Researcher basic information

• 理学博士, 京都大学

• https://researchmap.jp/shinichinakagawa?lang=en

• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=200901032447755154
• https://sites.google.com/rnabiol.com/home

• 50324679

• 200901032447755154

• intrinsically disordered protein
• noncoding RNA
• 4.5SH
• splicing
• Genome Editing
• Neat1
• paraspeckle
• nuclear bodies
• 核スペックル

• Life Science, Molecular biology
• Life Science, Developmental biology

• Bachelor's degree program, School of Pharmaceutical Sciences and Pharmacy
• Master's degree program, Graduate School of Life Science
• Doctoral (PhD) degree program, Graduate School of Life Science

Research activity information

• Lobe-Less, a Long Noncoding RNA That Regulates Drosophila Mushroom Body Morphogenesis.
  Sachi Inagaki; Natsuki Nakamura; Mitsutaka Kadota; Sean D Keeley; Shigehiro Kuraku; Masanao Sato; Shinichi Nakagawa; Mari Mito; Kevin G Nyberg; Kaori Niimi; Hidenori Kiyosawa; Satoru Kobayashi; Yuji Kageyama
  Genes to cells : devoted to molecular & cellular mechanisms, 31, 1, e70080, Jan. 2026, [International Magazine]
  English, Scientific journal, Long noncoding RNAs (lncRNAs) are abundantly transcribed in eukaryotes, but most of their physiological roles, especially in neural development, remain unclear due to limited in vivo studies. Here we show that Lobe-less (LOL) lncRNA of Drosophila is expressed in developing neuronal cells and is required for the development of the mushroom body, a center of memory and learning in the insect brain. lol mutant flies exhibit defective morphology of the mushroom body and axon branch patterns, as well as misregulation of neurogenic genes. LOL RNA forms nuclear puncta and genetically interacts with Polycomb group genes in the regulation of homeotic genes. These findings demonstrate that this long ncRNA plays a critical role in the epigenetic control of neural circuit formation.
• Architectural RNAs: blueprints for functional membraneless organelle assembly.
  Tetsuro Hirose; Naoko Fujiwara; Kensuke Ninomiya; Tetsuya Yamamoto; Shinichi Nakagawa; Tomohiro Yamazaki
  Trends in genetics : TIG, 12 Jun. 2025, [International Magazine]
  English, Scientific journal, Among the pervasive transcripts from eukaryotic genomes, a novel subset, referred to as architectural RNAs (arcRNAs), has an essential role in assembling membraneless organelles (MLOs). These arcRNAs sequester specific RNA-binding proteins (RBPs) and promote phase separation through multivalent interactions. NEAT1_2, an archetypal arcRNA, serves as a blueprint for paraspeckle architecture, characterized by a shell-and-core micelle-like configuration and immiscibility with other MLOs, relying on the cooperative contributions of distinct modular RNA domains. arcRNAs regulate gene expression through three of MLO action modes (crucible, sponge, and hub), guided by the functional blueprints embedded in arcRNA sequences. Advanced high-throughput analyses have identified thousands of arcRNA candidates, underscoring their potential in organizing transient intracellular compartments and driving dynamic cellular processes.
• Biophysical Aspect of Assembly and Regulation of Nuclear Bodies Scaffolded by Architectural RNA.
  Tetsuya Yamamoto; Tomohiro Yamazaki; Kensuke Ninomiya; Shinichi Nakagawa; Tetsuro Hirose
  Journal of molecular biology, 437, 9, 169016, 169016, Elsevier BV, 01 May 2025, [International Magazine]
  English, Scientific journal, A growing body of evidence suggests that nuclear bodies, condensates of RNAs and proteins within the nucleus, are assembled through liquid-liquid phase separation. Some nuclear bodies, such as paraspeckles, are scaffolded by a class of RNAs known as architectural RNAs. From a materials science perspective, RNAs are categorized as polymers, which have been extensively studied in soft matter physics. While soft matter physics has the potential to provide significant insights, it is not directly applicable because transcription and other biochemical processes differentiate RNAs from other polymers studied in this field. Therefore, an interdisciplinary research fusing molecular biology and soft matter physics offers a powerful approach to studying nuclear bodies. This review introduces the biophysical insights provided by such interdisciplinary research in the assembly and regulation of nuclear bodies.
• The Role of ESS2/DGCR14: Is It an Essential Factor in Splicing and Transcription?
  Ichiro Takada; Shinya Hidano; Tohru Nakagawa; Shinichi Nakagawa; Makoto Makishima; Sayuri Takahashi
  International journal of molecular sciences, 26, 9, 25 Apr. 2025, [International Magazine]
  English, Scientific journal, ESS2 (ess-2 splicing factor homolog, also known as DGCR14 or DGS-I) is a member of the deletion gene cluster in the 22q11.2 deletion syndrome (22q11.2DS, also known as DiGeorge syndrome or CATCH 22 syndrome). The ESS2 gene is not part of a gene family, and the coded protein has a coiled-coil structure (Es domain), which is conserved from yeast to humans. Recent studies have shown that ESS2 is involved in splicing C and C* complex, but other interactants, such as transcription factors and U1 snRNP, are also reported. Although the molecular mechanism is still under investigation, ESS2 plays a pivotal role in cell differentiation and proliferation. ESS2 knockout mice show embryonic lethal in the early stage, and recent studies show the association of ESS2 with cancer, autoimmune disease, and neurodevelopmental disorders. ESS2 can regulate mRNA splicing and transcriptional activity through interactions with other proteins, and ESS2-dependent gene expression regulation seems to be cell type-selective. In this review, we summarized the cloning history and functions of ESS2, including recent findings.
• Balancing RNA processing and innate immune response: Possible roles for SMN condensates in snRNP biogenesis.
  Hiroshi Maita; Shinichi Nakagawa
  Biochimica et biophysica acta. General subjects, 1869, 3, 130764, 130764, Mar. 2025, [International Magazine]
  English, Scientific journal, Biomolecular condensates like U-bodies are specialized cellular structures formed through multivalent interactions among intrinsically disordered regions. U-bodies sequester small nuclear ribonucleoprotein complexes (snRNPs) in the cytoplasm, and their formation in mammalian cells depends on stress conditions. Because of their location adjacent to P-bodies, U-bodies have been considered potential sites for snRNP storage or turnover. SMN, a chaperone for snRNP biogenesis, forms condensates through its Tudor domain. In fly models, defects in SMN trigger innate immune responses similar to those observed with excess cytoplasmic snRNA during viral infection in mammalian cells. Additionally, spinal muscular atrophy (SMA), caused by SMN deficiency, is associated with inflammation. Therefore, SMN may help prevent innate immune aberrant activation due to defective snRNP biogenesis by forming U-bodies to sequester these molecules. Further studies on U-body functions may provide therapeutic insights for diseases related to RNA metabolism.
• Downregulation of NEAT1 due to loss of TDP-43 function exacerbates motor neuron degeneration in amyotrophic lateral sclerosis.
  Yu Kawakami; Yohei Iguchi; Jiayi Li; Yoshinobu Amakusa; Takashi Yoshimura; Ryo Chikuchi; Satoshi Yokoi; Madoka Iida; Yuichi Riku; Yasushi Iwasaki; Tetsuro Hirose; Shinichi Nakagawa; Masahisa Katsuno
  Brain communications, 7, 4, fcaf261, 2025, [International Magazine]
  English, Scientific journal, TAR DNA-binding protein 43 (TDP-43) is of particular interest in the pathogenesis of amyotrophic lateral sclerosis (ALS). It has been speculated that loss of nuclear TDP-43 and its cytoplasmic aggregation contributes to neurodegeneration. Although considerable attention has been paid to RNA metabolism in TDP-43 function, TDP-43 is also known to act as a transcription factor. This study found that the expression of Nuclear-enriched abundant transcript 1 (NEAT1), a long-non-coding RNA, was substantially downregulated in motor neurons with nuclear TDP-43 loss, but upregulated in those with preserved nuclear TDP-43, in the postmortem spinal cords of patients with sporadic ALS. TDP-43 depletion induced Neat1 downregulation in Neuro2a cells, primary cortical neurons, and mouse spinal motor neurons. Furthermore, TDP-43 was found to positively regulate NEAT1 at the transcriptional level. Finally, Neat1 knockout exacerbates neurodegeneration of hSOD1G93A mice accompanied by increased misfolded superoxide dismutase 1 (SOD1) aggregations. Transcriptome analysis revealed that Neat1 knockout reduced protein folding-related genes, such as heat shock protein family A member 1A (Hspa1a), in the spinal cords of hSOD1G93A mice. Our results indicated that the loss of TDP-43 function enhances ALS neurodegeneration by losing the protective effect of NEAT1.
• Long non-coding RNA Malat1 fine-tunes bone homeostasis and repair by orchestrating cellular crosstalk and β-catenin-OPG/Jagged1 pathway.
  Yongli Qin; Jumpei Shirakawa; Cheng Xu; Ruge Chen; Xu Yang; Courtney Ng; Shinichi Nakano; Mahmoud Elguindy; Zhonghao Deng; Kannanganattu V Prasanth; Moritz F Eissmann; Shinichi Nakagawa; William M Ricci; Baohong Zhao
  eLife, 13, 23 Dec. 2024, [International Magazine]
  English, Scientific journal, The IncRNA Malat1 was initially believed to be dispensable for physiology due to the lack of observable phenotypes in Malat1 knockout (KO) mice. However, our study challenges this conclusion. We found that both Malat1 KO and conditional KO mice in the osteoblast lineage exhibit significant osteoporosis. Mechanistically, Malat1 acts as an intrinsic regulator in osteoblasts to promote osteogenesis. Interestingly, Malat1 does not directly affect osteoclastogenesis but inhibits osteoclastogenesis in a non-autonomous manner in vivo via integrating crosstalk between multiple cell types, including osteoblasts, osteoclasts, and chondrocytes. Our findings substantiate the existence of a novel remodeling network in which Malat1 serves as a central regulator by binding to β-catenin and functioning through the β-catenin-OPG/Jagged1 pathway in osteoblasts and chondrocytes. In pathological conditions, Malat1 significantly promotes bone regeneration in fracture healing. Bone homeostasis and regeneration are crucial to well-being. Our discoveries establish a previous unrecognized paradigm model of Malat1 function in the skeletal system, providing novel mechanistic insights into how a lncRNA integrates cellular crosstalk and molecular networks to fine tune tissue homeostasis, remodeling and repair.
• Identification of BAY61-3606 Derivatives With Improved Activity in Splicing Modulation That Induces Inclusion of Cassette Exons Similar to the Splicing Factor 3B Subunit 1 Mutation.
  Takanori Matsumaru; Toshiki Iwamatsu; Kana Ishigami; Makoto Inai; Wataru Kanto; Ayumi Ishigaki; Atsushi Toyoda; Satoshi Shuto; Katsumi Maenaka; Shinichi Nakagawa; Hiroshi Maita
  Chemical biology & drug design, 104, 4, e70002, Oct. 2024, [International Magazine]
  English, Scientific journal, Splicing modulation by a small compound offers therapeutic potential for diseases caused by splicing abnormality. However, only a few classes of compounds that can modulate splicing have been identified. We previously identified BAY61-3606, a multiple kinase inhibitor, as a compound that relaxes the splicing fidelity at the 3' splice site recognition. We have also reported the synthesis of derivatives of BAY61-3606. In this study, we tested those compounds for their splicing modulation capabilities and identified two contrasting compounds. These compounds were further investigated for their effects on the whole transcriptome, and analysis of changes in transcription and splicing revealed that the highly active derivative in the splicing reporter assay also showed significantly higher activity in modulating the splicing of endogenously expressed genes. Particularly, cassette exon inclusion was highly upregulated by this compound, and clustering analysis revealed that these effects resembled those in splicing factor 3b subunit 1 (SF3B1) K700E mutant cells but contrasted with those of the splicing inhibitor H3B-8800. Additionally, a group of serine/arginine-rich (SR) protein genes was identified as representatively affected, likely via modulation of poison exon inclusion. This finding could guide further analysis of the mode of action of these compounds on splicing, which could be valuable for developing drugs for diseases associated with splicing abnormalities.
• Dissecting the role of SMN multimerization in its dissociation from the Cajal body using harmine as a tool compound.
  Saki Ohazama; Akiko Fujimoto; Daisuke Konda; Ryota Yokoyama; Shinichi Nakagawa; Hiroshi Maita
  Journal of cell science, 137, 18, 15 Sep. 2024, [International Magazine]
  English, Scientific journal, Survival motor neuron protein (SMN), which is linked to spinal muscular atrophy, is a key component of the Gemin complex, which is essential for the assembly of small nuclear RNA-protein complexes (snRNPs). After initial snRNP assembly in the cytoplasm, both snRNPs and SMN migrate to the nucleus and associate with Cajal bodies, where final snRNP maturation occurs. It is assumed that SMN must be free from the Cajal bodies for continuous snRNP biogenesis. Previous observation of the SMN granules docked in the Cajal bodies suggests the existence of a separation mechanism. However, the precise processes that regulate the spatial separation of SMN complexes from Cajal bodies remain unclear. Here, we have employed a super-resolution microscope alongside the β-carboline alkaloid harmine, which disrupts the Cajal body in a reversible manner. Upon removal of harmine, SMN and Coilin first appear as small interconnected condensates. The SMN condensates mature into spheroidal structures encircled by Coilin, eventually segregating into distinct condensates. Expression of a multimerization-deficient SMN mutant leads to enlarged, atypical Cajal bodies in which SMN is unable to segregate into separate condensates. These findings underscore the importance of multimerization in facilitating the segregation of SMN from Coilin within Cajal bodies.
• An evolutionarily distinct Hmgn2 variant influences shape recognition in Medaka Fish.
  Shuntaro Inoue; Yume Masaki; Shinichi Nakagawa; Saori Yokoi
  Communications biology, 7, 1, 973, 973, 23 Aug. 2024, [International Magazine]
  English, Scientific journal, Protein sequence diversification significantly impacts physiological traits. In this study, using medaka fish (Oryzias latipes), we identify a novel protein variant affecting shape preference behavior. Re-analysis of sequencing data reveals that LOC101156433 encodes a unique Hmgn2 variant with unusual subnuclear localization, clustered separately from the Hmgn2 clades of other species. Medaka mutants with this variant showed reduce telencephalic regions and altered shape preference, suggesting a link between protein sequence variation and behavioral changes. Additionally, this Hmgn2 variant is common in Acanthopterygii fishes, which are adapted to a variety of environments, indicating its potential evolutionary significance. Our findings highlight the relationship between amino acid sequence variation and the development of new molecular and behavioral adaptations, providing insights into the visual shape perception system in fish.
• The Essential Role of Architectural Noncoding RNA Neat1 in Cold-Induced Beige Adipocyte Differentiation in Mice.
  Hikaru Toya; Yuko Okamatsu-Ogura; Saori Yokoi; Misuzu Kurihara; Mari Mito; Shintaro Iwasaki; Tetsuro Hirose; Shinichi Nakagawa
  RNA (New York, N.Y.), 01 May 2024, [International Magazine]
  English, Scientific journal, Neat1 is an architectural RNA that provides the structural basis for nuclear bodies known as paraspeckles. Although the assembly processes by which Neat1 organizes paraspeckle components are well-documented, the physiological functions of Neat1 remain less defined. This is partly because Neat1 knockout (KO) mice, lacking paraspeckles, do not exhibit overt phenotypes under normal laboratory conditions. During our search for conditions that elicit clear phenotypes in Neat1 KO mice, we discovered that the differentiation of beige adipocytes-inducible thermogenic cells that emerge upon cold exposure-is severely impaired in these mutant mice. Neat1_2, the architectural isoform of Neat1, is transiently upregulated during the early stages of beige adipocyte differentiation, coinciding with increased paraspeckle formation. Genes with altered expression during beige adipocyte differentiation typically cluster at specific chromosomal locations, some of which move closer to paraspeckles upon cold exposure. These observations suggest that paraspeckles might coordinate the regulation of these gene clusters by controlling the activity of certain transcriptional condensates that co-regulate multiple genes. We propose that our findings highlight a potential role for Neat1 and paraspeckles in modulating chromosomal organization and gene expression, potentially crucial processes for the differentiation of beige adipocytes.
• The early macrophage response to pathogens requires dynamic regulation of the nuclear paraspeckle
  Sikandar Azam; Kaitlyn S. Armijo; Chi G. Weindel; Morgan J. Chapman; Alice Devigne; Shinichi Nakagawa; Tetsuro Hirose; Susan Carpenter; Robert O. Watson; Kristin L. Patrick
  Proceedings of the National Academy of Sciences, 121, 9, e2312587121, Proceedings of the National Academy of Sciences, 21 Feb. 2024, [International Magazine]
  English, Scientific journal, To ensure a robust immune response to pathogens without risking immunopathology, the kinetics and amplitude of inflammatory gene expression in macrophages need to be exquisitely well controlled. There is a growing appreciation for stress-responsive membraneless organelles (MLOs) regulating various steps of eukaryotic gene expression in response to extrinsic cues. Here, we implicate the nuclear paraspeckle, a highly ordered biomolecular condensate that nucleates on the Neat1 lncRNA, in tuning innate immune gene expression in murine macrophages. In response to a variety of innate agonists, macrophage paraspeckles rapidly aggregate (0.5 h poststimulation) and disaggregate (2 h poststimulation). Paraspeckle maintenance and aggregation require active transcription and MAPK signaling, whereas paraspeckle disaggregation requires degradation of Neat1 via the nuclear RNA exosome. In response to lipopolysaccharide treatment, Neat1 KO macrophages fail to properly express a large cohort of proinflammatory cytokines, chemokines, and antimicrobial mediators. Consequently, Neat1 KO macrophages cannot control replication of Salmonella enterica serovar Typhimurium or vesicular stomatitis virus. These findings highlight a prominent role for MLOs in orchestrating the macrophage response to pathogens and support a model whereby dynamic assembly and disassembly of paraspeckles reorganizes the nuclear landscape to enable inflammatory gene expression following innate stimuli.
• 4.5SH RNA counteracts deleterious exonization of SINE B1 in mice.
  Rei Yoshimoto; Yuta Nakayama; Ikuko Nomura; Ikuko Yamamoto; Yumeka Nakagawa; Shigeyuki Tanaka; Misuzu Kurihara; Yu Suzuki; Takehiko Kobayashi; Hiroko Kozuka-Hata; Masaaki Oyama; Mari Mito; Shintaro Iwasaki; Tomohiro Yamazaki; Tetsuro Hirose; Kimi Araki; Shinichi Nakagawa
  Molecular cell, 83, 24, 4479, 4493, 21 Dec. 2023, [International Magazine]
  English, Scientific journal, 4.5SH RNA is a highly abundant, small rodent-specific noncoding RNA that localizes to nuclear speckles enriched in pre-mRNA-splicing regulators. To investigate the physiological functions of 4.5SH RNA, we have created mutant mice that lack the expression of 4.5SH RNA. The mutant mice exhibited embryonic lethality, suggesting that 4.5SH RNA is an essential species-specific noncoding RNA in mice. RNA-sequencing analyses revealed that 4.5SH RNA protects the transcriptome from abnormal exonizations of the antisense insertions of the retrotransposon SINE B1 (asB1), which would otherwise introduce deleterious premature stop codons or frameshift mutations. Mechanistically, 4.5SH RNA base pairs with complementary asB1-containing exons via the target recognition region and recruits effector proteins including Hnrnpm via its 5' stem loop region. The modular organization of 4.5SH RNA allows us to engineer a programmable splicing regulator to induce the skipping of target exons of interest. Our results also suggest the general existence of splicing regulatory noncoding RNAs.
• Shell protein composition specified by the lncRNA NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles.
  Hiro Takakuwa; Tomohiro Yamazaki; Sylvie Souquere; Shungo Adachi; Hyura Yoshino; Naoko Fujiwara; Tetsuya Yamamoto; Tohru Natsume; Shinichi Nakagawa; Gerard Pierron; Tetsuro Hirose
  Nature cell biology, 25, 11, 1664, 1675, Cold Spring Harbor Laboratory, Nov. 2023, [International Magazine]
  English, Scientific journal, Abstract
  
  Many membraneless organelles (MLOs) formed through phase separation play crucial roles in various cellular processes. Although these MLOs co-exist in cells, how they maintain their independence without coalescence or engulfment remains largely unknown. Here, we investigated the molecular mechanism by which paraspeckles with core-shell architecture scaffolded by NEAT1_2 lncRNAs exist as distinct MLOs. We identified NEAT1 deletion mutants that assemble paraspeckles that are incorporated into nuclear speckles. Several paraspeckle proteins, including SFPQ, HNRNPF, and BRG1, prevent this incorporation and thus contribute to the segregation of paraspeckles from nuclear speckles. Shell localization of these proteins in the paraspeckles, which is determined by NEAT1_2 lncRNA domains, is required for this segregation process. Conversely, U2-related spliceosomal proteins are involved in internalizing the paraspeckles into nuclear speckles. This study shows that the paraspeckle shell composition dictates the independence of MLOs in the nucleus, providing insights into the importance of the shell in defining features and functions of MLOs.
• SINE-derived short noncoding RNAs: their evolutionary origins, molecular mechanisms, and physiological significance
  Rei Yoshimoto; Shinichi Nakagawa
  Frontiers in RNA Research, 1, Frontiers Media SA, 10 Aug. 2023
  Scientific journal, Short Interspersed Elements (SINEs) comprise a significant portion of the genomes of higher eukaryotes, including humans and mice. This review focuses on SINE-derived noncoding RNAs (ncRNAs), particularly BC1, BC200, and 4.5SH RNA, which are expressed abundantly and in a species-specific manner. These ncRNAs seem to have independently evolved their functions during evolutionary processes: BC1 and BC200 have become cytoplasmic translation inhibitors, while 4.5SH RNA has developed into a nuclear ncRNA that regulates splicing. This review delves into the unique roles of these ncRNAs, with a special emphasis on the recently discovered splicing regulation function of 4.5SH RNA. Furthermore, we discuss their evolutionary trajectories and potential implications for understanding the complexities of gene regulation.
• Nondomain biopolymers: Flexible molecular strategies to acquire biological functions.
  Kazuharu Arakawa; Tetsuro Hirose; Toshifumi Inada; Takuhiro Ito; Toshie Kai; Masaaki Oyama; Yukihide Tomari; Takao Yoda; Shinichi Nakagawa
  Genes to cells : devoted to molecular & cellular mechanisms, 30 May 2023, [International Magazine]
  English, Scientific journal, A long-standing assumption in molecular biology posits that the conservation of protein and nucleic acid sequences emphasizes the functional significance of biomolecules. These conserved sequences fold into distinct secondary and tertiary structures, enable highly specific molecular interactions, and regulate complex yet organized molecular processes within living cells. However, recent evidence suggests that biomolecules can also function through primary sequence regions that lack conservation across species or gene families. These regions typically do not form rigid structures, and their inherent flexibility is critical for their functional roles. This review examines the emerging roles and molecular mechanisms of "nondomain biomolecules," whose functions are not easily predicted due to the absence of conserved functional domains. We propose the hypothesis that both domain- and nondomain-type molecules work together to enable flexible and efficient molecular processes within the highly crowded intracellular environment.
• Long noncoding RNA Malat1 inhibits Tead3-Nfatc1-mediated osteoclastogenesis to suppress osteoporosis and bone metastasis.
  Yang Zhao; Hongqi Teng; Yalan Deng; Marisela Sheldon; Consuelo Martinez; Jie Zhang; Annie Tian; Yutong Sun; Shinichi Nakagawa; Fan Yao; Hai Wang; Li Ma
  Research square, 20 Mar. 2023, [International Magazine]
  English, MALAT1, one of the few highly conserved nuclear long noncoding RNAs (IncRNAs), is abundantly expressed in normal tissues. Previously, targeted inactivation and genetic rescue experiments identified MALAT1 as a suppressor of breast cancer lung metastasis. On the other hand, Malat1-knockout mice are viable and develop normally. On a quest to discover new roles of MALAT1 in physiological and pathological processes, we found that this lncRNA is downregulated during osteoclastogenesis in humans and mice. Notably, Malat1 deficiency in mice promotes osteoporosis and bone metastasis, which can be rescued by genetic add-back of Malat1. Mechanistically, Malat1 binds to Tead3 protein, a macrophage-osteoclast-specific Tead family member, blocking Tead3 from binding and activating Nfatc1, a master regulator of osteoclastogenesis, which results in the inhibition of Nfatc1-mediated gene transcription and osteoclast differentiation. Altogether, these findings identify Malat1 as a lncRNA that suppresses osteoporosis and bone metastasis.
• Long non-coding RNAs: definitions, functions, challenges and recommendations
  John S. Mattick; Paulo P. Amaral; Piero Carninci; Susan Carpenter; Howard Y. Chang; Ling-Ling Chen; Runsheng Chen; Caroline Dean; Marcel E. Dinger; Katherine A. Fitzgerald; Thomas R. Gingeras; Mitchell Guttman; Tetsuro Hirose; Maite Huarte; Rory Johnson; Chandrasekhar Kanduri; Philipp Kapranov; Jeanne B. Lawrence; Jeannie T. Lee; Joshua T. Mendell; Timothy R. Mercer; Kathryn J. Moore; Shinichi Nakagawa; John L. Rinn; David L. Spector; Igor Ulitsky; Yue Wan; Jeremy E. Wilusz; Mian Wu
  Nature Reviews Molecular Cell Biology, Springer Science and Business Media LLC, 03 Jan. 2023
  Scientific journal
• BAY61-3606 Alters snRNP Composition and Enhances Usage of Suboptimal Splice Acceptor Site.
  Kenji Tomita; Shinichi Nakagawa; Hiroyoshi Ariga; Hiroshi Maita
  Biological & pharmaceutical bulletin, 46, 2, 147, 157, 2023, [Domestic magazines]
  English, Scientific journal, Intron recognition by the spliceosome mainly depends on conserved intronic sequences such as 5' splice sites, 3' splice sites, and branch sites. Therefore, even substitution of just a single nucleotide in a 5' or 3' splice site abolishes the splicing at the mutated site and leads to cryptic splice site usage. A number of disease-causative mutations have been found in 5' and 3' splice sites, but the genes with these mutations still maintain the correct protein-coding sequence, so recovery of splicing at the mutated splice site may produce a normal protein. Mutations in the spliceosome components have been shown to change the balance between the conformational transition and disassembly of the spliceosome, which affects the decision about whether the reaction of the incorporated substrate will proceed. In addition, the lower disassembly rate caused by such mutations induces splicing of the mutated splice site. We hypothesized that small compounds targeting the spliceosome may include a compound mimicking the effect of those mutations. Thus, we screened a small-compound library and identified a compound, BAY61-3606, that changed the cellular small nuclear ribonucleoprotein composition and also showed activity of enhancing splicing at the mutated 3' splice site of the reporter gene, as well as splicing at the suboptimal 3' splice site of endogenous cassette exons. These results indicate that further analysis of the mechanism of action of BAY61-3606 could enable modulation of the fidelity of splicing.
• tRNA-like Transcripts from the NEAT1-MALAT1 Genomic Region Critically Influence Human Innate Immunity and Macrophage Functions
  Martina Gast; Vanasa Nageswaran; Andreas W. Kuss; Ana Tzvetkova; Xiaomin Wang; Liliana H. Mochmann; Pegah Ramezani Rad; Stefan Weiss; Stefan Simm; Tanja Zeller; Henry Voelzke; Wolfgang Hoffmann; Uwe Völker; Stefan B. Felix; Marcus Dörr; Antje Beling; Carsten Skurk; David-Manuel Leistner; Bernhard H. Rauch; Tetsuro Hirose; Bettina Heidecker; Karin Klingel; Shinichi Nakagawa; Wolfram C. Poller; Filip K. Swirski; Arash Haghikia; Wolfgang Poller
  Cells, 11, 24, 3970, 3970, MDPI AG, 08 Dec. 2022
  Scientific journal, The evolutionary conserved NEAT1-MALAT1 gene cluster generates large noncoding transcripts remaining nuclear, while tRNA-like transcripts (mascRNA, menRNA) enzymatically generated from these precursors translocate to the cytosol. Whereas functions have been assigned to the nuclear transcripts, data on biological functions of the small cytosolic transcripts are sparse. We previously found NEAT1−/− and MALAT1−/− mice to display massive atherosclerosis and vascular inflammation. Here, employing selective targeted disruption of menRNA or mascRNA, we investigate the tRNA-like molecules as critical components of innate immunity. CRISPR-generated human ΔmascRNA and ΔmenRNA monocytes/macrophages display defective innate immune sensing, loss of cytokine control, imbalance of growth/angiogenic factor expression impacting upon angiogenesis, and altered cell–cell interaction systems. Antiviral response, foam cell formation/oxLDL uptake, and M1/M2 polarization are defective in ΔmascRNA/ΔmenRNA macrophages, defining first biological functions of menRNA and describing new functions of mascRNA. menRNA and mascRNA represent novel components of innate immunity arising from the noncoding genome. They appear as prototypes of a new class of noncoding RNAs distinct from others (miRNAs, siRNAs) by biosynthetic pathway and intracellular kinetics. Their NEAT1-MALAT1 region of origin appears as archetype of a functionally highly integrated RNA processing system.
• A guide to membraneless organelles and their various roles in gene regulation.
  Tetsuro Hirose; Kensuke Ninomiya; Shinichi Nakagawa; Tomohiro Yamazaki
  Nature reviews. Molecular cell biology, 23 Nov. 2022, [International Magazine]
  English, Scientific journal, Membraneless organelles (MLOs) are detected in cells as dots of mesoscopic size. By undergoing phase separation into a liquid-like or gel-like phase, MLOs contribute to intracellular compartmentalization of specific biological functions. In eukaryotes, dozens of MLOs have been identified, including the nucleolus, Cajal bodies, nuclear speckles, paraspeckles, promyelocytic leukaemia protein (PML) nuclear bodies, nuclear stress bodies, processing bodies (P bodies) and stress granules. MLOs contain specific proteins, of which many possess intrinsically disordered regions (IDRs), and nucleic acids, mainly RNA. Many MLOs contribute to gene regulation by different mechanisms. Through sequestration of specific factors, MLOs promote biochemical reactions by simultaneously concentrating substrates and enzymes, and/or suppressing the activity of the sequestered factors elsewhere in the cell. Other MLOs construct inter-chromosomal hubs by associating with multiple loci, thereby contributing to the biogenesis of macromolecular machineries essential for gene expression, such as ribosomes and spliceosomes. The organization of many MLOs includes layers, which might have different biophysical properties and functions. MLOs are functionally interconnected and are involved in various diseases, prompting the emergence of therapeutics targeting them. In this Review, we introduce MLOs that are relevant to gene regulation and discuss their assembly, internal structure, gene-regulatory roles in transcription, RNA processing and translation, particularly in stress conditions, and their disease relevance.
• Transcriptional coregulator Ess2 controls survival of post-thymic CD4+ T cells through the Myc and IL-7 signaling pathways.
  Ichiro Takada; Shinya Hidano; Sayuri Takahashi; Kaori Yanaka; Hidesato Ogawa; Megumi Tsuchiya; Atsushi Yokoyama; Shingo Sato; Hiroki Ochi; Tohru Nakagawa; Takashi Kobayashi; Shinichi Nakagawa; Makoto Makishima
  The Journal of biological chemistry, 298, 9, 102342, 102342, Sep. 2022, [International Magazine]
  English, Scientific journal, Ess2, also known as Dgcr14, is a transcriptional co-regulator of CD4+ T cells. Ess2 is located in a chromosomal region, the loss of which has been associated with 22q11.2 deletion syndrome (22q11DS), which causes heart defects, skeletal abnormalities, and immunodeficiency. However, the specific association of Ess2 with 22q11DS remains unclear. To elucidate the role of Ess2 in T-cell development, we generated Ess2 floxed (Ess2fl/fl) and CD4+ T cell-specific Ess2 KO (Ess2ΔCD4/ΔCD4) mice using the Cre/loxP system. Interestingly, Ess2ΔCD4/ΔCD4 mice exhibited reduced naïve T-cell numbers in the spleen, while the number of thymocytes (CD4-CD8-, CD4+CD8+, CD4+CD8-, and CD4-CD8+) in the thymus remained unchanged. Furthermore, Ess2ΔCD4/ΔCD4 mice had decreased NKT cells and increased γδT cells in the thymus and spleen. A genome-wide expression analysis using RNA-seq revealed that Ess2 deletion alters the expression of many genes in CD4 single-positive thymocytes, including genes related to the immune system and Myc target genes. In addition, Ess2 enhanced the transcriptional activity of c-Myc. Some genes identified as Ess2 targets in mice show expressional correlation with ESS2 in human immune cells. Moreover, Ess2ΔCD4/ΔCD4 naïve CD4+ T cells did not maintain survival in response to IL-7. Our results suggest that Ess2 plays a critical role in post-thymic T-cell survival through the Myc and IL-7 signaling pathways.
• Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat.
  Akihiro Yamada; Hikaru Toya; Mayuko Tanahashi; Misuzu Kurihara; Mari Mito; Shintaro Iwasaki; Satoshi Kurosaka; Toru Takumi; Archa Fox; Yoshimi Kawamura; Kyoko Miura; Shinichi Nakagawa
  RNA (New York, N.Y.), 28, 8, 1128, 1143, Aug. 2022, [Peer-reviewed], [Last author, Corresponding author], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, Paraspeckles are mammalian-specific nuclear bodies built on the long noncoding RNA NEAT1_2 The molecular mechanisms of paraspeckle formation have been mainly studied using human or mouse cells, and it is not known if the same molecular components are involved in the formation of paraspeckles in other mammalian species. We thus investigated the expression pattern of NEAT1_2 in naked mole-rats (nNEAT1_2), which exhibit extreme longevity and lower susceptibility to cancer. In the intestine, nNEAT1_2 is widely expressed along the entire intestinal epithelium, which is different from the expression of mNeat1_2 that is restricted to the cells of the distal tip in mice. Notably, the expression of FUS, a FET family RNA binding protein, essential for the formation of paraspeckles both in humans and mice, was absent in the distal part of the intestinal epithelium in naked mole-rats. Instead, mRNAs of other FET family proteins EWSR1 and TAF15 were expressed in the distal region. Exogenous expression of these proteins in Fus-deficient murine embryonic fibroblast cells rescued the formation of paraspeckles. These observations suggest that nNEAT1_2 recruits a different set of RNA binding proteins in a cell type-specific manner during the formation of paraspeckles in different organisms.
• lncRNA Neat1 regulates neuronal dysfunction post-sepsis via stabilization of hemoglobin subunit beta.
  Yan Wu; Pengfei Li; Liu Liu; Andrew J Goodwin; Perry V Halushka; Tetsuro Hirose; Shinichi Nakagawa; Jiliang Zhou; Meng Liu; Hongkuan Fan
  Molecular therapy : the journal of the American Society of Gene Therapy, 30, 7, 2618, 2632, 06 Jul. 2022, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, Sepsis-associated encephalopathy (SAE) is characterized by acute and diffuse brain dysfunction and correlates with long-term cognitive impairments with no targeted therapy. We used a mouse model of sepsis-related cognitive impairment to examine the role of lncRNA nuclear enriched abundant transcript 1 (Neat1) in SAE. We observed that Neat1 expression was increased in neuronal cells from septic mice and that it directly interacts with hemoglobin subunit beta (Hbb), preventing its degradation. The Neat1/Hbb axis suppressed postsynaptic density protein 95 (PSD-95) levels and decreased dendritic spine density. Neat1 knockout mice exhibited decreased Hbb levels, which resulted in increased PSD-95 levels, increased neuronal dendritic spine density, and decreased anxiety and memory impairment. Neat1 silencing via the antisense oligonucleotide GapmeR ameliorated anxiety-like behavior and cognitive impairment post-sepsis. In conclusion, we uncovered a previously unknown mechanism of the Neat1/Hbb axis in regulating neuronal dysfunction, which may lead to a novel treatment strategy for SAE.
• MiR-150 Attenuates Maladaptive Cardiac Remodeling Mediated by Long Noncoding RNA MIAT and Directly Represses Profibrotic Hoxa4.
  Tatsuya Aonuma; Bruno Moukette; Satoshi Kawaguchi; Nipuni P Barupala; Marisa N Sepúlveda; Kyle Frick; Yaoliang Tang; Maya Guglin; Subha V Raman; Chenleng Cai; Suthat Liangpunsakul; Shinichi Nakagawa; Il-Man Kim
  Circulation. Heart failure, 15, 4, CIRCHEARTFAILURE121008686, 10 Jan. 2022, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, BACKGROUND: MicroRNA-150 (miR-150) plays a protective role in heart failure (HF). Long noncoding RNA, myocardial infarction-associated transcript (MIAT) regulates miR-150 function in vitro by direct interaction. Concurrent with miR-150 downregulation, MIAT is upregulated in failing hearts, and gain-of-function single-nucleotide polymorphisms in MIAT are associated with increased risk of myocardial infarction (MI) in humans. Despite the correlative relationship between MIAT and miR-150 in HF, their in vivo functional relationship has never been established, and molecular mechanisms by which these 2 noncoding RNAs regulate cardiac protection remain elusive. METHODS: We use MIAT KO (knockout), Hoxa4 (homeobox a4) KO, MIAT TG (transgenic), and miR-150 TG mice. We also develop DTG (double TG) mice overexpressing MIAT and miR-150. We then use a mouse model of MI followed by cardiac functional, structural, and mechanistic studies by echocardiography, immunohistochemistry, transcriptome profiling, Western blotting, and quantitative real-time reverse transcription-polymerase chain reaction. Moreover, we perform expression analyses in hearts from patients with HF. Lastly, we investigate cardiac fibroblast activation using primary adult human cardiac fibroblasts and in vitro assays to define the conserved MIAT/miR-150/HOXA4 axis. RESULTS: Using novel mouse models, we demonstrate that genetic overexpression of MIAT worsens cardiac remodeling, while genetic deletion of MIAT protects hearts against MI. Importantly, miR-150 overexpression attenuates the detrimental post-MI effects caused by MIAT. Genome-wide transcriptomic analysis of MIAT null mouse hearts identifies Hoxa4 as a novel downstream target of the MIAT/miR-150 axis. Hoxa4 is upregulated in cardiac fibroblasts isolated from ischemic myocardium and subjected to hypoxia/reoxygenation. HOXA4 is also upregulated in patients with HF. Moreover, Hoxa4 deficiency in mice protects the heart from MI. Lastly, protective actions of cardiac fibroblast miR-150 are partially attributed to the direct and functional repression of profibrotic Hoxa4. CONCLUSIONS: Our findings delineate a pivotal functional interaction among MIAT, miR-150, and Hoxa4 as a novel regulatory mechanism pertinent to ischemic HF.
• UPA-Seq-Based Search Method for Functional lncRNA Candidates.
  Saori Yokoi; Shinichi Nakagawa
  Methods in molecular biology (Clifton, N.J.), 2509, 269, 278, 2022, [Peer-reviewed], [Invited], [Last author], [International Magazine]
  English, Scientific journal, Long noncoding RNAs (lncRNAs) constitute a large fraction of the transcriptome in mammals, and recent studies have revealed important functions of lncRNAs in a variety of biological processes. However, the fraction of lncRNAs that have been functionally validated is small, and only sequence and expression information are available for most lncRNAs. Here, we describe the procedures for UV-phenol aqueous-phase RNA sequencing (UPA-seq), a method for searching for functional lncRNA candidates among whole genomes based on the assumption that functional lncRNAs exert their functions through associations with proteins.
• The cell type-specific ER membrane protein UGS148 is not essential in mice.
  Osamu Takahashi; Mayuko Tanahashi; Saori Yokoi; Mari Kaneko; Kaori Yanaka; Shinichi Nakagawa; Hiroshi Maita
  Genes to cells : devoted to molecular & cellular mechanisms, 27, 1, 43, 60, Jan. 2022, [Peer-reviewed], [Corresponding author], [International Magazine]
  English, Scientific journal, Genomes of higher eukaryotes encode many uncharacterized proteins, and the functions of these proteins cannot be predicted from the primary sequences due to a lack of conserved functional domains. In this study, we focused on a poorly characterized protein UGS148 that is highly expressed in a specialized cell type called tanycytes that line the ventral wall of the third ventricle in the hypothalamus. Immunostaining of UGS148 revealed the fine morphology of tanycytes with highly branched apical ER membranes. Immunoprecipitation revealed that UGS148 associated with mitochondrial ATPase at least in vitro, and ER and mitochondrial signals occasionally overlapped in tanycytes. Mutant mice lacking UGS148 did not exhibit overt phenotypes, suggesting that UGS148 was not essential in mice reared under normal laboratory conditions. We also found that RNA probes that were predicted to uniquely detect UGS148 mRNA cross-reacted with uncharacterized RNAs, highlighting the importance of experimental validation of the specificity of probes during the hybridization-based study of RNA localization.
• NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis.
  Mi Kyung Park; Li Zhang; Kyung-Won Min; Jung-Hyun Cho; Chih-Chen Yeh; Hyesu Moon; Daniel Hormaechea-Agulla; Hyejin Mun; Seungbeom Ko; Ji Won Lee; Sonali Jathar; Aubrey S Smith; Yixin Yao; Nguyen Thu Giang; Hong Ha Vu; Victoria C Yan; Mary C Bridges; Antonis Kourtidis; Florian Muller; Jeong Ho Chang; Su Jung Song; Shinichi Nakagawa; Tetsuro Hirose; Je-Hyun Yoon; Min Sup Song
  Cell metabolism, 33, 12, 2380, 2397, 07 Dec. 2021, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, Accelerated glycolysis is the main metabolic change observed in cancer, but the underlying molecular mechanisms and their role in cancer progression remain poorly understood. Here, we show that the deletion of the long noncoding RNA (lncRNA) Neat1 in MMTV-PyVT mice profoundly impairs tumor initiation, growth, and metastasis, specifically switching off the penultimate step of glycolysis. Mechanistically, NEAT1 directly binds and forms a scaffold bridge for the assembly of PGK1/PGAM1/ENO1 complexes and thereby promotes substrate channeling for high and efficient glycolysis. Notably, NEAT1 is upregulated in cancer patients and correlates with high levels of these complexes, and genetic and pharmacological blockade of penultimate glycolysis ablates NEAT1-dependent tumorigenesis. Finally, we demonstrate that Pinin mediates glucose-stimulated nuclear export of NEAT1, through which it exerts isoform-specific and paraspeckle-independent functions. These findings establish a direct role for NEAT1 in regulating tumor metabolism, provide new insights into the Warburg effect, and identify potential targets for therapy.
• NEAT1 lncRNA and amyotrophic lateral sclerosis.
  Yoshinori Nishimoto; Shinichi Nakagawa; Hideyuki Okano
  Neurochemistry international, 150, 105175, 105175, 02 Sep. 2021, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Amyotrophic lateral sclerosis (ALS) is a representative neurological disease that is known to devastate entire motor neurons within a period of just a few years. Discoveries of the specific pathologies of relevant RNA-binding proteins, including TAR DNA-binding protein-43 (TDP-43) and fused in sarcoma/translocated in liposarcoma (FUS/TLS), and the causative genes of both familial and sporadic ALS have provided crucial information that could lead to a cure. In recent ALS research the GGGGCC-repeat expansion in the C9orf72 gene was identified as one of the most important pathological findings, suggesting the significance of both nuclear dysfunction due to dipeptide repeat proteins (DPRs) and RNA toxicity (such as pathological alterations of non-coding RNAs). In research on model animals carrying ALS-related molecules, the determination of whether a factor is protective or toxic has been controversial. Herein, we review the findings regarding NEAT1 RNA and C9orf72 GGGGCC repeats associated with ALS, from the viewpoint of conversion from the protective stage in the nucleus in early-phase ALS to late-phase induction of cell death. This review will provide insights for the development of RNA effectors as novel ALS treatments.
• A histone modifier, ASXL1, interacts with NONO and is involved in paraspeckle formation in hematopoietic cells.
  Keita Yamamoto; Susumu Goyama; Shuhei Asada; Takeshi Fujino; Taishi Yonezawa; Naru Sato; Reina Takeda; Akiho Tsuchiya; Tomofusa Fukuyama; Yosuke Tanaka; Akihiko Yokoyama; Hikaru Toya; Ayana Kon; Yasuhito Nannya; Rena Onoguchi-Mizutani; Shinichi Nakagawa; Tetsuro Hirose; Seishi Ogawa; Nobuyoshi Akimitsu; Toshio Kitamura
  Cell reports, 36, 8, 109576, 109576, 24 Aug. 2021, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Paraspeckles are membraneless organelles formed through liquid-liquid phase separation and consist of multiple proteins and RNAs, including NONO, SFPQ, and NEAT1. The role of paraspeckles and the component NONO in hematopoiesis remains unknown. In this study, we show histone modifier ASXL1 is involved in paraspeckle formation. ASXL1 forms phase-separated droplets, upregulates NEAT1 expression, and increases NONO-NEAT1 interactions through the C-terminal intrinsically disordered region (IDR). In contrast, a pathogenic ASXL mutant (ASXL1-MT) lacking IDR does not support the interaction of paraspeckle components. Furthermore, paraspeckles are disrupted and Nono localization is abnormal in the cytoplasm of hematopoietic stem and progenitor cells (HSPCs) derived from ASXL1-MT knockin mice. Nono depletion and the forced expression of cytoplasmic NONO impair the repopulating potential of HSPCs, as does ASXL1-MT. Our study indicates a link between ASXL1 and paraspeckle components in the maintenance of normal hematopoiesis.
• Identification of the cell-type-specific ER membrane protein Tanmp expressed in hypothalamic tanycytes and subsets of neurons
  Osamu Takahashi; Mayuko Tanahashi; Saori Yokoi; Mari Kaneko; Tomoko Tokuhara; Kaori Yanaka; Shinichi Nakagawa; Hiroshi Maita
  Cold Spring Harbor Laboratory, 06 Jul. 2021
  AbstractGenomes of higher eukaryotes encode many uncharacterized proteins, and the functions of these proteins cannot be predicted from the primary sequences due to a lack of conserved functional domains. During a screening of novel noncoding RNAs abundantly expressed in mouse brains, we incidentally identified a gene termed Tanmp, which encoded an endoplasmic reticulum (ER) protein without known functional domains. Tanmp is specifically expressed in the nervous system, and the highest expression was observed in a specialized cell type called tanycyte that aligns the ventral wall of the third ventricle in the hypothalamus. Immunostaining of Tanmp revealed the fine morphology of tanycytes with highly branched apical ER membranes. Immunoprecipitation revealed that Tanmp associates with mitochondrial ATPase at least in vitro, and ER and mitochondrial signals occasionally overlapped in tanycytes. Mutant mice lacking Tanmp did not exhibit overt phenotypes, suggesting that Tanmp is not essential in mice reared under normal laboratory conditions. We also found that RNA probes that are predicted to uniquely detect Tanmp mRNA cross-reacted with uncharacterized RNAs, highlighting the importance of experimental validation of the specificity of probes during the hybridization-based study of RNA localization.
• Paraspeckles are constructed as block copolymer micelles.
  Tomohiro Yamazaki; Tetsuya Yamamoto; Hyura Yoshino; Sylvie Souquere; Shinichi Nakagawa; Gerard Pierron; Tetsuro Hirose
  The EMBO journal, 40, 12, e107270, 15 Jun. 2021, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, Paraspeckles are constructed by NEAT1_2 architectural long noncoding RNAs. Their characteristic cylindrical shapes, with highly ordered internal organization, distinguish them from typical liquid-liquid phase-separated condensates. We experimentally and theoretically investigated how the shape and organization of paraspeckles are determined. We identified the NEAT1_2 RNA domains responsible for shell localization of the NEAT1_2 ends, which determine the characteristic internal organization. Using the soft matter physics, we then applied a theoretical framework to understand the principles that determine NEAT1_2 organization as well as shape, number, and size of paraspeckles. By treating paraspeckles as amphipathic block copolymer micelles, we could explain and predict the experimentally observed behaviors of paraspeckles upon NEAT1_2 domain deletions or transcriptional modulation. Thus, we propose that paraspeckles are block copolymer micelles assembled through a type of microphase separation, micellization. This work provides an experiment-based theoretical framework for the concept that ribonucleoprotein complexes (RNPs) can act as block copolymers to form RNA-scaffolding biomolecular condensates with optimal sizes and structures in cells.
• ArcRNAs and the formation of nuclear bodies.
  Shinichi Nakagawa; Tomohiro Yamazaki; Taro Mannen; Tetsuro Hirose
  Mammalian genome : official journal of the International Mammalian Genome Society, 33, 2, 382, 401, 03 Jun. 2021, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
  English, Scientific journal, Long noncoding RNAs (lncRNAs) have long been collectively and passively defined as transcripts that do not encode proteins. However, extensive functional studies performed over the last decade have enabled the classification of lncRNAs into multiple categories according to their functions and/or molecular properties. Architectual RNAs (arcRNAs) are a group of lncRNAs that serve as architectural components of submicron-scale cellular bodies or nonmembranous organelles, which are composed of specific sets of proteins and nucleic acids involved in particular molecular processes. In this review, we focus on arcRNAs that function in the nucleus, which provide a structural basis for the formation of nuclear bodies, nonmembranous organelles in the cell nucleus. We will summarize the current list of arcRNAs and proteins associated with classic and more recently discovered nuclear bodies and discuss general rules that govern the formation of nuclear bodies, emphasizing weak multivalent interactions mediated by innately flexible biomolecules.
• The lncRNA Caren antagonizes heart failure by inactivating DNA damage response and activating mitochondrial biogenesis.
  Michio Sato; Tsuyoshi Kadomatsu; Keishi Miyata; Junco S Warren; Zhe Tian; Shunshun Zhu; Haruki Horiguchi; Aman Makaju; Anna Bakhtina; Jun Morinaga; Taichi Sugizaki; Kaname Hirashima; Kumiko Yoshinobu; Mai Imasaka; Masatake Araki; Yoshihiro Komohara; Tomohiko Wakayama; Shinichi Nakagawa; Sarah Franklin; Koichi Node; Kimi Araki; Yuichi Oike
  Nature communications, 12, 1, 2529, 2529, 05 May 2021, [Peer-reviewed], [International Magazine]
  English, Scientific journal, In the past decade, many long noncoding RNAs (lncRNAs) have been identified and their in vitro functions defined, although in some cases their functions in vivo remain less clear. Moreover, unlike nuclear lncRNAs, the roles of cytoplasmic lncRNAs are less defined. Here, using a gene trapping approach in mouse embryonic stem cells, we identify Caren (short for cardiomyocyte-enriched noncoding transcript), a cytoplasmic lncRNA abundantly expressed in cardiomyocytes. Caren maintains cardiac function under pathological stress by inactivating the ataxia telangiectasia mutated (ATM)-DNA damage response (DDR) pathway and activating mitochondrial bioenergetics. The presence of Caren transcripts does not alter expression of nearby (cis) genes but rather decreases translation of an mRNA transcribed from a distant gene encoding histidine triad nucleotide-binding protein 1 (Hint1), which activates the ATM-DDR pathway and reduces mitochondrial respiratory capacity in cardiomyocytes. Therefore, the cytoplasmic lncRNA Caren functions in cardioprotection by regulating translation of a distant gene and maintaining cardiomyocyte homeostasis.
• Spliceostatin A interaction with SF3B limits U1 snRNP availability and causes premature cleavage and polyadenylation.
  Rei Yoshimoto; Jagat K Chhipi-Shrestha; Tilman Schneider-Poetsch; Masaaki Furuno; A Maxwell Burroughs; Shohei Noma; Harukazu Suzuki; Yoshihide Hayashizaki; Akila Mayeda; Shinichi Nakagawa; Daisuke Kaida; Shintaro Iwasaki; Minoru Yoshida
  Cell chemical biology, 28, 9, 1356, 1365, 23 Mar. 2021, [Peer-reviewed], [International Magazine]
  English, Scientific journal, RNA splicing, a highly conserved process in eukaryotic gene expression, is seen as a promising target for anticancer agents. Splicing is associated with other RNA processing steps, such as transcription and nuclear export; however, our understanding of the interaction between splicing and other RNA regulatory mechanisms remains incomplete. Moreover, the impact of chemical splicing inhibition on long non-coding RNAs (lncRNAs) has been poorly understood. Here, we demonstrate that spliceostatin A (SSA), a chemical splicing modulator that binds to the SF3B subcomplex of the U2 small nuclear ribonucleoprotein particle (snRNP), limits U1 snRNP availability in splicing, resulting in premature cleavage and polyadenylation of MALAT1, a nuclear lncRNA, as well as protein-coding mRNAs. Therefore, truncated transcripts are exported into the cytoplasm and translated, resulting in aberrant protein products. Our work demonstrates that active recycling of the splicing machinery maintains homeostasis of RNA processing beyond intron excision.
• Ablation of lncRNA Miat attenuates pathological hypertrophy and heart failure.
  Liu Yang; Jianxin Deng; Wenxia Ma; Aijun Qiao; Shiyue Xu; Yang Yu; Chan Boriboun; Xiang Kang; Dunzheng Han; Patrick Ernst; Lufang Zhou; Jiawei Shi; Eric Zhang; Tao-Sheng Li; Hongyu Qiu; Shinichi Nakagawa; Seth Blackshaw; Jianyi Zhang; Gangjian Qin
  Theranostics, 11, 16, 7995, 8007, 2021, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, Rationale: The conserved long non-coding RNA (lncRNA) myocardial infarction associate transcript (Miat) was identified for its multiple single-nucleotide polymorphisms that are strongly associated with susceptibility to MI, but its role in cardiovascular biology remains elusive. Here we investigated whether Miat regulates cardiac response to pathological hypertrophic stimuli. Methods: Both an angiotensin II (Ang II) infusion model and a transverse aortic constriction (TAC) model were used in adult WT and Miat-null knockout (Miat-KO) mice to induce pathological cardiac hypertrophy. Heart structure and function were evaluated by echocardiography and histological assessments. Gene expression in the heart was evaluated by RNA sequencing (RNA-seq), quantitative real-time RT-PCR (qRT-PCR), and Western blotting. Primary WT and Miat-KO mouse cardiomyocytes were isolated and used in Ca2+ transient and contractility measurements. Results: Continuous Ang II infusion for 4 weeks induced concentric hypertrophy in WT mice, but to a lesser extent in Miat-KO mice. Surgical TAC for 6 weeks resulted in decreased systolic function and heart failure in WT mice but not in Miat-KO mice. In both models, Miat-KO mice displayed reduced heart-weight to tibia-length ratio, cardiomyocyte cross-sectional area, cardiomyocyte apoptosis, and cardiac interstitial fibrosis and a better-preserved capillary density, as compared to WT mice. In addition, Ang II treatment led to significantly reduced mRNA and protein expression of the Ca2+ cycling genes Sarcoplasmic/endoplasmic reticulum Ca2+ ATPase 2a (SERCA2a) and ryanodine receptor 2 (RyR2) and a dramatic increase in global RNA splicing events in the left ventricle (LV) of WT mice, and these changes were largely blunted in Miat-KO mice. Consistently, cardiomyocytes isolated from Miat-KO mice demonstrated more efficient Ca2+ cycling and greater contractility. Conclusions: Ablation of Miat attenuates pathological hypertrophy and heart failure, in part, by enhancing cardiomyocyte contractility.
• Inhibition of the long non-coding RNA NEAT1 protects cardiomyocytes from hypoxia in vitro via decreased pri-miRNA processing.
  Olof Gidlöf; Kerstin Bader; Selvi Celik; Mario Grossi; Shinichi Nakagawa; Tetsuro Hirose; Bernhard Metzler; Björn Olde; David Erlinge
  Cell death & disease, 11, 8, 677, 677, 13 Aug. 2020, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, While restoration of coronary blood flow to the ischemic heart is the most effective strategy for reducing infarct size, reperfusion injury represents a significant limiting factor on clinical outcomes in myocardial infarction patients. Ischemic preconditioning (IPC) has been shown to inhibit reperfusion injury and represents an attractive model for studying cardioprotective signal transduction pathways. Long non-coding RNAs (lncRNAs) are a structurally and functionally heterogenous class of RNA transcripts with unknown roles in IPC-induced cardioprotection. Through microarray-based expression profiling of 31,423 lncRNAs in cardiac tissue from IPC mice, we identified the nuclear transcript Neat1 to be rapidly and robustly decreased in response to IPC. siRNA-mediated knock down of Neat1 reduced apoptosis and necrosis in murine cardiomyocytes (CM) and human iPS-derived CMs in response to prolonged hypoxia and hypoxia-reoxygenation, assessed with Annexin V/propidium iodide-staining, a Caspase 3/7 activity assay, LDH release, and western blot for cleaved Caspase 3. Mechanistically, Neat1 was shown to regulate processing of pro-apoptotic microRNA-22 (miR-22) in murine and human CM nuclei using a luciferase reporter assay. Hypoxia-induced downregulation of Neat1 was shown to result in accumulation of unprocessed pri-miRNA and decreased availability of biologically active miRNA, including miR-22. Addition of exogenous synthetic miR-22 reversed the protective effect of Neat1 knock down in human iPS-CM. In conclusion, we have identified the nuclear lncRNA Neat1 as part of a conserved oxygen-sensitive feedback mechanism by regulation of miRNA processing and a potential target in cardioprotection.
• Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice.
  Michail S Kukharsky; Natalia N Ninkina; Haiyan An; Vsevolod Telezhkin; Wenbin Wei; Camille Rabesahala de Meritens; Johnathan Cooper-Knock; Shinichi Nakagawa; Tetsuro Hirose; Vladimir L Buchman; Tatyana A Shelkovnikova
  Translational psychiatry, 10, 1, 171, 171, 28 May 2020, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, NEAT1 is a highly and ubiquitously expressed long non-coding RNA (lncRNA) which serves as an important regulator of cellular stress response. However, the physiological role of NEAT1 in the central nervous system (CNS) is still poorly understood. In the current study, we addressed this by characterising the CNS function of the Neat1 knockout mouse model (Neat1-/- mice), using a combination of behavioural phenotyping, electrophysiology and expression analysis. RNAscope® in situ hybridisation revealed that in wild-type mice, Neat1 is expressed across the CNS regions, with high expression in glial cells and low expression in neurons. Loss of Neat1 in mice results in an inadequate reaction to physiological stress manifested as hyperlocomotion and panic escape response. In addition, Neat1-/- mice display deficits in social interaction and rhythmic patterns of activity but retain normal motor function and memory. Neat1-/- mice do not present with neuronal loss, overt neuroinflammation or gross synaptic dysfunction in the brain. However, cultured Neat1-/- neurons are characterised by hyperexcitability and dysregulated calcium homoeostasis, and stress-induced neuronal activity is also augmented in Neat1-/- mice in vivo. Gene expression analysis showed that Neat1 may act as a weak positive regulator of multiple genes in the brain. Furthermore, loss of Neat1 affects alternative splicing of genes important for the CNS function and implicated in neurological diseases. Overall, our data suggest that Neat1 is involved in stress signalling in the brain and fine-tunes the CNS functions to enable adaptive behaviour in response to physiological stress.
• Sexually dimorphic role of oxytocin in medaka mate choice.
  Saori Yokoi; Kiyoshi Naruse; Yasuhiro Kamei; Satoshi Ansai; Masato Kinoshita; Mari Mito; Shintaro Iwasaki; Shuntaro Inoue; Teruhiro Okuyama; Shinichi Nakagawa; Larry J Young; Hideaki Takeuchi
  Proceedings of the National Academy of Sciences of the United States of America, 117, 9, 4802, 4808, 03 Mar. 2020, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, Oxytocin is a central neuromodulator required for facilitating mate preferences for familiar individuals in a monogamous rodent (prairie vole), irrespective of sex. While the role of oxytocin in mate choice is only understood in a few monogamous species, its function in nonmonogamous species, comprising the vast majority of vertebrate species, remains unclear. To address this issue, we evaluated the involvement of an oxytocin homolog (isotocin, referred herein as oxt) in mate choice in medaka fish (Oryzias latipes). Female medaka prefer to choose familiar mates, whereas male medaka court indiscriminately, irrespective of familiarity. We generated mutants of the oxt ligand (oxt) and receptor genes (oxtr1 and oxtr2) and revealed that the oxt-oxtr1 signaling pathway was essential for eliciting female mate preference for familiar males. This pathway was also required for unrestricted and indiscriminate mating strategy in males. That is, either oxt or oxtr1 mutation in males decreased the number of courtship displays toward novel females, but not toward familiar females. Further, males with these mutations exhibited enhanced mate-guarding behaviors toward familiar females, but not toward novel females. In addition, RNA-sequencing (seq) analysis revealed that the transcription of genes involved in gamma-amino butyric acid metabolism as well as those encoding ion-transport ATPase are up-regulated in both oxt and oxtr1 mutants only in female medaka, potentially explaining the sex difference of the mutant phenotype. Our findings provide genetic evidence that oxt-oxtr1 signaling plays a role in the mate choice for familiar individuals in a sex-specific manner in medaka fish.
• Forced isoform switching of Neat1_1 to Neat1_2 leads to the loss of Neat1_1 and the hyperformation of paraspeckles but does not affect the development and growth of mice.
  Momo Isobe; Hikaru Toya; Mari Mito; Tomoki Chiba; Hiroshi Asahara; Tetsuro Hirose; Shinichi Nakagawa
  RNA (New York, N.Y.), 26, 3, 251, 264, Mar. 2020, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
  English, Scientific journal, Neat1 is a long noncoding RNA (lncRNA) that serves as an architectural component of the nuclear bodies known as paraspeckles. Two isoforms of Neat1, the short isoform Neat1_1 and the long isoform Neat1_2, are generated from the same gene locus by alternative 3' processing. Neat1_1 is the most abundant and the best conserved isoform expressed in various cell types, whereas Neat1_2 is expressed in a small population of particular cell types, including the tip cells of the intestinal epithelium. To investigate the physiological significance of isoform switching, we created mutant mice that solely expressed Neat1_2 by deleting the upstream polyadenylation (poly-A) signal (PAS) required for the production of Neat1_1. We observed the loss of Neat1_1 and strong up-regulation of Neat1_2 in various tissues and cells and the subsequent hyperformation of paraspeckles, especially in cells that normally express Neat1_2. However, the mutant mice were born at the expected Mendelian ratios and did not exhibit obvious external and histological abnormalities. These observations suggested that the hyperformation of paraspeckles does not interfere with the development and growth of these animals under normal laboratory conditions.
• Architectural RNAs for Membraneless Nuclear Body Formation.
  Tomohiro Yamazaki; Shinichi Nakagawa; Tetsuro Hirose
  Cold Spring Harbor symposia on quantitative biology, 84, 227, 237, 04 Feb. 2020, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Long noncoding RNAs (lncRNAs) are fundamental regulators of various cellular processes. A subset of lncRNAs, termed architectural RNAs (arcRNAs), function in the formation and maintenance of phase-separated membraneless organelles in multiple eukaryotic species. These membraneless organelles represent an important type of compartmentalization in the crowded cellular environment and have several distinct features. The NEAT1_2 lncRNA is a well-characterized arcRNA that functions as an essential scaffold of paraspeckle nuclear bodies. Here, we describe the biogenesis of paraspeckles on arcRNAs through phase separation, focusing on the specific functions of multiple NEAT1_2 RNA domains and their partner RNA-binding proteins. Finally, we present an updated model of paraspeckle formation and discuss future perspectives of research into arcRNA-instructed architectures of phase-separated nuclear bodies.
• What is the switch for coupling transcription and splicing? RNA Polymerase II C-terminal domain phosphorylation, phase separation and beyond.
  Hiroshi Maita; Shinichi Nakagawa
  Wiley interdisciplinary reviews. RNA, 11, 1, e1574, Jan. 2020, [Peer-reviewed], [Last author], [International Magazine]
  English, Phosphorylation of the RNA polymerase II C-terminal domain (Pol II CTD) has important roles in the kinetic coupling of splicing with transcription, which is essential for many genes to maintain correct splicing patterns. However, because of the extensively repeated low complexity sequences of Pol II CTD, it was unclear how phosphorylation-dependent molecular interactions were able to provide sufficient specificity to spatiotemporally partition various cotranscriptional events. Here we try to view the molecular mechanisms governing cotranscriptional splicing from the role of phase separation based on recent studies showing the ability of Pol II CTD to form droplets. This article is categorized under:   RNA Processing > Splicing Regulation/Alternative Splicing   RNA Processing > Splicing Mechanisms   RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
• The long noncoding RNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth.
  Adriaens C; Rambow F; Bervoets G; Silla T; Mito M; Chiba T; Asahara H; Hirose T; Nakagawa S; Jensen TH; Marine JC
  RNA (New York, N.Y.), 25, 12, 1681, 1695, Dec. 2019, [Peer-reviewed], ［Internationally co-authored］
  Scientific journal
• Creation of CRISPR-based germline-genome-engineered mice without ex vivo handling of zygotes by i-GONAD.
  Gurumurthy CB; Sato M; Nakamura A; Inui M; Kawano N; Islam MA; Ogiwara S; Takabayashi S; Matsuyama M; Nakagawa S; Miura H; Ohtsuka M
  Nature protocols, 14, 8, 2452, 2482, Aug. 2019, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, Methods to create genetically engineered mice involve three major steps: harvesting embryos from one set of females, microinjection of reagents into embryos ex vivo and their surgical transfer to another set of females. Although tedious, these methods have been used for more than three decades to create mouse models. We recently developed a method named GONAD (genome editing via oviductal nucleic acids delivery), which bypasses these steps. GONAD involves injection of CRISPR components (Cas9 mRNA and guide RNA (gRNA)) into the oviducts of pregnant females 1.5 d post conception, followed by in vivo electroporation to deliver the components into the zygotes in situ. Using GONAD, we demonstrated that target genes can be disrupted and analyzed at different stages of mouse embryonic development. Subsequently, we developed improved GONAD (i-GONAD) by delivering CRISPR ribonucleoproteins (RNPs; Cas9 protein or Cpf1 protein and gRNA) into day-0.7 pregnant mice, which made it suitable for routine generation of knockout and large-deletion mouse models. i-GONAD can also generate knock-in models containing up to 1-kb inserts when single-stranded DNA (ssDNA) repair templates are supplied. i-GONAD offers other advantages: it does not require vasectomized males and pseudo-pregnant females, the females used for i-GONAD are not sacrificed and can be used for other experiments, it can be easily adopted in laboratories lacking sophisticated microinjection equipment, and can be implemented by researchers skilled in small-animal surgery but lacking embryo-handling skills. Here, we provide a step-by-step protocol for establishing the i-GONAD method. The protocol takes ∼6 weeks to generate the founder mice.
• Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs.
  Shinoda S; Kitagawa S; Nakagawa S; Wei FY; Tomizawa K; Araki K; Araki M; Suzuki T; Suzuki T
  Nucleic acids research, 47, 16, 8734, 8745, Jul. 2019, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Post-transcriptional modifications in mitochondrial tRNAs (mt-tRNAs) play critical roles in mitochondrial protein synthesis, which produces respiratory chain complexes. In this study, we took advantage of mass spectrometric analysis to map 5-methylcytidine (m5C) at positions 48-50 in eight mouse and six human mt-tRNAs. We also confirmed the absence of m5C in mt-tRNAs isolated from Nsun2 knockout (KO) mice, as well as from NSUN2 KO human culture cells. In addition, we successfully reconstituted m5C at positions 48-50 of mt-tRNA in vitro with NSUN2 protein in the presence of S-adenosylmethionine. Although NSUN2 is predominantly localized to the nucleus and introduces m5C into cytoplasmic tRNAs and mRNAs, structured illumination microscopy clearly revealed NSUN2 foci inside mitochondria. These observations provide novel insights into the role of NSUN2 in the physiology and pathology of mitochondrial functions.
• Molecular anatomy of the architectural NEAT1 noncoding RNA: The domains, interactors, and biogenesis pathway required to build phase-separated nuclear paraspeckles.
  Hirose T; Yamazaki T; Nakagawa S
  Wiley interdisciplinary reviews. RNA, 10, 6, e1545, May 2019, [Peer-reviewed], [Last author], [International Magazine]
  English, Scientific journal, Long noncoding RNAs (lncRNAs) are extremely diverse and have various significant physiological functions. lncRNAs generally associate with specific sets of RNA-binding proteins (RBPs) to form functional ribonucleoprotein (RNP) complexes. NEAT1 is a highly abundant lncRNA in the mammalian cell nucleus that associates with specific RBPs to form NEAT1 RNPs. Intriguingly, cellular NEAT1 RNPs are extraordinarily large and can be detected using an optical microscope. These gigantic RNPs, so-called paraspeckles, are a type of membraneless nuclear body. Paraspeckles contain approximately 50 NEAT1 RNA molecules together with characteristic RBPs possessing aggregation-prone prion-like domains. Paraspeckle formation proceeds on the nascent NEAT1 transcript in conjunction with NEAT1 biogenesis, which exhibits various features that differ from those exhibited by mRNA biogenesis, including a lack of introns, noncanonical 3' end formation, and nuclear retention. These unique features may be required for the mechanism of paraspeckle formation. NEAT1 possesses three distinct RNA domains (A, B, and C), which function in stabilization (A), isoform switching (B), and paraspeckle assembly (C). In particular, the central C domain contains smaller subdomains that are high-affinity binding sites for the essential paraspeckle proteins (NONO and SFPQ) that subsequently polymerize along NEAT1. Subsequent recruitment of additional essential PSPs (FUS and RBM14) induces liquid-liquid phase separation to build a massive paraspeckle structure. Thus, the molecular anatomy of the NEAT1 arcRNA provides an ideal model to understand how lncRNAs form the functional RNP machinery. This article is characterized under: RNA Export and Localization > Nuclear Export/Import RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
• Long noncoding RNA NEAT1 modulates immune cell functions and is suppressed in early onset myocardial infarction patients.
  Gast M; Rauch B; Haghikia A; Nakagawa S; Haas J; Stroux A; Schmidt D; Schumann P; Weiss S; Jensen L; Kratzer A; Kraenkel N; Müller C; Börnigen D; Hirose T; Blankenberg S; Escher F; Kühl A; Kuss A; Meder B; Landmesser U; Zeller T; Poller W
  Cardiovascular research, Mar. 2019, [Peer-reviewed], ［Internationally co-authored］
• TChIP-Seq: Cell-Type-Specific Epigenome Profiling.
  Mari Mito; Mitsutaka Kadota; Shinichi Nakagawa; Shintaro Iwasaki
  Journal of visualized experiments : JoVE, 143, 23 Jan. 2019, [Peer-reviewed], [International Magazine]
  English, Epigenetic regulation plays central roles in gene expression. Since histone modification was discovered in the 1960s, its physiological and pathological functions have been extensively studied. Indeed, the advent of next-generation deep sequencing and chromatin immunoprecipitation (ChIP) via specific histone modification antibodies has revolutionized our view of epigenetic regulation across the genome. Conversely, tissues typically consist of diverse cell types, and their complex mixture poses analytic challenges to investigating the epigenome in a particular cell type. To address the cell type-specific chromatin state in a genome-wide manner, we recently developed tandem chromatin immunoprecipitation sequencing (tChIP-Seq), which is based on the selective purification of chromatin by tagged core histone proteins from cell types of interest, followed by ChIP-Seq. The goal of this protocol is the introduction of best practices of tChIP-Seq. This technique provides a versatile tool for tissue-specific epigenome investigation in diverse histone modifications and model organisms.
• The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription.
  Katsel P; Roussos P; Fam P; Khan S; Tan W; Hirose T; Nakagawa S; Pletnikov MV; Haroutunian V
  NPJ schizophrenia, 5, 1, 3, Jan. 2019, [Peer-reviewed], ［Internationally co-authored］
• UPA-seq: prediction of functional lncRNAs using differential sensitivity to UV crosslinking.
  Taiwa Komatsu; Saori Yokoi; Koichi Fujii; Mari Mito; Yusuke Kimura; Shintaro Iwasaki; Shinichi Nakagawa
  RNA (New York, N.Y.), 24, 12, 1785, 1802, Dec. 2018, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
  English, While a large number of long noncoding RNAs (lncRNAs) are transcribed from the genome of higher eukaryotes, systematic prediction of their functionality has been challenging due to the lack of conserved sequence motifs or structures. Assuming that some lncRNAs function as large ribonucleoprotein complexes and thus are easily crosslinked to proteins upon UV irradiation, we performed RNA-seq analyses of RNAs recovered from the aqueous phase after UV irradiation and phenol-chloroform extraction (UPA-seq). As expected, the numbers of UPA-seq reads mapped to known functional lncRNAs were remarkably reduced upon UV irradiation. Comparison with ENCODE eCLIP data revealed that lncRNAs that exhibited greater decreases upon UV irradiation preferentially associated with proteins containing prion-like domains (PrLDs). Fluorescent in situ hybridization (FISH) analyses revealed the nuclear localization of novel functional lncRNA candidates, including one that accumulated at the site of transcription. We propose that UPA-seq provides a useful tool for the selection of lncRNA candidates to be analyzed in depth in subsequent functional studies.
• Long noncoding RNA MALAT1 suppresses breast cancer metastasis.
  Kim J; Piao HL; Kim BJ; Yao F; Han Z; Wang Y; Xiao Z; Siverly AN; Lawhon SE; Ton BN; Lee H; Zhou Z; Gan B; Nakagawa S; Ellis MJ; Liang H; Hung MC; You MJ; Sun Y; Ma L
  Nature genetics, 50, 12, 1705, 1715, Dec. 2018, [Peer-reviewed], ［Internationally co-authored］
• Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu.
  Nakagawa S; Yamazaki T; Hirose T
  Open biology, 8, 10, Oct. 2018, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
  English, Scientific journal, Paraspeckles are nuclear bodies built on an architectural long noncoding RNA, NEAT1, and a series of studies have revealed their molecular components, fine internal structures and cellular and physiological functions. Emerging lines of evidence suggest that paraspeckle formation is elicited by phase separation of associating RNA-binding proteins containing intrinsically disordered regions, which induce ordered arrangement of paraspeckle components along NEAT1. In this review, we will summarize the history of paraspeckle research over the last couple of decades, especially focusing on the function and structure of the nuclear bodies. We also discuss the future directions of research on long noncoding RNAs that form 'RNP milieux', large and flexible phase-separated ribonucleoprotein complexes.
• Long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1) is critical for phenotypic switching of vascular smooth muscle cells.
  Ahmed ASI; Dong K; Liu J; Wen T; Yu L; Xu F; Kang X; Osman I; Hu G; Bunting KM; Crethers D; Gao H; Zhang W; Liu Y; Wen K; Agarwal G; Hirose T; Nakagawa S; Vazdarjanova A; Zhou J
  Proceedings of the National Academy of Sciences of the United States of America, 115, 37, E8660, E8667, Sep. 2018, [Peer-reviewed], ［Internationally co-authored］
• Immune system-mediated atherosclerosis caused by deficiency of long noncoding RNA MALAT1 in ApoE-/- mice.
  Gast M; Rauch BH; Nakagawa S; Haghikia A; Jasina A; Haas J; Nath N; Jensen L; Stroux A; Böhm A; Friebel J; Rauch U; Skurk C; Blankenberg S; Zeller T; Prasanth KV; Meder B; Kuss A; Landmesser U; Poller W
  Cardiovascular research, Aug. 2018, [Peer-reviewed], ［Internationally co-authored］
• Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation
  Tomohiro Yamazaki; Sylvie Souquere; Takeshi Chujo; Simon Kobelke; Yee Seng Chong; Archa H. Fox; Charles S. Bond; Shinichi Nakagawa; Gerard Pierron; Tetsuro Hirose
  Molecular Cell, 70, 6, 1038, 1053.e7, Cell Press, 21 Jun. 2018, [Peer-reviewed], ［Internationally co-authored］
  English, Scientific journal
• CO2-sensitive tRNA modification associated with human mitochondrial disease.
  Huan Lin; Kenjyo Miyauchi; Tai Harada; Ryo Okita; Eri Takeshita; Hirofumi Komaki; Kaoru Fujioka; Hideki Yagasaki; Yu-Ichi Goto; Kaori Yanaka; Shinichi Nakagawa; Yuriko Sakaguchi; Tsutomu Suzuki
  Nature communications, 9, 1, 1875, 1875, 14 May 2018, [Peer-reviewed], [International Magazine]
  English, Scientific journal, It has been generally thought that tRNA modifications are stable and static, and their frequencies are rarely regulated. N6-threonylcarbamoyladenosine (t6A) occurs at position 37 of five mitochondrial (mt-)tRNA species. We show that YRDC and OSGEPL1 are responsible for t6A37 formation, utilizing L-threonine, ATP, and CO2/bicarbonate as substrates. OSGEPL1-knockout cells exhibit respiratory defects and reduced mitochondrial translation. We find low level of t6A37 in mutant mt-tRNA isolated from the MERRF-like patient's cells, indicating that lack of t6A37 results in pathological consequences. Kinetic measurements of t6A37 formation reveal that the Km value of CO2/bicarbonate is extremely high (31 mM), suggesting that CO2/bicarbonate is a rate-limiting factor for t6A37 formation. Consistent with this, we observe a low frequency of t6A37 in mt-tRNAs isolated from human cells cultured without bicarbonate. These findings indicate that t6A37 is regulated by sensing intracellular CO2/bicarbonate concentration, implying that mitochondrial translation is modulated in a codon-specific manner under physiological conditions.
• Paraspeckles: Where Long Noncoding RNA Meets Phase Separation
  Archa H. Fox; Shinichi Nakagawa; Tetsuro Hirose; Charles S. Bond
  Trends in Biochemical Sciences, 43, 2, 124, 135, Elsevier Ltd, 01 Feb. 2018, [Peer-reviewed], ［Internationally co-authored］
  English
• Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing.
  Mari Mito; Mitsutaka Kadota; Kaori Tanaka; Yasuhide Furuta; Kuniya Abe; Shintaro Iwasaki; Shinichi Nakagawa
  Scientific reports, 8, 1, 1143, 1143, 18 Jan. 2018, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
  English, The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). FLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3-a chromatin modification mainly associated with active promoters-allowed us to survey the histone modifications in Camk2a-positive neurons. Indeed, tChIP-Seq identified hundreds of H3K4me3 modifications in promoter regions located upstream of genes associated with neuronal functions and genes with unknown functions in cortical neurons. tChIP-Seq provides a versatile approach to investigating the epigenetic modifications of particular cell types in vivo.
• Neat1 is a p53-inducible lincRNA essential for transformation suppression
  Stephano S. Mello; Carolyn Sinow; Nitin Raj; Pawel K. Mazur; Kathryn Bieging-Rolett; Daniela Kenzelmann Broz; Jamie F. Conklin Imam; Hannes Vogel; Laura D. Wood; Julien Sage; Tetsuro Hirose; Shinichi Nakagawa; John Rinn; Laura D. Attardi
  GENES & DEVELOPMENT, 31, 11, 1095, 1108, Jun. 2017, [Peer-reviewed]
  English, Scientific journal
• Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs
  Takeshi Chujo; Tomohiro Yamazaki; Tetsuya Kawaguchi; Satoshi Kurosaka; Toru Takumi; Shinichi Nakagawa; Tetsuro Hirose
  EMBO JOURNAL, 36, 10, 1447, 1462, May 2017, [Peer-reviewed]
  English, Scientific journal
• Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives.
  Poller W; Dimmeler S; Heymans S; Zeller T; Haas J; Karakas M; Leistner DM; Jakob P; Nakagawa S; Blankenberg S; Engelhardt S; Thum T; Weber C; Meder B; Hajjar R; andmesser U
  European heart journal, Apr. 2017, [Peer-reviewed]
• Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity
  Xiaona Chen; Liangqiang He; Yu Zhao; Yuying Li; Suyang Zhang; Kun Sun; Karl So; Fengyuan Chen; Liang Zhou; Leina Lu; Lijun Wang; Xihua Zhu; Xichen Bao; Miguel A. Esteban; Shinichi Nakagawa; Kannanganattu V. Prasanth; Zhenguo Wu; Hao Sun; Huating Wang
  CELL DISCOVERY, 3, 17002, Mar. 2017, [Peer-reviewed]
  English, Scientific journal
• Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders
  Mathieu Quesnel-Vallieres; Zahra Dargaei; Manuel Irimia; Thomas Gonatopoulos-Pournatzis; Joanna Y. Ip; Mingkun Wu; Timothy Sterne-Weiler; Shinichi Nakagawa; Melanie A. Woodin; Benjamin J. Blencowe; Sabine P. Cordes
  MOLECULAR CELL, 64, 6, 1023, 1034, Dec. 2016, [Peer-reviewed]
  English, Scientific journal
• Control of Chromosomal Localization of Xist by hnRNP U Family Molecules
  Takehisa Sakaguchi; Yuko Hasegawa; Neil Brockdorff; Ken Tsutsui; Kimiko M. Tsutsui; Takashi Sado; Shinichi Nakagawa
  DEVELOPMENTAL CELL, 39, 1, 11, 12, Oct. 2016, [Peer-reviewed]
  English
• Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization
  Jason A. West; Mari Mito; Satoshi Kurosaka; Toru Takumi; Chiharu Tanegashima; Takeshi Chujo; Kaori Yanaka; Robert E. Kingston; Tetsuro Hirose; Charles Bond; Archa Fox; Shinichi Nakagawa
  JOURNAL OF CELL BIOLOGY, 214, 7, 817, 830, Sep. 2016, [Peer-reviewed]
  English, Scientific journal
• Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA
  Aparna Anantharaman; Mahdieh Jadaliha; Vidisha Tripathi; Shinichi Nakagawa; Tetsuro Hirose; Michael F. Jantsch; Supriya G. Prasanth; Kannanganattu V. Prasanth
  SCIENTIFIC REPORTS, 6, 34043, Sep. 2016, [Peer-reviewed]
  English, Scientific journal
• p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity
  Carmen Adriaens; Laura Standaert; Jasmine Barra; MathilDe latil; Annelien Verfaillie; Peter Kalev; Bram Boeckx; Paul W. G. Wijnhoven; Enrico Radaelli; William Vermi; Eleonora Leucci; Gaelle Lapouge; Benjamin Beck; Joost van den Oord; Shinichi Nakagawa; Tetsuro Hirose; Anna A. Sablina; Diether Lambrechts; Stein Aerts; Cedric Blanpain; Jean-Christophe Marine
  NATURE MEDICINE, 22, 8, 861, +, Aug. 2016, [Peer-reviewed]
  English, Scientific journal
• Gomafu IncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine
  Joanna Y. Ip; Masamitsu Sone; Chieko Nashiki; Qun Pan; Kiyoyuki Kitaichi; Kaori Yanaka; Takaya Abe; Keizo Takao; Tsuyoshi Miyakawa; Benjamin J. Blencowe; Shinichi Nakagawa
  SCIENTIFIC REPORTS, 6, 27204, Jun. 2016, [Peer-reviewed]
  English, Scientific journal
• Simultaneous multicolor detection of RNA and proteins using super-resolution microscopy
  Mari Mito; Tetsuya Kawaguchi; Tetsuro Hirose; Shinichi Nakagawa
  METHODS, 98, 158, 165, Apr. 2016, [Peer-reviewed]
  English, Scientific journal
• Long noncoding RNA MALAT1-derived mascRNA is involved in cardiovascular innate immunity
  Martina Gast; Blanche Schroen; Antje Voigt; Jan Haas; Uwe Kuehl; Dirk Lassner; Carsten Skurk; Felicitas Escher; Xiaomin Wang; Adelheid Kratzer; Katharina Michalik; Anna Papageorgiou; Tim Peters; Madlen Loebel; Sabrina Wilk; Nadine Althof; Kannanganattu V. Prasanth; Hugo Katus; Benjamin Meder; Shinichi Nakagawa; Carmen Scheibenbogen; Heinz-Peter Schultheiss; Ulf Landmesser; Stefanie Dimmeler; Stephane Heymans; Wolfgang Poller
  JOURNAL OF MOLECULAR CELL BIOLOGY, 8, 2, 178, 181, Apr. 2016, [Peer-reviewed]
  English
• Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA
  Xinying Zong; Shinichi Nakagawa; Susan M. Freier; Jingyi Fei; Taekjip Ha; Supriya G. Prasanth; Kannanganattu V. Prasanth
  NUCLEIC ACIDS RESEARCH, 44, 6, 2898, 2908, Apr. 2016, [Peer-reviewed]
  English, Scientific journal
• Long Non-Coding RNA Malat-1 Is Dispensable during Pressure Overload-Induced Cardiac Remodeling and Failure in Mice
  Tim Peters; Steffie Hermans-Beijnsberger; Abdelaziz Beqqali; Nicole Bitsch; Shinichi Nakagawa; Kannanganattu V. Prasanth; Leon J. de Windt; Ralph J. van Oort; Stephane Heymans; Blanche Schroen
  PLOS ONE, 11, 2, e0150236, Feb. 2016, [Peer-reviewed]
  English, Scientific journal
• MALAT1 long non-coding RNA in cancer
  Rei Yoshimoto; Akila Mayeda; Minoru Yoshida; Shinichi Nakagawa
  BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, 1859, 1, 192, 199, Jan. 2016, [Peer-reviewed]
  English, Scientific journal
• Clues to long noncoding RNA taxonomy.
  Hirose T; Nakagawa S
  Biochimica et biophysica acta, 1859, 1, 1, 2, Jan. 2016, [Peer-reviewed]
• Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNA(H)
  Kentaro Ishida; Kenjyo Miyauchi; Yuko Kimura; Mari Mito; Shunpei Okada; Tsutomu Suzuki; Shinichi Nakagawa
  GENES TO CELLS, 20, 11, 887, 901, Nov. 2015, [Peer-reviewed]
  English, Scientific journal
• MALAT1 long non-coding RNA in cancer.
  Yoshimoto R; Mayeda A; Yoshida M; Nakagawa S
  Biochimica et biophysica acta, 1859, 1, 192, 199, Oct. 2015, [Peer-reviewed]
• Xist Exon 7 Contributes to the Stable Localization of Xist RNA on the Inactive X-Chromosome
  Norishige Yamada; Yuko Hasegawa; Minghui Yue; Tomofumi Hamada; Shinichi Nakagawa; Yuya Ogawa
  PLoS Genetics, 11, 8, e1005430, Public Library of Science, 01 Aug. 2015, [Peer-reviewed]
  English, Scientific journal
• Lessons from reverse-genetic studies of lncRNAs.
  Nakagawa S
  Biochimica et biophysica acta, 1859, 1, 177, 183, Jun. 2015, [Peer-reviewed]
• Long noncoding RNA in epigenetic gene regulation
  Yuko Hasegawa; Shinichi Nakagawa
  Long Noncoding RNAs Structures and Functions, 133, 149, Springer Japan, 01 Jan. 2015, [Peer-reviewed]
  English, In book
• Super-resolution imaging of nuclear bodies by STED microscopy.
  Yasushi Okada; Shinichi Nakagawa
  Methods in molecular biology (Clifton, N.J.), 1262, 21, 35, 2015, [Peer-reviewed], [International Magazine]
  English, The sizes of nuclear bodies and other nuclear structures are normally no more than a few hundred nanometers. This size is below the resolution limit of light microscopy and thus requires electron microscopy for direct observation. Recent developments in super-resolution microscopy have extended the resolution of light microscopy to beyond 100 nm. Here, we describe a super-resolution technique, gated STED, for the analysis of the structure of nuclear bodies, with emphasis on the sample preparation and other technical tips that are important to obtain high-quality super-resolution images.
• SiRNA screening of nuclear proteins.
  Hasegawa Y; Nakagawa S
  Methods in molecular biology (Clifton, N.J.), 1262, 333, 348, 2015, [Peer-reviewed]
• The long noncoding RNA Neat1 is required for mammary gland development and lactation
  Laura Standaert; Carmen Adriaens; Enrico Radaelli; Alexandra Van Keymeulen; Cedric Blanpain; Tetsuro Hirose; Shinichi Nakagawa; Jean-Christophe Marine
  RNA, 20, 12, 1844, 1849, Dec. 2014, [Peer-reviewed]
  English, Scientific journal
• The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice
  Shinichi Nakagawa; Masayuki Shimada; Kaori Yanaka; Mari Mito; Takashi Arai; Eiki Takahashi; Youko Fujita; Toshihiko Fujimori; Laura Standaert; Jean-Christophe Marine; Tetsuro Hirose
  DEVELOPMENT, 141, 23, 4618, 4627, Dec. 2014, [Peer-reviewed]
  English, Scientific journal
• The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer
  Dimple Chakravarty; Andrea Sboner; Sujit S. Nair; Eugenia Giannopoulou; Ruohan Li; Sven Hennig; Juan Miguel Mosquera; Jonathan Pauwels; Kyung Park; Myriam Kossai; Theresa Y. MacDonald; Jacqueline Fontugne; Nicholas Erho; Ismael A. Vergara; Mercedeh Ghadessi; Elai Davicioni; Robert B. Jenkins; Nallasivam Palanisamy; Zhengming Chen; Shinichi Nakagawa; Tetsuro Hirose; Neil H. Bander; Himisha Beltran; Archa H. Fox; Olivier Elemento; Mark A. Rubin
  NATURE COMMUNICATIONS, 5, 5, 5383, Nov. 2014, [Peer-reviewed]
  English, Scientific journal
• Analysis of the subcellular distribution of RNA by fluorescence in situ hybridization
  Shinichi Nakagawa
  Regulatory Non-Coding RNAs: Methods and Protocols, 1206, 107, 122, Springer New York, 20 Sep. 2014, [Peer-reviewed]
  English, In book
• Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1
  Akira Ishizuka; Yuko Hasegawa; Kentaro Ishida; Kaori Yanaka; Shinichi Nakagawa
  GENES TO CELLS, 19, 9, 704, 721, Sep. 2014, [Peer-reviewed]
  English, Scientific journal
• Yb Integrates piRNA Intermediates and Processing Factors into Perinuclear Bodies to Enhance piRISC Assembly
  Yukiko Murota; Hirotsugu Ishizu; Shinichi Nakagawa; Yuka W. Iwasaki; Shinsuke Shibata; Miharu K. Kamatani; Kuniaki Saito; Hideyuki Okano; Haruhiko Siomi; Mikiko C. Siomi
  CELL REPORTS, 8, 1, 103, 113, Jul. 2014, [Peer-reviewed]
  English, Scientific journal
• Nuclear lncRNAs as epigenetic regulators-beyond skepticism.
  Nakagawa S; Kageyama Y
  Biochimica et biophysica acta, 1839, 3, 215, 222, Mar. 2014, [Peer-reviewed]
• Gathering around Firre
  Shinichi Nakagawa; Tatsuya Hirano
  NATURE STRUCTURAL & MOLECULAR BIOLOGY, 21, 3, 207, 208, Mar. 2014, [Peer-reviewed]
  English
• The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing
  G. Barry; J. A. Briggs; D. P. Vanichkina; E. M. Poth; N. J. Beveridge; V. S. Ratnu; S. P. Nayler; K. Nones; J. Hu; T. W. Bredy; S. Nakagawa; F. Rigo; R. J. Taft; M. J. Cairns; S. Blackshaw; E. J. Wolvetang; J. S. Mattick
  Molecular Psychiatry, 19, 4, 486, 494, Nature Publishing Group, 2014, [Peer-reviewed]
  English, Scientific journal
• NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies
  Tetsuro Hirose; Giorgio Virnicchi; Akie Tanigawa; Takao Naganuma; Ruohan Li; Hiroshi Kimura; Takahide Yokoi; Shinichi Nakagawa; Marianne Benard; Archa H. Fox; Gerard Pierron
  MOLECULAR BIOLOGY OF THE CELL, 25, 1, 169, 183, Jan. 2014, [Peer-reviewed]
  English, Scientific journal
• The long non-coding RNA nuclear-enriched abundant transcript 1_2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis
  T. Naganuma; S. Nakagawa; A. Tanigawa; Y.F. Sasaki; N. Goshima; T. Hirose
  EMBO J, 31, 4020, 4034, Jul. 2013, [Peer-reviewed], [International Magazine]
  English, Scientific journal, BACKGROUND: A long non-coding RNA (lncRNA), nuclear-enriched abundant transcript 1_2 (NEAT1_2), constitutes nuclear bodies known as "paraspeckles". Mutations of RNA binding proteins, including TAR DNA-binding protein-43 (TDP-43) and fused in sarcoma/translocated in liposarcoma (FUS/TLS), have been described in amyotrophic lateral sclerosis (ALS). ALS is a devastating motor neuron disease, which progresses rapidly to a total loss of upper and lower motor neurons, with consciousness sustained. The aim of this study was to clarify the interaction of paraspeckles with ALS-associated RNA-binding proteins, and to identify increased occurrence of paraspeckles in the nucleus of ALS spinal motor neurons. RESULTS: In situ hybridization (ISH) and ultraviolet cross-linking and immunoprecipitation were carried out to investigate interactions of NEAT1_2 lncRNA with ALS-associated RNA-binding proteins, and to test if paraspeckles form in ALS spinal motor neurons. As the results, TDP-43 and FUS/TLS were enriched in paraspeckles and bound to NEAT1_2 lncRNA directly. The paraspeckles were localized apart from the Cajal bodies, which were also known to be related to RNA metabolism. Analyses of 633 human spinal motor neurons in six ALS cases showed NEAT1_2 lncRNA was upregulated during the early stage of ALS pathogenesis. In addition, localization of NEAT1_2 lncRNA was identified in detail by electron microscopic analysis combined with ISH for NEAT1_2 lncRNA. The observation indicating specific assembly of NEAT1_2 lncRNA around the interchromatin granule-associated zone in the nucleus of ALS spinal motor neurons verified characteristic paraspeckle formation. CONCLUSIONS: NEAT1_2 lncRNA may act as a scaffold of RNAs and RNA binding proteins in the nuclei of ALS motor neurons, thereby modulating the functions of ALS-associated RNA-binding proteins during the early phase of ALS. These findings provide the first evidence of a direct association between paraspeckle formation and a neurodegenerative disease, and may shed light on the development of novel therapeutic targets for the treatment of ALS.
• The long non-coding RNA nuclear-enriched abundant transcript 1-2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis
  Yoshinori Nishimoto; Shinichi Nakagawa; Tetsuro Hirose; Hirotaka James Okano; Masaki Takao; Shinsuke Shibata; Satoshi Suyama; Ken-Ichiro Kuwako; Takao Imai; Shigeo Murayama; Norihiro Suzuki; Hideyuki Okano
  Molecular Brain, 6, 1, 31, 2013, [Peer-reviewed]
  English, Scientific journal
• Alternative 3 '-end processing of long noncoding RNA initiates construction of nuclear paraspeckles
  Takao Naganuma; Shinichi Nakagawa; Akie Tanigawa; Yasnory F. Sasaki; Naoki Goshima; Tetsuro Hirose
  EMBO JOURNAL, 31, 20, 4020, 4034, Oct. 2012, [Peer-reviewed]
  English, Scientific journal
• Paraspeckles: Possible nuclear hubs by the RNA for the RNA
  Tetsuro Hirose; Shinichi Nakagawa
  Biomolecular Concepts, 3, 5, 415, 428, De Gruyter Mouton, 01 Oct. 2012, [Peer-reviewed]
  English
• Paraspeckle nuclear bodies-useful uselessness?
  Shinichi Nakagawa; Tetsuro Hirose
  CELLULAR AND MOLECULAR LIFE SCIENCES, 69, 18, 3027, 3036, Sep. 2012, [Peer-reviewed]
  English
• Malat1 is not an essential component of nuclear speckles in mice
  Shinichi Nakagawa; Joanna Y. Ip; Go Shioi; Vidisha Tripathi; Xinying Zong; Tetsuro Hirose; Kannanganattu V. Prasanth
  RNA-A PUBLICATION OF THE RNA SOCIETY, 18, 8, 1487, 1499, Aug. 2012, [Peer-reviewed]
  English, Scientific journal
• Long non-coding RNAs in nuclear bodies
  Joanna Y. Ip; Shinichi Nakagawa
  DEVELOPMENT GROWTH & DIFFERENTIATION, 54, 1, 44, 54, Jan. 2012, [Peer-reviewed]
  English
• Tsukushi functions as a Wnt signaling inhibitor by competing with Wnt2b for binding to transmembrane protein Frizzled4
  Kunimasa Ohta; Ayako Ito; Sei Kuriyama; Giuseppe Lupo; Mitsuko Kosaka; Shin-Ichi Ohnuma; Shinichi Nakagawa; Hideaki Tanaka
  Proceedings of the National Academy of Sciences of the United States of America, 108, 36, 14962, 14967, 06 Sep. 2011, [Peer-reviewed]
  English, Scientific journal
• Revisiting the function of nuclear scaffold/matrix binding proteins in X chromosome inactivation
  Yuko Hasegawa; Shinichi Nakagawa
  RNA BIOLOGY, 8, 5, 735, 739, Sep. 2011, [Peer-reviewed]
  English
• eXIST with matrix-associated proteins
  Shinichi Nakagawa; Kannanganattu V. Prasanth
  TRENDS IN CELL BIOLOGY, 21, 6, 321, 327, Jun. 2011, [Peer-reviewed]
  English
• Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1
  Hitomi Tsuiji; Rei Yoshimoto; Yuko Hasegawa; Masaaki Furuno; Minoru Yoshida; Shinichi Nakagawa
  GENES TO CELLS, 16, 5, 479, 490, May 2011, [Peer-reviewed]
  English, Scientific journal
• Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice
  Shinichi Nakagawa; Takao Naganuma; Go Shioi; Tetsuro Hirose
  JOURNAL OF CELL BIOLOGY, 193, 1, 31, 39, Apr. 2011, [Peer-reviewed]
  English, Scientific journal
• Ectopic Mitf in the Embryonic Chick Retina by Co-transfection of beta-Catenin and Otx2
  Peter D. Westenskow; Jon B. McKean; Fumi Kubo; Shinichi Nakagawa; Sabine Fuhrmann
  INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, 51, 10, 5328, 5335, Oct. 2010, [Peer-reviewed]
  English, Scientific journal
• The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA
  Yuko Hasegawa; Neil Brockdorff; Shinji Kawano; Kimiko Tsutui; Ken Tsutui; Shinichi Nakagawa
  DEVELOPMENTAL CELL, 19, 3, 469, 476, Sep. 2010, [Peer-reviewed]
  English, Scientific journal
• Cath6, a bHLH Atonal Family Proneural Gene, Negatively Regulates Neuronal Differentiation in the Retina
  Fumi Kubo; Shinichi Nakagawa
  DEVELOPMENTAL DYNAMICS, 239, 9, 2492, 2500, Sep. 2010, [Peer-reviewed]
  English, Scientific journal
• LIM family transcription factors regulate the subtype-specific morphogenesis of retinal horizontal cells at post-migratory stages
  Akiko Suga; Masanori Taira; Shinichi Nakagawa
  DEVELOPMENTAL BIOLOGY, 330, 2, 318, 328, Jun. 2009, [Peer-reviewed]
  English, Scientific journal
• Hairy1 acts as a node downstream of Wnt signaling to maintain retinal stem cell-like progenitor cells in the chick ciliary marginal zone
  Fumi Kubo; Shinichi Nakagawa
  DEVELOPMENT, 136, 11, 1823, 1833, Jun. 2009, [Peer-reviewed]
  English, Scientific journal
• Wnt signaling in retinal stem cells and regeneration
  Fumi Kubo; Shinichi Nakagawa
  DEVELOPMENT GROWTH & DIFFERENTIATION, 50, 4, 245, 251, May 2008, [Peer-reviewed]
  English
• Transposon-mediated stable integration and tetracycline-inducible expression of electroporated transgenes in chicken embryos
  Yoshiko Takahashi; Tadayoshi Watanabe; Shinichi Nakagawa; Koichi Kawakami; Yuki Sato
  AVIAN EMBRYOLOGY, 2ND EDITION, 87, 271, +, 2008, [Peer-reviewed]
  English, In book
• Tsukushi is a Frizzled4 ligand that regulates the proliferation of retinal stem cells in competition with Wnt2b
  Kunimasa Ohta; Ayako Ito; Sei Kuriyama; Rika Nakayama; Naoko Oshima; Mitsuko Kosaka; Shinichi Ohnuma; Shinichi Nakagawa; Hideaki Tanaka
  NEUROSCIENCE RESEARCH, 61, S42, S42, 2008, [Peer-reviewed]
  English
• Melanocortin 2 receptor is required for adrenal gland development, steroidogenesis, and neonatal gluconeogenesis
  Dai Chida; Shinichi Nakagawa; So Nagai; Hiroshi Sagara; Harumi Katsumata; Toshihiro Imaki; Harumi Suzuki; Fumiko Mitani; Tadashi Ogishima; Chikara Shimizu; Hayato Kotaki; Shigeru Kakuta; Katsuko Sudo; Takao Koike; Mitsurnasa Kubo; Yoichiro Iwakura
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104, 46, 18205, 18210, Nov. 2007, [Peer-reviewed]
  English, Scientific journal
• The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons
  Masamitsu Sone; Tetsutaro Hayashi; Hiroshi Tarui; Kiyokazu Agata; Masatoshi Takeichi; Shinichi Nakagawa
  JOURNAL OF CELL SCIENCE, 120, 15, 2498, 2506, Aug. 2007, [Peer-reviewed]
  English, Scientific journal
• Tsukushi inhibits the proliferation of retinal stem/progenitor cells
  Kunimasa Ohta; Ayako Ito; Sei Kuriyama; Shinichi Ohnuma; Mitsuko Kosaka; Shinichi Nakagawa; H. Tanaka
  DEVELOPMENTAL BIOLOGY, 306, 1, 391, 391, Jun. 2007, [Peer-reviewed]
  English
• Tet-on inducible system combined with in ovo electroporation dissects multiple roles of genes in somitogenesis of chicken embryos
  Tadayoshi Watanabe; Daisuke Saito; Koji Tanabe; Rinako Suetsugu; Yukiko Nakaya; Shinichi Nakagawa; Yoshiko Takahashi
  DEVELOPMENTAL BIOLOGY, 305, 2, 625, 636, May 2007, [Peer-reviewed]
  English, Scientific journal
• Stable integration and conditional expression of electroporated transgenes in chicken embryos
  Yuki Sato; Toshiharu Kasai; Shinichi Nakagawa; Koji Tanabe; Tadayoshi Watanabe; Koichi Kawakami; Yoshiko Takahashi
  DEVELOPMENTAL BIOLOGY, 305, 2, 616, 624, May 2007, [Peer-reviewed]
  English, Scientific journal
• Cadherin is required for dendritic morphogenesis and synaptic terminal organization of retinal horizontal cells
  Koji Tanabe; Yoshiko Takahashi; Yuki Sato; Koichi Kawakami; Masatoshi Takeichi; Shinichi Nakagawa
  DEVELOPMENT, 133, 20, 4085, 4096, Oct. 2006, [Peer-reviewed]
  English, Scientific journal
• Embryonic stem cells that differentiate into RPE cell precursors in vitro develop into RPE cell monolayers in vivo
  H Aoki; A Hara; S Nakagawa; T Motohashi; M Hirano; Y Takahashi; T Kunisada
  EXPERIMENTAL EYE RESEARCH, 82, 2, 265, 274, Feb. 2006, [Peer-reviewed]
  English, Scientific journal
• Wnt2b inhibits differentiation of retinal progenitor cells in the absence of Notch activity by downregulating the expression of proneural genes
  F Kubo; M Takeichi; S Nakagawa
  DEVELOPMENT, 132, 12, 2759, 2770, Jun. 2005, [Peer-reviewed]
  English, Scientific journal
• Identification of a nonchordate-type classic cadherin in vertebrates: Chicken Hz-cadherin is expressed in horizontal cells of the neural retina and contains a nonchordate-specific domain complex
  K Tanabe; M Takeichi; S Nakagawa
  DEVELOPMENTAL DYNAMICS, 229, 4, 899, 906, Apr. 2004, [Peer-reviewed]
  English, Scientific journal
• Identification of the laminar-inducing factor: Wnt-signal from the anterior rim induces correct laminar formation of the neural retina in vitro
  S Nakagawa; S Takada; R Takada; M Takeichi
  DEVELOPMENTAL BIOLOGY, 260, 2, 414, 425, Aug. 2003, [Peer-reviewed]
  English, Scientific journal
• Wnt2b controls retinal cell differentiation at the ciliary marginal zone
  F Kubo; M Takeichi; S Nakagawa
  DEVELOPMENT, 130, 3, 587, 598, Feb. 2003, [Peer-reviewed]
  English, Scientific journal
• Cadherin-dependent cell-cell adhesion.
  Takeichi M; Nakagawa S
  Current protocols in cell biology, Chapter 9, Unit 9.3, May 2001, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Differential treatment of cells with trypsin can be used to distinguish Ca(2+)-dependent adhesion (CDS) from Ca(2+)-independent adhesion (CIDS). Cadherins appear to be a unique family of molecules whose structure and function as adhesion molecules are protected from trypsin in the presence of Ca(2+). This unit provides protocols for preparation and analysis of cells for cadherin-dependent adhesion in short-term and long-term aggregation assays. The functions of different cadherins can be assessed in mixed aggregate assays. Fluorescence antibody-based assays are used to identify specific cadherins and their associated catenins, and transformation of cells with specific constructs can be used to assay adhesion in cells with loss of cadherin activity.
• Patterning of cell assemblies regulated by adhesion receptors of the cadherin superfamily
  M Takeichi; S Nakagawa; S Aono; T Usui; T Uemura
  PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES, 355, 1399, 885, 890, Jul. 2000, [Peer-reviewed]
  English, Scientific journal
• Morphologic fate of diencephalic prosomeres and their subdivisions revealed by mapping cadherin expression
  C Redies; M Ast; S Nakagawa; M Takeichi; M Martinez-de-la-Torre; L Puelles
  JOURNAL OF COMPARATIVE NEUROLOGY, 421, 4, 481, 514, Jun. 2000, [Peer-reviewed]
  English
• Blockade of cadherin-6B activity perturbs the distribution of PSD-95 family proteins in retinal neurones
  Y Honjo; S Nakagawa; M Takeichi
  GENES TO CELLS, 5, 4, 309, 318, Apr. 2000, [Peer-reviewed]
  English, Scientific journal
• Ephrin-B regulates the ipsilateral routing of retinal axons at the optic chiasm
  S Nakagawa; C Brennan; KG Johnson; D Shewan; WA Harris; CE Holt
  NEURON, 25, 3, 599, 610, Mar. 2000, [Peer-reviewed]
  English, Scientific journal
• p120(ctn) acts as an inhibitory regulator of cadherin function in colon carcinoma cells
  S Aono; S Nakagawa; AB Reynolds; M Takeichi
  JOURNAL OF CELL BIOLOGY, 145, 3, 551, 562, May 1999, [Peer-reviewed]
  English, Scientific journal
• Combinatorial expression of cadherins in the tectum and the sorting of neurites in the tectofugal pathways of the chicken embryo
  JCP Wohrn; S Nakagawa; M Ast; M Takeichi; C Redies
  NEUROSCIENCE, 90, 3, 985, 1000, 1999, [Peer-reviewed]
  English, Scientific journal
• Neural crest emigration from the neural tube depends on regulated cadherin expression
  S Nakagawa; M Takeichi
  DEVELOPMENT, 125, 15, 2963, 2971, Aug. 1998, [Peer-reviewed]
  English, Scientific journal
• Cadherin expression in the retina and retinofugal pathways of the chicken embryo
  JCP Wohrn; L Puelles; S Nakagawa; M Takeichi; C Redies
  JOURNAL OF COMPARATIVE NEUROLOGY, 396, 1, 20, 38, Jun. 1998, [Peer-reviewed]
  English, Scientific journal
• Cadherin-defined segments and parasagittal cell ribbons in the developing chicken cerebellum
  K Arndt; S Nakagawa; M Takeichi; C Redies
  MOLECULAR AND CELLULAR NEUROSCIENCE, 10, 5-6, 211, 228, Apr. 1998, [Peer-reviewed]
  English, Scientific journal
• Cadherin-defined segments and parasagittal cell ribbons in the developing chicken cerebellum
  K Arndt; S Nakagawa; M Takeichi; C Redies
  MOLECULAR AND CELLULAR NEUROSCIENCE, 10, 5-6, 211, 228, Apr. 1998, [Peer-reviewed]
  English, Scientific journal
• N-cadherin is crucial for heart formation in the chick embryo
  S Nakagawa; M Takeichi
  DEVELOPMENT GROWTH & DIFFERENTIATION, 39, 4, 451, 455, Aug. 1997, [Peer-reviewed]
  English, Scientific journal
• In vivo evidence of the critical role of cadherin-5 in murine vascular integrity.
  N Matsuyoshi; K Toda; Y Horiguchi; T Tanaka; S Nakagawa; M Takeichi; S Imamura
  Proceedings of the Association of American Physicians, 109, 4, 362, 71, Jul. 1997, [International Magazine]
  English, Scientific journal, Vascular endothelial cell-cell adhesion is crucial for the regulation of vascular functions and is associated with many circulatory disorders. We isolated a rat monoclonal antibody (VECD1) recognizing the mouse vascular endothelial cell adhesion molecule and found that it inhibited vascular endothelial cell-cell association. We sequenced a full-length cDNA of the antigen that was identical to mouse cadherin-5. L-cells transfected with its cDNA acquired cell-cell adhesiveness, and these transfectants reacted with VECD1 at cell-cell contact areas. We studied the role of mouse cadherin-5 in vascular functions. The addition of VECD1 antibody to a cultured vascular endothelial cell line (F-2) caused the detachment of each cell. Although normal F-2 cells formed tubular structures on Matrigel, VECD1 disturbed the tubulogenesis. VECD1 also increased the permeability through the F-2 cell layer. To clarify the in vivo function of mouse cadherin-5, we intraperitoneally injected the hybridomas producing VECD1 into adult mice. Severe venous stasis and subcutaneous hemorrhage were induced within several days after the injection, resulting in the early death of the animals. These findings are evidence of an essential role of cadherin-5 in the regulation of vascular endothelial cell-cell adhesion in vivo.
• 11 Selective Aggregation Assays for Embryonic Brain Cells and Cell lines
  Shinichi Nakagawa; Hiroaki Matsunami; Masatoshi Takeichi
  Current Topics in Developmental Biology, 36, C, 197, 210, 01 Jan. 1997, [Peer-reviewed]
  English, Scientific journal
• NEURAL CREST CELL-CELL ADHESION CONTROLLED BY SEQUENTIAL AND SUBPOPULATION-SPECIFIC EXPRESSION OF NOVEL CADHERINS
  S NAKAGAWA; M TAKEICHI
  DEVELOPMENT, 121, 5, 1321, 1332, May 1995, [Peer-reviewed]
  English, Scientific journal

• ブロック共重合体ミセル化:RNA-タンパク質複合体構築の新たな設計原理
  山崎智弘; 山崎智弘; 谷口一郎; 山本哲也; SOUQUERE Sylvie; 梅崎創太; 中川真一; PIERRON Gerard; 廣瀬哲郎; 廣瀬哲郎; 廣瀬哲郎, 日本分子生物学会年会プログラム・要旨集(Web), 48th, 2025
• Exon-skipping for Fukuyama congenital muscular dystrophy
  池田真理子; 芳本玲; 中川真一, 日本小児科学会雑誌, 129, 2, 2025
• 4.5SH RNA as a natural gene therapeutic
  中川真一; 芳本玲, 医学のあゆみ, 292, 11, 2025
• Functions of cytoplasmic lncRNAs - circRNA, Cyrano, and NORAD
  中川真一, 実験医学, 42, 15, 2024
• Cajal Bodyの形成と機能におけるCoilin天然変性領域の解析
  横山涼太; 米田宏; 中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 47th, 2024
• PML bodyによるY染色体遺伝子の転写制御のメカニズム
  後藤早紀; 中川真一; 栗原美寿々, 日本分子生物学会年会プログラム・要旨集(Web), 47th, 2024
• 非ドメイン型バイオポリマーの生理機能解析
  中川真一; 坪山幸太郎; 泊幸秀, 日本生化学会大会(Web), 97th, 2024
• General remarks: Non-domain biopolymers and biological control
  中川真一, 月刊メディカル・サイエンス・ダイジェスト, 49, 9, 2023
• Identification of the cell-cycle dependent U-body-like structure that contains factors for snRNP maturation
  嶋田雄大; 湯浅博晶; 杉栞太朗; 中川真一; 中川真一; 米田宏; 米田宏, 日本薬学会年会要旨集(Web), 143rd, 2023
• Shell protein composition specified by NEAT1 domains dictates the paraspeckle segregation from nuclear speckles
  高桑央; 高桑央; 山崎智弘; SOUQUERE Sylvie; 足達俊吾; 藤原奈央子; 吉野彪羅; 山本哲也; 中川真一; 村上正晃; PIERRON Gerard; 廣瀬哲郎; 廣瀬哲郎; 廣瀬哲郎, 日本分子生物学会年会プログラム・要旨集(Web), 46th, 2023
• Regulation of cellular differentiation and cancer progression by arcRNAs
  中川真一, 月刊細胞, 54, 8, 2022
• Establishment of an animal model of bone senescence
  右近裕一朗; 立岩大輔; 中川真一; 萩澤宏樹; 平井宏昌; 高橋惇司; 生田雅人; 今村健志; 岡田誠司; 海渡貴司, Journal of Spine Research (Web), 13, 3, 2022
• Development of designable splicing regulators using the effector-binding module of 4.5SH RNA
  芳本玲; 中山雄太; 荒木喜美; 中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 45th, 2022
• The long noncoding RNA Neat1 regulates beige cell differentiation upon cold stimulation.
  戸谷ひかる; 岡松優子; 山口良文; 廣瀬哲郎; 中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 45th, 2022
• Analysis of the principles of formation of membraneless organelles scaffolded by RNAs using theoretical and reconstitution approaches
  山崎智弘; 山本哲也; 吉野彪羅; 高桑央; 高桑央; SOUQEURE Slyvie; 一色和奏; 岩田瑞季; 土井理恵; 中川真一; PIERRON Gerard; 廣瀬哲郎; 廣瀬哲郎, 日本分子生物学会年会プログラム・要旨集(Web), 45th, 2022
• Regulation of Cajal body by Arginine Dimethylation of Coilin
  大峽咲希; 中川真一; 中川真一; 米田宏; 米田宏, 日本分子生物学会年会プログラム・要旨集(Web), 45th, 2022
• Physiological analyses of super-disordered proteins using mutant mice
  中川真一, 日本生化学会大会(Web), 95th, 2022
• メダカにおけるHmgn2の生理機能解析
  正木佑芽; 中川真一; 横井佐織, 日本神経化学会大会抄録集(Web), 65th, 2022
• メダカで脳特異的に発現するfarp1_2遺伝子の機能解析
  櫻井玖美; 井ノ上俊太郎; 中川真一; 横井佐織, 日本神経化学会大会抄録集(Web), 65th, 2022
• 4.5SHクラスタから転写される新規noncoding RNAの解析
  梅木孔信; 中川真一; 栗原美寿々, 日本遺伝学会大会プログラム要旨集(CD-ROM), 94th, 2022
• メダカを用いた大胆/臆病に関わる個性の遺伝子基盤解析
  田中豪; 成瀬清; 郷康広; 辰本将司; 豊田敦; 勝村啓史; 中川真一; 横井佐織, 日本遺伝学会大会プログラム要旨集(CD-ROM), 94th, 2022
• Analysis of physiological funtions of malat1 in medaka fish
  横井佐織; 水戸麻里; 岩崎信太郎; 中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 45th, 2022
• メダカをモデルとした行動に関わる性格の分子神経基盤解析
  田中豪; 成瀬清; 郷康広; 辰本将司; 豊田敦; 勝村啓史; 中川真一; 横井佐織, 日本神経化学会大会抄録集(Web), 65th, 2022
• Comprehensive understanding the nature of Cajal body’s multi-functionality and flexibility
  大峽咲希; 中川真一; 中川真一; 米田宏; 米田宏, 実験医学, 39, 10, 1509, 1514, Jun. 2021
  (株)羊土社, Japanese
• LncRNA Neat1 regulate differentiation of beige cells under cold stimulation.
  戸谷ひかる; 岡松優子; 山口良文; 廣瀬哲郎; 中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 44th, 2021
• Regulation of embryogenesis by a repeat-associated Myodonta clade-specific noncoding RNA 4.5SH
  中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 44th, 2021
• Analysis of the mechanism of nuclear aggregation formation of TDP43 induced by Dehydrocostus lactone treatment
  田中慧; 中川真一; 中川真一; 米田宏; 米田宏, 日本分子生物学会年会プログラム・要旨集(Web), 44th, 2021
• 細胞内ティール組織化:マルチバレント相互作用と相分離が織りなす細胞内プロセスの理解 ティール相互作用によって作られる核内非膜オルガネラの形成機構
  中川 真一; 大峽 咲希; 米田 宏, 日本細胞生物学会大会講演要旨集, 72回, W2, 4, Jun. 2020
  (一社)日本細胞生物学会, Japanese
• Analyses of fine internal structures of RNA-containing nonmembranous bodies and roles of intrinsically disordered regions
  中川真一, 実験医学, 38, 5, 762, 768, Mar. 2020
  (株)羊土社, Japanese
• 配偶者選択におけるオキシトシンの役割の性的二形性
  横井佐織; 成瀬清; 亀井保博; 安齋賢; 木下政人; 水戸麻理; 岩崎信太郎; 井ノ上俊太郎; 奥山輝大; 中川真一; YOUNG Larry J.; 竹内秀明, 日本分子生物学会年会プログラム・要旨集(Web), 43rd, 2020
• パラスペックル:RNAを骨格として形成されるミクロ相分離構造体
  山崎智弘; 山本哲也; 吉野彪羅; 高桑央; 高桑央; SOUQUERE Sylvie; 中川真一; PIERRON Gerard; 廣瀬哲郎, 日本分子生物学会年会プログラム・要旨集(Web), 43rd, 2020
• 長鎖ノンコーディングRNAであるGomafuの核内繋留機構におけるSF3b2の寄与の解明
  上原 理加; 梅本 銀河; 中川 真一; 吉田 稔; 服部 光治; 築地 仁美, 日本生化学会大会プログラム・講演要旨集, 92回, [2P, 242], Sep. 2019
  (公社)日本生化学会, Japanese
• 小型齧歯類特異的4.5SHクラスタの欠損マウスは胎生致死となる
  山本育子; 杉本道彦; 荒木喜美; 鈴木雄; 小林武彦; 中川真一, 日本RNA学会年会要旨集, 21st, 2019
• Neat1 lncRNA KOマウスの表現型解析
  戸谷ひかる; 屋中香織; 戸田知得; 岡松優子; 中川真一, 日本RNA学会年会要旨集, 21st, 2019
• メダカ成魚脳で発現する機能性lncRNAの探索
  横井佐織; 中川真一, 日本RNA学会年会要旨集, 21st, 2019
• 相分離構造体パラスペックルの性状・機能を規定するNEAT1lncRNAモジュール
  山崎智弘; 高桑央; SOUQUERE Sylvie; 小松リチャード馨; 吉野彪羅; FOX Archa H.; BOND Charles S.; 中川真一; 齊藤博英; PIERRON Gerard; 廣瀬哲郎, 日本分子生物学会年会プログラム・要旨集(Web), 42nd, 2019
• 核内相分離構造体パラスペックルの生物物理的性質を規定するNEAT1 lncRNAのRNPモジュール
  山崎智弘; 高桑央; SOUQUERE Sylvie; 吉野彪羅; FOX Archa H.; BOND Charles S.; 中川真一; PIERRON Gerard; 廣瀬哲郎, 日本RNA学会年会要旨集, 21st, 2019
• Dehydrocostus lactoneによるCajal Body消失機構の解析
  大峽咲希; 中川真一; 米田宏, 日本RNA学会年会要旨集, 21st, 2019
• Dehydrocostus lactoneによるCajal Body消失機構の解析
  大峽咲希; 中川真一; 米田宏, 日本分子生物学会年会プログラム・要旨集(Web), 42nd, 2019
• snRNP生合成の調節機構のケミカルバイオロジー
  大峡咲希; 中川真一; 中川真一; 米田宏; 米田宏, 日本分子生物学会年会プログラム・要旨集(Web), 42nd, 2019
• ストレス顆粒形成促進因子NFAR2の天然変性領域が担う液-液相分離の生理的意義の解析
  山下映; 山下映; 藤井一希; 藤井一希; 腰高由美恵; 安達真由美; 笹川恵理; 中川真一; 高雄啓三; 高雄啓三; 椎名伸之; 椎名伸之; 椎名伸之, 日本分子生物学会年会プログラム・要旨集(Web), 42nd, 2019
• Myodonta clade特異的4.5SH遺伝子クラスタはマウスの発生に必須である
  山本育子; 杉本道彦; 荒木喜美; 鈴木雄; 小林武彦; 中川真一, 日本進化学会大会プログラム・講演要旨集(Web), 21st, 2019
• 核内構造体パラスペックルの生理機能
  中川 真一, 臨床神経学, 58, Suppl., S56, S56, Dec. 2018
  (一社)日本神経学会, Japanese
• UPA‐Seq:UVへの感受性を利用した機能性lncRNAの同定
  中川真一; 小松太和; 水戸麻理; 竹本愛菜; 藤居光一; 岩崎信太郎, 日本RNA学会年会要旨集, 20th, 40, 09 Jul. 2018
  Japanese
• 核内構造体パラスペックルはNEAT1lncRNAの複数のモジュールドメインの協調した機能により構築される
  山崎智弘; SOUQUERE Sylvie; 吉野彪羅; 高桑央; 中條岳志; FOX Archa H.; BOND Charles S.; 中川真一; PIERRON Gerard; 廣瀬哲郎, 日本分子生物学会年会プログラム・要旨集(Web), 41st, 2018
• 翻訳抑制効果を示す化合物によるU-body誘導機構の解析
  米田宏; 中川真一, 日本RNA学会年会要旨集, 20th, 2018
• membrane-less organelleによるRNA制御機構の化合物を用いた解析
  米田宏; 大峡咲希; 中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 41st, 2018
• ストレス応答性翻訳制御因子NFAR2の天然変性領域欠損マウスの網羅的行動解析
  山下映; 山下映; 藤井一希; 藤井一希; 腰高由美恵; 安達真由美; 笹川恵理; 中川真一; 高雄啓三; 椎名伸之; 椎名伸之; 椎名伸之, 日本分子生物学会年会プログラム・要旨集(Web), 41st, 2018
• NEAT1 lncRNA機能ドメイン上でのNONOオリゴマー化が相分離した核内構造体パラスペックル形成を誘導する
  山崎智弘; SOUQUERE Sylvie; 吉野彪羅; 高桑央; 中條岳志; FOX Archa H.; BOND Charles S.; 中川真一; PIERRON Gerard; 廣瀬哲郎, 日本RNA学会年会要旨集, 20th, 2018
• 核内構造体パラスペックルはNEAT1 lncRNAの複数のモジュールドメインの協調した機能により構築される
  山崎智弘; SOUQUERE Sylvie; 吉野彪羅; 高桑央; 中條岳志; FOX Archa H.; BOND Charles S.; 中川真一; PIERRON Gerard; 廣瀬哲郎, RNAフロンティアミーティング, 2018, 2018
• 核内構造体パラスペックルはNEAT1 IncRNAの複数の機能ドメインにより構築される
  山崎 智弘; Souquere Sylvie; 木立 尚孝; Fox Archa; 中川 真一; Gerard Pierron; 廣瀬 哲郎, 生命科学系学会合同年次大会, 2017年度, [1P, 0764], Dec. 2017
  生命科学系学会合同年次大会運営事務局, Japanese
• 分子共生-RNAタンパク質相互作用による機能創発 UV照射に対する異なる感受性を利用した新規機能的lncRNA候補の同定(Identification of novel functional IncRNA candidates using differential sensitivities to UV-irradiation)
  中川 真一, 生命科学系学会合同年次大会, 2017年度, [4AW09, 7], Dec. 2017
  生命科学系学会合同年次大会運営事務局, English
• DISTURBED EXPRESSION OF IMMUNOREGULATORY LONG NONCODING RNAS IN CIRCULATING IMMUNE CELLS FROM PATIENTS WITH EARLY MYOCARDIAL INFARCTION
  Wolfgang Poller; Martina Gast; Shinichi Nakagawa; Jan Haas; Andrea Stroux; Christian Mueller; Daniela Boernigen; Dirk Westermann; Carsten Skurk; Ursula Rauch-Kroehnert; Kannanganattu Prasanth; Stefan Blankenberg; Benjamin Meder; Ulf Landmesser; Tanja Zeller, JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY, 69, 11, 2036, 2036, Mar. 2017
  English, Summary international conference
• DEFICIENCY OF LONG NONCODING RNA MALAT1 CAUSES IMMUNE SYSTEM DEREGULATION AND ACCELERATED ATHEROSCLEROSIS IN APO E-/- MICE
  Wolfgang Poller; Martina Gast; Bernhard Rauch; Shinichi Nakagawa; Kannanganattu Prasanth; Andrea Stroux; Jan Haas; Benjamin Meder; Carsten Skurk; Ursula Rauch-Kroehnert; Ulf Landmesser, JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY, 69, 11, 2031, 2031, Mar. 2017
  English, Summary international conference
• NEAT1長鎖ノンコーディングRNAは液相分離を誘導することで核内構造体パラスペックルを構築する
  山崎智弘; SOUQUERE Sylvie; 木立尚孝; FOX Archa H.; 中川真一; PIERRON Gerard; 廣瀬哲郎, 日本RNA学会年会要旨集, 19th, 2017
• 「長鎖ノンコーディングRNAにできること~マウスからのメッセージ」
  中川真一, 千里ライフサイエンスセミナー講演要旨集, 2017, L2, 2017
• スプライス部位認識の正確性を緩める化合物の作用機構
  米田宏; 芳本玲; 中川真一, 日本RNA学会年会要旨集, 19th, 2017
• UV-Phenol RNA-seqによる機能性長鎖非コードRNAの同定
  小松太和; 小松太和; 中川真一, 日本RNA学会年会要旨集, 19th, 2017
• Lessons from reverse-genetic studies of lncRNAs
  Shinichi Nakagawa, Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1859, 1, 177, 183, 01 Jan. 2016
  Elsevier, English, Book review
• Clues to long noncoding RNA taxonomy
  Tetsuro Hirose; Shinichi Nakagawa, BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, 1859, 1, 1, 2, Jan. 2016
  English, Others
• ncRNA研究をはじめよう 6.RNA細胞内局在の高解像度解析
  水戸麻理; 中川真一, 実験医学, 33, 20, 3402, 3406, 10 Dec. 2015
  Japanese
• 長鎖ノンコーディングRNAのマイルストーン研究 核内構造体lncRNA 13.染色体機能とlncRNA
  若井道仁; 中川真一, 実験医学, 33, 20, 3296, 3297, 10 Dec. 2015
  Japanese
• 長鎖ノンコーディングRNAのマイルストーン研究 その他のlncRNA関連トピック 17.lncRNA複合体解析法の登場
  中川真一, 実験医学, 33, 20, 3304, 3305, 10 Dec. 2015
  Japanese
• 長鎖ノンコーディングRNAのマイルストーン研究 その他のlncRNA関連トピック 19.lncRNA解析の問題点と遺伝学的解析
  中川真一, 実験医学, 33, 20, 3308, 3309, 10 Dec. 2015
  Japanese
• RNAと生命現象 長鎖ノンコーディングRNAによる妊孕性の制御
  中川 真一, 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, 88回・38回, [2S15, 2], Dec. 2015
  (公社)日本生化学会, English
• 【ノンコーディングRNAテキストブック 最新の医学・創薬研究、方法論とマイルストーン論文200報】 (第2章)長鎖ノンコーディングRNAのマイルストーン研究 総論 長鎖ncRNA研究の歴史と現状
  中川 真一, 実験医学, 33, 20, 3266, 3269, Dec. 2015
  (株)羊土社, Japanese
• 【ノンコーディングRNAテキストブック 最新の医学・創薬研究、方法論とマイルストーン論文200報】 (第2章)長鎖ノンコーディングRNAのマイルストーン研究 核内構造体IncRNA 染色体機能とIncRNA
  若井 道仁; 中川 真一, 実験医学, 33, 20, 3296, 3297, Dec. 2015
  (株)羊土社, Japanese
• 【ノンコーディングRNAテキストブック 最新の医学・創薬研究、方法論とマイルストーン論文200報】 (第2章)長鎖ノンコーディングRNAのマイルストーン研究 その他のIncRNA関連トピック IncRNA複合体解析法の登場
  中川 真一, 実験医学, 33, 20, 3304, 3305, Dec. 2015
  (株)羊土社, Japanese
• 【ノンコーディングRNAテキストブック 最新の医学・創薬研究、方法論とマイルストーン論文200報】 (第2章)長鎖ノンコーディングRNAのマイルストーン研究 その他のIncRNA関連トピック IncRNA解析の問題点と遺伝学的解析
  中川 真一, 実験医学, 33, 20, 3308, 3309, Dec. 2015
  (株)羊土社, Japanese
• 【ノンコーディングRNAテキストブック 最新の医学・創薬研究、方法論とマイルストーン論文200報】 (第4章)ncRNA研究をはじめよう RNA細胞内局在の高解像度解析
  水戸 麻理; 中川 真一, 実験医学, 33, 20, 3402, 3406, Dec. 2015
  (株)羊土社, Japanese
• NEAT1lncRNAの難溶性を考慮したパラスペックル構造因子の再定量と構造構築原理の探究
  中條岳志; 中川真一; 川口哲哉; 内匠透; 廣瀬哲郎, 日本生化学会大会(Web), 88回・38回, [2T25p, 08(2P0765)], Dec. 2015
  (公社)日本生化学会, Japanese
• RNA制御のケミカルバイオロジー スプライシング阻害剤Spliceostatin Aの感受性を決定づけるイントロンの特徴とは?
  芳本 玲; 甲斐田 大輔; 古野 正朗; 鈴木 治和; 林崎 良英; 前田 明; 中川 真一; 吉田 稔, 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, 88回・38回, [4W10, 4], Dec. 2015
  (公社)日本生化学会, Japanese
• Close Up実験法 Series266 簡単RNA蛍光in situハイブリダイゼーション実験
  川口哲哉; 廣瀬哲郎; 中川真一, 実験医学, 33, 14, 2283, 2289, Sep. 2015
  (株)羊土社, Japanese
• 教えて!エコ実験RETURNS 工夫&節約のメリハリ研究術 第4回 染物屋のカイゼン術
  中川真一, 実験医学, 33, 11, 1802, 1806, 01 Jul. 2015
  (株)羊土社, Japanese
• 核内構造体を形成する長鎖ノンコーディングRNAの生理機能解析
  中川真一, 日本核酸医薬学会年会講演要旨集, 1st, 2015
• 超解像顕微鏡による核内構造体パラスペックルの微細構造観察
  中川真一; 水戸麻理; 廣瀬哲郎, 日本RNA学会年会要旨集, 17th, 2015
• スプライシング阻害剤Spliceostatin Aの感受性を決定づけるイントロンの特徴とは?
  芳本玲; 芳本玲; 甲斐田大輔; 甲斐田大輔; 古野正朗; 鈴木治和; 林崎良英; 前田明; 中川真一; 吉田稔, 日本生化学会大会(Web), 88th, 4W10-P-4 (WEB ONLY), 2015
  Japanese
• 長鎖ノンコーディングRNA:遺伝子発現制御メカニズム別・機能リファレンス【メカニズム 4):mRNAと相互作用するlncRNA】レトロトランスポゾン配列を介して形成される二本鎖RNAによる遺伝子発現制御
  石田賢太郎; 中川真一, 細胞工学, 34, 1, 38, 42, 22 Dec. 2014
  Japanese
• 【長鎖ノンコーディングRNA:遺伝子発現制御メカニズム別・機能リファレンス】 【メカニズム mRNAと相互作用するIncRNA】 レトロトランスポゾン配列を介して形成される二本鎖RNAによる遺伝子発現制御
  石田 賢太郎; 中川 真一, 細胞工学, 34, 1, 38, 42, Dec. 2014
  (株)学研メディカル秀潤社, Japanese
• The Long Noncoding MALAT1-MascRNA System is a Novel Regulator of Cardiac Innate Immunity
  Wolfgang Poller; Martina Gast; Blanche Schroen; Antje Voigt; Jan Haas; Anna Papageorgiou; Uwe Kuehl; Dirk Lassner; Xiaomin Wang; Madlen Loebel; Sabrina Wilk; Nadine Althof; Tim Peters; Kannanganattu Prasanth; Hugo Katus; Benjamin Meder; Shinichi Nakagawa; Carmen Scheibenbogen; Stephane Heymans, CIRCULATION, 130, Nov. 2014
  English, Summary international conference
• YbによるpiRNA生合成因子/piRNA前駆体の制御機構
  室田友紀子; 石津大嗣; 中川真一; 岩崎由香; 芝田晋介; 鎌谷太陽; 齋藤都暁; 岡野栄之; 塩見春彦; 塩見美喜子, 日本RNA学会年会要旨集, 16th, 122, 23 Jul. 2014
  Japanese
• スプライシングがMalat1 RNAの局在と安定化を保証している!
  芳本玲; 古野正明; 鈴木治和; 林崎良英; 中川真一; 吉田稔, 日本RNA学会年会要旨集, 16th, 229, 23 Jul. 2014
  Japanese
• hnRNP Uにより制御される新規インプリンティング遺伝子の同定
  長谷川優子; 中川真一, 日本RNA学会年会要旨集, 16th, 114, 23 Jul. 2014
  Japanese
• Nuclear lncRNAs as epigenetic regulators-Beyond skepticism
  Shinichi Nakagawa; Yuji Kageyama, Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1839, 3, 215, 222, Mar. 2014
  Book review
• Global regulation of gene expression by a nuclear noncoding RNA highly homologous to SINE B1
  Shinichi Nakagawa; Kentaro Ishida, GENES & GENETIC SYSTEMS, 88, 6, 343, 343, Dec. 2013
  English, Summary international conference
• レトロトランスポゾンSINE B1と相同配列を持つ核内ノンコーディングRNAによるグローバルな遺伝子発現制御
  中川真一; 石田賢太郎, 日本遺伝学会大会プログラム・予稿集, 85th, 75, 31 Aug. 2013
  Japanese
• 核内構造体パラスペックルはGAリッチな配列を含むイントロンを繋留している
  WEST Jason; 工樂樹洋; KINGSTON Robert; 廣瀬哲郎; 中川真一, 日本RNA学会年会要旨集, 15th, 100, 24 Jul. 2013
  Japanese
• 【生命分子を統合するRNA-その秘められた役割と制御機構 分子進化・サイレンシング・non-coding RNAからRNA修飾・編集・RNA-タンパク質間相互作用まで】 (第2章)転移因子・ウイルスと宿主の"せめぎ合い"と遺伝子サイレンシング 概論 転移因子・ウイルスと宿主のせめぎ合いによりもたらされるゲノム進化
  中川 真一, 実験医学, 31, 7, 1047, 1054, May 2013
  (株)羊土社, Japanese
• 転移因子・ウイルスと宿主の“せめぎ合い”と遺伝子サイレンシング 概論 転移因子・ウイルスと宿主のせめぎ合いによりもたらされるゲノム進化
  中川真一, 実験医学, 31, 7, 1047, 1054, 01 May 2013
  Japanese
• 転移因子・ウイルスと宿主の“せめぎ合い”と遺伝子サイレンシング 4.mRNA非翻訳領域のレトロトランスポゾン挿入配列による転写後遺伝子発現制御―潜在的な遺伝的変異の蓄積と表現型としての多様性の急激な解放
  中川真一; 石田賢太郎, 実験医学, 31, 7, 1079, 1085, May 2013
  (株)羊土社, Japanese
• 長鎖非コードRNAの局在と機能に対するRNA結合タンパク質hnRNP Uの役割
  長谷川優子; 中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 36th, 2013
• プロテアソーム阻害に応答した核内構造体noncoding RNAの転写抑制機能
  廣瀬哲郎; 谷川明恵; VIRNICCHI Giorgio; BENARD Marianne; 長沼孝雄; 佐々木保典; 中川真一; FOX Archa; PIRRON Gerard, 日本RNA学会年会要旨集, 14th, 52, 18 Jul. 2012
  Japanese
• 核内構造体パラスペックルの骨格ncRNAであるNEAT1を欠損するマウスは早期に不妊になる
  中川真一; 廣瀬哲郎, 日本RNA学会年会要旨集, 14th, 48, 18 Jul. 2012
  Japanese
• 4.5SH RNAによる核内繋留を介した遺伝子発現制御におけるdsRNA結合タンパク質Ilf3の役割
  石田賢太郎; 中川真一, 日本RNA学会年会要旨集, 14th, 140, 18 Jul. 2012
  Japanese
• 核内ノンコーディングRNA Gomafuは新規核内構造体であるCelf3/SF1体と相互作用する
  石塚明; 長谷川優子; 中川真一, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 2012
• ショウジョウバエ卵巣体細胞におけるprimary piRNA生合成機構
  室田友紀子; 石津大嗣; 芝田晋介; 鎌谷太陽; 齋藤都暁; 中川真一; 岡野栄之; 塩見春彦; 塩見美喜子, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 2P-0287 (WEB ONLY), 2012
  Japanese
• 【細胞核-構造と機能】 その他 核内ノンコーディングRNAの役割
  石塚 明; 中川 真一, 生体の科学, 62, 5, 502, 503, Oct. 2011
  (公財)金原一郎記念医学医療振興財団, Japanese
• hnRNP UはXist RNA局在制御を通じてX染色体不活性化に関与する
  長谷川優子; 筒井公子; 筒井研; 鈴木勉; 中川真一, 生化学, 84回, 1S1p, 4, Sep. 2011
  (公社)日本生化学会, Japanese
• 【ゲノムの"ダークマター"長鎖ncRNAが制御する多彩な生命現象】 概論 長鎖ncRNA研究のはじまりの終わり
  中川 真一; 影山 裕二, 実験医学, 29, 11, 1702, 1708, Jul. 2011
  (株)羊土社, Japanese
• ゲノムの“ダークマター”長鎖ncRNAが制御する多彩な生命現象 長鎖ncRNA研究のはじまりの終わり
  中川真一; 影山裕二, 実験医学, 29, 11, 1702, 1708, 01 Jul. 2011
  Japanese
• ノンコーディングRNAによるエピジェネティック制御機構:設計図にはない多様な細胞機能を生み出す仕組み 核内構造体に活躍の場を求めたノンコーディングRNAたち
  中川真一, 細胞工学, 30, 7, 734, 739, Jun. 2011
  (株)学研メディカル秀潤社, Japanese
• ショウジョウバエ卵巣由来体細胞におけるprimary piRNA生合成機構
  室田友紀子; 石津大嗣; 齋藤都暁; 小谷葉月; 中川真一; 塩見春彦; 塩見美喜子, 日本分子生物学会年会プログラム・要旨集(Web), 34th, 2011
• 90塩基の低分子ノンコーディングRNAによる核内繋留を介した新規遺伝子発現制御(A novel gene expression regulatory mechanism controlled by 90nt nuclear non-coding RNA through the nuclear retention)
  石田 賢太郎; 中川 真一, 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, 83回・33回, 4P, 0796, Dec. 2010
  (公社)日本生化学会, English
• 大量に蓄積する核内ノンコーディングRNAの機能解析―Gomafuを例にとって
  中川真一, 生化学, 83回・33回, 2W8, 6, Dec. 2010
  (公社)日本生化学会, Japanese
• 核内構造構築に必要なnoncoding RNAの選択的3’末端プロセシングの分子機構
  長沼孝雄; 中川真一; 青木一真; 五島直樹; 佐々木保典; 廣瀬哲郎, 生化学, 83回・33回, 3P, 0795, Dec. 2010
  (公社)日本生化学会, Japanese
• 核内構造体noncoding RNAの選択的プロセシング制御機構
  長沼孝雄; 中川真一; 青木一真; 五島直樹; 佐々木保典; 廣瀬哲郎, 日本RNA学会年会要旨集, 12th, 72, 27 Jul. 2010
  Japanese
• 核内長鎖ノンコーディングRNA Gomafuは動物の行動を制御する
  曽根正光; 築地仁美; 芳本玲; 吉田稔; 北市清幸; 山本経之; 阿部高也; 高雄啓三; 宮川剛; 中川真一, 日本RNA学会年会要旨集, 12th, 70, 27 Jul. 2010
  Japanese
• 拡大・進展を続けるRNA研究の最先端 長鎖noncoding RNA・small RNAからRNA修飾・編集・品質管理まで 第1章 noncoding RNAの分子機構と生命現象,疾患との関わり 1.進化的に「新しい」バイオマテリアル―核内mRNA型noncoding RNAに何ができるのか
  中川真一, 実験医学, 28, 10, 1496-1501,1490(1), 10 Jun. 2010
  Japanese
• 【拡大・進展を続けるRNA研究の最先端 長鎖noncoding RNA・small RNAからRNA修飾・編集・品質管理まで】 noncoding RNAの分子機構と生命現象、疾患との関わり 進化的に「新しい」バイオマテリアル 核内mRNA型noncoding RNAに何ができるのか
  中川 真一, 実験医学, 28, 10, 1496, 1501, Jun. 2010
  (株)羊土社, Japanese
• hnRNP UはXist RNAの不活性化X染色体上への局在を制御する
  長谷川優子; 長谷川優子; BROCKDORFF Neil; 筒井公子; 筒井研; 中川真一, 日本RNA学会年会要旨集, 12th, 2010
• Emerging world of nuclear long noncoding RNAs
  Shinichi Nakagawa, Seikagaku, 82, 1, 42, 46, 2010, [Peer-reviewed]
  1, Japanese
• 中枢神経系の層形成時に細胞タイプ特異的に発現する新規遺伝子の機能解析
  中川真一, 脳の神経回路の機能解明 平成16-21年度 No.16069101, 118, 119, 2010
  Japanese
• 核内高分子ノンコーディングRNAの世界
  中川真一, 生化学, 82, 1, 42, 46, Jan. 2010
  これまでに知られている機能性核内高分子ノンコーティングRNAの主な機能について、転移座からみてcisに働いて転写サイト付近の転写を制御するもの、transに働いて核内構造体を形成するものの二つに分けて概説した。パラスペックルの構造維持に必要なMENε/β、核スペックルに局在するMalat1、および著者等によって同定された、神経系に特異的に発現する新規核内構造物を形成するGomafuなどの発現、構造、機能などについて述べた。, (公社)日本生化学会, Japanese
• 新規核内高分子ノンコーディングRNA Gomafuの機能解析
  中川真一, 生化学, 82回, 2S12a, 1, Sep. 2009
  (公社)日本生化学会, Japanese
• Tsukushi is a Frizzled ligand that, in competition with Wnt2b, regulates the proliferation of retinal stem/progenitor cells
  Kunimasa Ohta; Ayako Ito; Sei Kuriyama; Giuseppe Lupo; Rika Nakayama; Naoko Ohshima; Mitsuko Kosaka; Shin-ichi Ohnuma; Shinichi Nakagawa; Hideaki Tanaka, MECHANISMS OF DEVELOPMENT, 126, S273, S273, Aug. 2009
  English, Summary international conference
• 齧歯類特異的な核内低分子ノンコーディングRNA4.5S RNA_Hによる新規遺伝子発現抑制機構
  石田賢太郎; 中川真一, 日本RNA学会年会要旨集, 11th, 42, 27 Jul. 2009
  Japanese
• hnRNP UはXist RNAの不活性化X染色体上への局在を制御する
  長谷川優子; 河野真二; 筒井公子; 筒井研; 鈴木勉; 中川真一, 日本RNA学会年会要旨集, 11th, 2009
• mRNA様non-coding RNAであるGomafuによるスプライシング制御
  築地仁美; 芳本玲; 吉田稔; 中川真一, 日本分子生物学会年会講演要旨集, 32nd, Vol.1, 2009
• Molecular function of Tsukushi on neuronal stem cells
  Kunimasa Ohta; Ayako Ito; Sei Kuriyama; Giuseppe Lupo; Rika Nakayama; Naoko Ohshima; Mitsuko Kosaka; Shin-ichi Ohnuma; Shinichi Nakagawa; Hideaki Tanaka, NEUROSCIENCE RESEARCH, 65, S91, S91, 2009
  English, Summary international conference
• 核内構造構築を司る長鎖noncoding RNAの選択的3’末端形成を介した機能発現機構
  長沼孝雄; 佐々木保典; 中川真一; 廣瀬哲郎, 日本分子生物学会年会講演要旨集, 32nd, Vol.1, 24, 2009
  Japanese
• 大量の核内mRNA型ノンコーディングRNAが語るもの (特集 ノンコーディングRNA--現状と問題点)
  中川真一; 石田賢太郎, 蛋白質核酸酵素, 53, 15, 1932, 1939, Dec. 2008
  共立出版
• [Lessons from abundant nuclear mRNA-like noncoding RNAs]
  Nakagawa S; Ishida K, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, 53, 1932, 1939, Dec. 2008, [Peer-reviewed]
  15
• ノンコーディングRNA:現状と問題点 大量の核内mRNA型ノンコーディングRNAが語るもの
  中川真一; 石田賢太郎, 蛋白質 核酸 酵素, 53, 15, 1932, 1939, Dec. 2008
  共立出版(株), Japanese
• 非コードRNA研究の新領域 新規mRNA様非コードRNA Gomafuの機能解析(Functional analysis of a novel mRNA-like noncoding RNA Gomafu)
  中川 真一, 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, 81回・31回, 1S3, 1, Nov. 2008
  (公社)日本生化学会, English
• 神経特異的mRNA様non‐codingRNAであるGomafuの核内繋留メカニズムの解析
  曽根正光; 築地仁美; 甲斐田大輔; 吉田稔; 中川真一, 日本RNA学会年会要旨集, 10th, 4, 23 Jul. 2008
  Japanese
• 機能性RNAの生理学 7.核内mRNA型non‐coding RNA
  中川真一, 実験医学, 26, 10, 1552-1556,HYOSHI,1474(2), 10 Jun. 2008
  Japanese
• 【RNAの機能解明と医療応用 最新の解析戦略と機能性RNAの知見から、RNA異常と疾患の関わり、RNA医薬・診断への応用まで】 機能性RNAの生理学 核内mRNA型non-coding RNA
  中川 真一, 実験医学, 26, 10, 1552, 1556, Jun. 2008
  (株)羊土社, Japanese
• 【命名から20年を超えて Wnt研究の新機軸】 概論 Wnt研究の現在 基礎研究の広がりと臨床応用への予兆
  中川 真一, 実験医学, 26, 3, 356, 360, Feb. 2008
  (株)羊土社, Japanese
• hnRNP UはXist RNAの不活性化X染色体上への局在を制御する
  長谷川優子; 河野真二; 筒井公子; 筒井研; 中川真一, 生化学, 2T5-2, 2008
  Japanese
• 核内に局在する4.5S RNA_Hの遺伝子発現調整
  石田賢太郎; 中川真一, 生化学, 1P-0918, 2008
  Japanese
• mRNA型ノンコーディングRNAであるGomafuの生化学的性質の検討
  築地仁美; 曽根正光; 中川真一, 日本RNA学会年会要旨集, 9th, 234, 28 Jul. 2007
  Japanese
• 核に局在するmRNA‐like ncRNA Gomafuの機能解析
  曽根正光; 稲垣智子; 竹市雅俊; 中川真一, 日本RNA学会年会要旨集, 9th, 231, 28 Jul. 2007
  Japanese
• 精子形成における哺乳類piRNAメチル化酵素の機能解析
  長岡真; 大原智也; 中川真一; 加藤敬行; 五島直樹; 野村信夫; 鈴木健夫; 坂口裕理子; 鈴木勉, 日本RNA学会年会要旨集, 9th, 22, 28 Jul. 2007
  Japanese
• 網膜幹細胞の未分化性を制御する分子メカニズム
  中川真一; 竹市雅俊; 久保郁; 久保郁, 日本眼科学会雑誌, 111, 101, 15 Mar. 2007
  Japanese
• 網膜細胞分化の分子メカニズム 網膜幹細胞の未分化性を制御する分子メカニズム
  中川 真一; 竹市 雅俊; 久保 郁, 日本眼科学会雑誌, 111, 臨増, 101, 101, Mar. 2007
  (公財)日本眼科学会, Japanese
• 核内ノンコーディングRNAの探索及び解析
  石田賢太郎; 中川真一, 日本RNA学会年会要旨集, 9th, 2007
• Tsukushi inhibits proliferation of retinal stem cells by Wnt signalling inhibition
  Kunimasa Ohta; Ayako Ito; Sei Kuriyama; Shin-Ichi Ohnuma; Mitsuko Kosaka; Shin-Ichi Nakagawa; Hideaki Tanaka, NEUROSCIENCE RESEARCH, 58, S56, S56, 2007
  English, Summary international conference
• メラノコルチン2型受容体は,副腎皮質の発生,ステロイド合成,糖新生に必要である
  千田大; 中川真一; 相良洋; 鈴木春巳; 久保光正; 岩倉洋一郎, 生化学, 3P-1139, 2007
  Japanese
• 網膜水平細胞の形態形成における,サブタイプ特異的な転写因子の機能解析
  須賀晶子; 中川真一, 生化学, 4P-0753, 2007
  Japanese
• 核に局在する新規ノンコーディングRNAgomafuの同定
  曽根正光; 竹市雅俊; 中川真一, 日本RNA学会年会要旨集, 8th, 37, 18 Jul. 2006
  Japanese
• 核に局在する新規ノンコーディングRNAの探索
  石田賢太郎; 中川真一, 日本RNA学会年会要旨集, 8th, 2006
• The molecular function of Tsukushi in retinal progenitor cells
  Kunimasa Ohta; Ayako Ito; Ryu Gejima; Sei Kuriyama; Mitsuyo Kosaka; Shin-ichi Nakagawa; Hideaki Tanaka, NEUROSCIENCE RESEARCH, 55, S53, S53, 2006
  English, Summary international conference
• Molecular network controlling retinal stem cell differentiation
  Shinichi Nakagawa; Masatoshi Takeichi; Fumi Kubo, NEUROSCIENCE RESEARCH, 55, S18, S18, 2006
  English, Summary international conference
• 新規核スペックル構造を形成するノンコーディングRNA遺伝子の同定
  曽根正光; 竹市雅俊; 中川真一, 日本分子生物学会年会講演要旨集, 28th, 74, 25 Nov. 2005
  Japanese
• Wntシグナルによる培養条件下での層形成の誘導と幹細胞の維持活性 (特集 視聴覚の再生)
  中川真一, 再生医療, 4, 2, 277, 282,200, May 2005
  メディカルレビュー社
• 【視聴覚の再生】 Wntシグナルによる培養条件下での層形成の誘導と幹細胞の維持活性
  中川 真一, 再生医療, 4, 2, 277, 282, May 2005
  (株)メディカルレビュー社, Japanese
• Wntシグナルによる培養条件下での層形成の誘導と幹細胞の維持活性
  中川真一, 再生医療, 4, 2, 277-282,200, 01 May 2005
  Japanese
• 網膜水平細胞における樹状突起の形態形成
  田辺光志; 竹市雅俊; 中川真一, 日本発生生物学会大会発表要旨集, 38th, 2005
• カドヘリンは網膜水平細胞の樹状突起形態形成を制御する
  田辺光志; 田辺光志; 竹市雅俊; 竹市雅俊; 中川真一, 日本分子生物学会年会講演要旨集, 28th, 2005
• 眼の器官形成におけるWntの役割
  中川真一, 生化学, 76, 12, 1573, 1576, 25 Dec. 2004
  (公社)日本生化学会, Japanese
• The role of Wnt signaling in eye organogenesis
  S Nakagawa, SEIKAGAKU, 76, 12, 1573, 1576, Dec. 2004, [Peer-reviewed]
  Japanese, Book review
• 網膜の組織形成とWntの活性 (特集 Wntシグナルとその多彩な機能--細胞極性・細胞運動・幹細胞の自己複製・発癌)
  中川真一, 細胞工学, 23, 6, 651, 654, Jun. 2004
  秀潤社, Japanese
• Wnt and the Retinal Histogenesis
  中川真一, 細胞工学, 23, 6, 651, 654, Jun. 2004
  Japanese
• 網膜層形成における細胞体移動を制御する遺伝子のスクリーニング
  曽根正光; 竹市雅俊; 中川真一, 日本発生生物学会大会発表要旨集, 37th, 77, 10 May 2004
  Japanese
• 【Wntシグナルとその多彩な機能 細胞極性・細胞運動・幹細胞の自己複製・発癌】 網膜の組織形成とWntの活性
  中川 真一, 細胞工学, 23, 6, 651, 654, May 2004
  発生期の網膜の細胞はいったんばらばらにしても再集合して組織塊を形成することができるが,そこでは特徴的な網膜の層構造は決して再生されず,内腔面に細胞が同心円状に並んだロゼットと呼ばれる異常な構造体ができてしまう.最近になって,Wntがこのロゼット形成を阻害し,正しい層構造を持った組織の再生を誘導することが明らかになった.この層形成誘導因子研究の歴史的背景と網膜の辺縁部の特殊性に焦点を当てて解説した, (株)学研メディカル秀潤社, Japanese
• Notchシグナルと独立なWntシグナルによる網膜前駆細胞の分化抑制機構
  中川真一, 日本分子生物学会年会プログラム・講演要旨集, 27th, 2004
• 網膜の再集合実験から見えてきたWnt2bの役割
  中川真一, 日本発生生物学会大会発表要旨集, 37th, 2004
• 網膜の幹細胞の維持と層形成におけるWnt-2bの役割
  久保郁; 竹市雅俊; 中川真一, 日本発生生物学会大会発表要旨集, 35th, 2002
• Axon sorting at the chiasm in xenopus
  CE Holt; S Nakagawa, EUROPEAN JOURNAL OF NEUROSCIENCE, 12, 184, 184, 2000
  English, Summary international conference
• The metamorphosis antidote
  S Nakagawa; WA Harris, NEURON, 24, 4, 763, 764, Dec. 1999
  English, Others
• p120はカドヘリンの負の制御因子である
  青野真也; 中川真一; 竹市雅俊, 日本細胞生物学会大会講演要旨集, 52nd, 36, 1999
  Japanese
• 組換えアデノウイルスを用いた神経冠細胞への遺伝子強制発現
  中川 真一; 森吉 弘毅; 中西 重忠; 竹市 雅敏, 日本分子生物学会年会プログラム・講演要旨集, 19, 675, 675, 01 Aug. 1996
  Japanese
• Functional Analysis of c-cad6B and c-cad7 during neural tube/crest formation.
  中川真一; 竹市雅俊, 日本発生生物学会大会発表要旨集, 29th, 1996
• Identification of Novel Cadherins Expressed in Neural Crest Cells.
  中川真一; 竹市雅俊, 日本発生生物学会大会発表要旨集, 27th, 1994
• Transitional expression of novel cadherins during neural crest development.
  中川真一; 竹市雅俊, 日本分子生物学会年会プログラム・講演要旨集, 17th, 1994
• Reexamination of the properties of epimorphin and its possible roles
  Yohei Hirai; Shin-ichi Nakagawa; Masatoshi Takeichi, Cell, 73, 3, 426, 427, 07 May 1993
  English, Report scientific journal

• 情報からマテリアルへ : ノンコーディングRNA研究 : 機能分子としてのRNAを見つけ、知り、創薬に使う新時代
  中川, 真一; 廣瀬, 哲郎; 松本, 有樹修
  羊土社, Sep. 2024, 9784758104210, 205p, Japanese
• フロントランナー直伝 : 相分離解析プロトコール : 今すぐ実験したくなる、論文にはないコツや技
  加藤, 昌人; 白木, 賢太郎; 中川, 真一
  羊土社, Jul. 2022, 9784758122597, 245p, Japanese
• 相分離 : メカニズムと疾患 : “膜のないオルガネラ"はいかに機能するか? 神経変性疾患・ウイルス感染とどう関わるか?
  廣瀬, 哲郎; 加藤, 昌人; 中川, 真一
  羊土社, Jun. 2021, 9784758103954, 221p, Japanese
• ノンコーディングRNAテキストブック : 最新の医学・創薬研究、方法論とマイルストーン論文200報
  塩見 美喜子; 中川 真一; 浅原 弘嗣
  羊土社, 2015, 9784758103510, 249p, Japanese

• Preferential association of prion-like-domain-containing RNA binding proteins to functional lncRNA candidates
  shinichi nakagawa
  30 Nov. 2018, English, Nominated symposium
  [Invited], [Domestic Conference]
• Prediction of functional lncRNAs using UPA-seq
  shinichi nakagawa
  CSHL Asia, 31 Oct. 2018, English, Invited oral presentation
  [International presentation]
• UPA‐Seq:UVへの感受性を利用した機能性lncRNAの同定
  中川真一; 小松太和; 水戸麻理; 竹本愛菜; 藤居光一; 岩崎信太郎
  日本RNA学会年会要旨集, 09 Jul. 2018, Japanese
• Attempts towards identification of novel functional lncRNAs
  shinichi nakagawa
  EMBO workshop, 11 Apr. 2018, English, Invited oral presentation
  [International presentation]
• Towards Identification of Novel Functional Long noncoding RNAs
  Shinichi Nakagawa
  Kumamoto Key Forum, 12 Jan. 2018, English, Invited oral presentation
  [Domestic Conference]
• 核内構造体パラスペックルの生理機能
  中川真一
  日本神経学会学術大会プログラム・抄録集, 2018, Japanese
• Identification of novel functional lncRNA candidates using differential sensitivities to UV-irradiation
  shinichi nakagawa
  ConBio 2017, 09 Dec. 2017, English, Invited oral presentation
  [Invited], [International presentation]
• Analyses of physiological function of lncRNAs
  shinichi nakagawa
  IIBMP2017, 29 Sep. 2017, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• UV‐Phenol RNA‐seqによる機能性長鎖非コードRNAの同定
  小松太和; 小松太和; 中川真一
  日本RNA学会年会要旨集, 19 Jul. 2017, Japanese
• Observation of sub-micron size nuclear bodies using super-resolution microscopy
  shinichi nakagawa
  The 43th Naito Conference「Noncoding RNA: Biology, Chemistry, & Diseases」, 29 Jun. 2017, English, Invited oral presentation
  [Invited], [International presentation]
• Fine structural analyses of nuclear body paraspeckle using SIM
  Shinichi Nakagawa
  50th JSDB meeting, 10 May 2017, English, Oral presentation
  [Domestic Conference]
• 「長鎖ノンコーディングRNAにできること~マウスからのメッセージ」
  中川真一
  千里ライフサイエンスセミナー講演要旨集, 2017, Japanese
• Observation of nuclear bodies using super-resolution microscopy
  Shinichi Nakagawa
  第39回 日本分子生物学会年会, 01 Dec. 2016, English, Invited oral presentation
  Yokohama, [Invited], [Domestic Conference]
• 核内構造体パラスペックルの 生理機能と微細構造解析
  中川 真一
  第53回日本生化学会北海道支部例会, 08 Jul. 2016, Japanese, Keynote oral presentation
  [Domestic Conference]
• RNAと生命現象 長鎖ノンコーディングRNAによる妊孕性の制御
  中川 真一
  日本生化学会大会・日本分子生物学会年会合同大会, Dec. 2015, English
• 核内構造体を形成する長鎖ノンコーディングRNAの生理機能解析
  中川真一
  日本核酸医薬学会年会講演要旨集, 15 Nov. 2015, Japanese
• 超解像顕微鏡による核内構造体パラスペックルの微細構造観察
  中川真一; 水戸麻理; 廣瀬哲郎
  日本RNA学会年会要旨集, 15 Jul. 2015, Japanese
• hnRNP Uにより制御される新規インプリンティング遺伝子の同定
  長谷川優子; 中川真一
  日本RNA学会年会要旨集, 23 Jul. 2014, Japanese
• レトロトランスポゾンSINE B1と相同配列を持つ核内ノンコーディングRNAによるグローバルな遺伝子発現制御
  中川真一; 石田賢太郎
  日本遺伝学会大会プログラム・予稿集, 31 Aug. 2013, Japanese
• 核内構造体パラスペックルはGAリッチな配列を含むイントロンを繋留している
  WEST Jason; 工樂樹洋; KINGSTON Robert; 廣瀬哲郎; 中川真一
  日本RNA学会年会要旨集, 24 Jul. 2013, Japanese
• 長鎖非コードRNAの局在と機能に対するRNA結合タンパク質hnRNP Uの役割
  長谷川優子; 中川真一
  日本分子生物学会年会プログラム・要旨集(Web), 2013, Japanese
• 核内構造体パラスペックルの骨格ncRNAであるNEAT1を欠損するマウスは早期に不妊になる
  中川真一; 廣瀬哲郎
  日本RNA学会年会要旨集, 18 Jul. 2012, Japanese
• 4.5SH RNAによる核内繋留を介した遺伝子発現制御におけるdsRNA結合タンパク質Ilf3の役割
  石田賢太郎; 中川真一
  日本RNA学会年会要旨集, 18 Jul. 2012, Japanese
• 核内ノンコーディングRNA Gomafuは新規核内構造体であるCelf3/SF1体と相互作用する
  石塚明; 長谷川優子; 中川真一
  日本分子生物学会年会プログラム・要旨集(Web), 2012, Japanese
• ショウジョウバエ卵巣由来体細胞におけるprimary piRNA生合成機構
  室田友紀子; 石津大嗣; 齋藤都暁; 小谷葉月; 中川真一; 塩見春彦; 塩見美喜子
  日本分子生物学会年会プログラム・要旨集(Web), 2011, Japanese
• 非コードRNA作用マシナリー 動作原理の分子基盤と生理機能 大量に蓄積する核内ノンコーディングRNAの機能解析 Gomafuを例にとって
  中川 真一
  日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, Dec. 2010, Japanese
• 90塩基の低分子ノンコーディングRNAによる核内繋留を介した新規遺伝子発現制御(A novel gene expression regulatory mechanism controlled by 90nt nuclear non-coding RNA through the nuclear retention)
  石田 賢太郎; 中川 真一
  日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, Dec. 2010, English
• hnRNP UはXist RNAの不活性化X染色体上への局在を制御する
  長谷川優子; BROCKDORFF Neil; 筒井公子; 筒井研; 中川真一
  日本RNA学会年会要旨集, 27 Jul. 2010, Japanese
• 核内構造体noncoding RNAの選択的プロセシング制御機構
  長沼孝雄; 中川真一; 青木一真; 五島直樹; 佐々木保典; 廣瀬哲郎
  日本RNA学会年会要旨集, 27 Jul. 2010, Japanese
• 核内長鎖ノンコーディングRNA Gomafuは動物の行動を制御する
  曽根正光; 築地仁美; 芳本玲; 吉田稔; 北市清幸; 山本経之; 阿部高也; 高雄啓三; 宮川剛; 中川真一
  日本RNA学会年会要旨集, 27 Jul. 2010, Japanese
• ノンコーディングRNAが制御する多様な機能 新規核内高分子ノンコーディングRNA Gomafuの機能解析
  中川 真一
  日本生化学会大会プログラム・講演要旨集, Sep. 2009, Japanese
• hnRNP UはXist RNAの不活性化X染色体上への局在を制御する
  長谷川優子; 河野真二; 筒井公子; 筒井研; 鈴木勉; 中川真一
  日本RNA学会年会要旨集, 27 Jul. 2009, Japanese
• mRNA様non‐coding RNAであるGomafuによるスプライシング制御
  築地仁美; 芳本玲; 吉田稔; 中川真一
  日本分子生物学会年会講演要旨集, 2009, Japanese
• 非コードRNA研究の新領域 新規mRNA様非コードRNA Gomafuの機能解析(Functional analysis of a novel mRNA-like noncoding RNA Gomafu)
  中川 真一
  日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, Nov. 2008, English
• 核に局在するmRNA‐like ncRNA Gomafuの機能解析
  曽根正光; 稲垣智子; 竹市雅俊; 中川真一
  日本RNA学会年会要旨集, 28 Jul. 2007, Japanese
• mRNA型ノンコーディングRNAであるGomafuの生化学的性質の検討
  築地仁美; 曽根正光; 中川真一
  日本RNA学会年会要旨集, 28 Jul. 2007, Japanese
• 核内ノンコーディングRNAの探索及び解析
  石田賢太郎; 中川真一
  日本RNA学会年会要旨集, 28 Jul. 2007, Japanese
• Wntシグナル伝達の新たな展望 Wntシグナル伝達下流における網膜幹細胞維持の毛様体境界帯でのNotchシグナル伝達とは独立したC-hairy1による制御(New horizon of Wnt signaling c-hairy1 controls retinal stem cell maintenance downstream of Wnt signaling, independently of Notch singnaling at the ciliary marginal zone)
  久保 郁; 竹市 雅俊; 中川 真一
  日本発生生物学会・日本細胞生物学会合同大会要旨集, May 2007, English
• 核に局在する新規ノンコーディングRNAgomafuの同定
  曽根正光; 竹市雅俊; 中川真一
  日本RNA学会年会要旨集, 18 Jul. 2006, Japanese
• 核に局在する新規ノンコーディングRNAの探索
  石田賢太郎; 中川真一
  日本RNA学会年会要旨集, 18 Jul. 2006, Japanese
• 新規核スペックル構造を形成するノンコーディングRNA遺伝子の同定
  曽根正光; 竹市雅俊; 中川真一
  日本分子生物学会年会講演要旨集, 25 Nov. 2005, Japanese
• カドヘリンは網膜水平細胞の樹状突起形態形成を制御する
  田辺光志; 竹市雅俊; 中川真一
  日本分子生物学会年会講演要旨集, 25 Nov. 2005, Japanese
• 網膜水平細胞における樹状突起の形態形成
  田辺光志; 竹市雅俊; 中川真一
  日本発生生物学会大会発表要旨集, May 2005, Japanese
• Notchシグナルと独立なWntシグナルによる網膜前駆細胞の分化抑制機構
  中川真一
  日本分子生物学会年会プログラム・講演要旨集, 25 Nov. 2004, Japanese
• 網膜層形成における細胞体移動を制御する遺伝子のスクリーニング
  曽根正光; 竹市雅俊; 中川真一
  日本発生生物学会大会発表要旨集, 10 May 2004, Japanese
• 網膜の再集合実験から見えてきたWnt2bの役割
  中川真一
  日本発生生物学会大会発表要旨集, 10 May 2004, Japanese
• 網膜の幹細胞の維持と層形成におけるWnt‐2bの役割
  久保郁; 竹市雅俊; 中川真一
  日本発生生物学会大会発表要旨集, 2002, Japanese
• 組換えアデノウイルスを用いた神経冠細胞への遺伝子強制発現
  中川真一; 森吉弘毅; 中西重忠; 竹市雅敏
  日本分子生物学会年会プログラム・講演要旨集, 01 Aug. 1996
• 組換えアデノウイルスを用いた神経冠細胞への遺伝子強制発現
  中川真一; 森吉弘毅; 中西重忠; 竹市雅俊
  日本分子生物学会年会プログラム・講演要旨集, Jul. 1996, Japanese
• Functional Analysis of c-cad6B and c-cad7 during neural tube/crest formation.
  中川真一; 竹市雅俊
  日本発生生物学会大会発表要旨集, 1996, Japanese
• Transitional expression of novel cadherins during neural crest development.
  中川真一; 竹市雅俊
  日本分子生物学会年会プログラム・講演要旨集, Nov. 1994, Japanese
• Identification of Novel Cadherins Expressed in Neural Crest Cells.
  中川真一; 竹市雅俊
  日本発生生物学会大会発表要旨集, 1994, Japanese

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• 日本分子生物学会
• 日本RNA学会
• 日本発生生物学会

• Elucidation of the Mechanism of Action of srRNA Controlling Splicing and Identification of Novel srRNAs
  Grants-in-Aid for Scientific Research
  01 Apr. 2024 - 31 Mar. 2029
  中川 真一; 芳本 玲
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Hokkaido University, 24H00546
• Funtional analyses of non-domain RNAs using mutant mice
  Grants-in-Aid for Scientific Research
  10 Sep. 2021 - 31 Mar. 2026
  中川 真一; 荒木 喜美
  Japan Society for the Promotion of Science, Grant-in-Aid for Transformative Research Areas (A), Hokkaido University, 21H05274
• Management of non-domain biopolymer research group
  Grants-in-Aid for Scientific Research
  10 Sep. 2021 - 31 Mar. 2026
  中川 真一; 廣瀬 哲郎; 尾山 大明; 稲田 利文; 荒川 和晴; 甲斐 歳恵; 依田 隆夫; 伊藤 拓宏; 泊 幸秀
  本領域では、種間で高度に保存された配列を持たずに機能を発揮するRNAやタンパク質を非ドメイン型バイオポリマーと定義し、その生理的な役割から分子レベルの分子機構まで階層横断的な研究を進め、新たな動作原理に基づく画期的な生体制御技術を開発することを目指している。
  今年度は領域立ち上げの初年度に当たり、班員間の連携を深めるために、領域班会議を10月9-10日の二日間にわたって北広島のクラッセホテルにてハイブリッド形式にて開催した。また、研究者間の交流をより深めるために、ワールドポスター形式でのディスカッションを同日程でオンラインで行った。対面での総括班会議では今後の活動方針について確認を行い、技術講習会についてはZoomを利用したオンライン形式でのハンズオンセミナーを取り入れてゆくこと、若手支援の海外ミーティング参加支援は新型コロナウイルス感染症の流行の状況を見ながら、渡航可能になり次第開始すること、公募班を含めた次回の領域会議は東京で行うことを確認した。
  班員間のコミュニケーションを深めるために、Slackのワークスペースを立ち上げた。各計画研究ごとのスレッドを作製して研究代表者、分担者、領域代表者で打ち合わせを随時行ったほか、汎用的な技術に関するスレッドも作製し、領域全体で共同研究のノウハウを共有できるプラットフォームを立ち上げた。また、変異マウスの作製の共同研究ならびに近位ビオチンラベルによる相互作用因子の質量分析による解析の共同研究をアレンジし、それら共同研究に係る経費の一部を支援した。
  若手育成に関してはRNAフロンティアミーティングの会場費の支援を予定していたが、オンライン開催になったため、班員の研究室からの積極的な参加という形で活動の支援を行った。
  Japan Society for the Promotion of Science, Grant-in-Aid for Transformative Research Areas (A), Hokkaido University, 21H05273
• Biology of Non-domain Biopolymer
  Grants-in-Aid for Scientific Research
  10 Sep. 2021 - 31 Mar. 2026
  中川 真一
  Japan Society for the Promotion of Science, Grant-in-Aid for Transformative Research Areas (A), 21A304
• 超天然変性タンパク質の個体レベルでの生理機能解析
  科学研究費助成事業
  09 Jul. 2021 - 31 Mar. 2024
  中川 真一; 泊 幸秀
  本研究は全長に渡って天然変性領域を持つ超天然変性タンパク質に注目し、その変異体を作製することで、機能未知の超天然変性タンパク質の生理機能を明らかにすることを目的としている。これまでの研究によって、病原性の凝集体形成を阻害したりタンパク質を変性から保護する活性を持つ超天然変性タンパク質が少なくとも6種類あることが明らかとなっていた。そこでこれらの遺伝子全てについてゲノム編集マウスを作製したところ、Hero11とHero45の二種類の遺伝子のホモ個体の生体は観察されず、胎生致死になることが予想された。さらに詳細な解析を行ったところ、Hero11は胎生5.5日目から7.5日目の間に、Hero45は胎生14日目以降に致死になることが明らかとなった。また、Hero11のノックアウトマウスから樹立したES細胞は野生型のES細胞に比べて増殖が大きく低下することが明らかとなった。さらに、Hero45のメスのヘテロマウスは、交尾をして妊娠しても正常に出産できない個体が頻繁に見られることが分かった。
  Hero11とHero45の分子動作機構を明らかにするために、これらのタンパク質にタグを付けた分子を培養細胞に発現させたところ、Hero11は核に局在し、核小体に特に濃縮すること、Hero45は主として細胞質に局在することが明らかとなった。また、Hero11がタンパク質の凝集体形成を抑制する際に、その細胞内局在が変化することも明らかとなった。
  これらに加え、小胞体に局在し、細胞内ドメインが天然変性領域からなる機能未知タンパク質UGS148についても変異マウスを作製し、その表現型解析を行った。その結果、UGS148は間脳脳室腹側に存在するタニサイト細胞の小胞体に特異的に分布するほかオレキシンニューロンにも強い発現が見られること、しかしながらノックアウトマウスは大きな異常を示さないことが明らかとなった。
  日本学術振興会, 挑戦的研究(萌芽), 北海道大学, 21K19246
• Biochemical approaches to understanding the reaction platforms of the piRNA pathway
  Grants-in-Aid for Scientific Research
  11 Jun. 2018 - 31 Mar. 2023
  泊 幸秀; 中川 真一
  これまでに、遺伝学的スクリーニングと、タンパク質-タンパク質相互作用の探索によって、膨大な数のpiRNA関連因子が存在することが明らかになっている、その中で生化学活性が特定されているものは、我々が発見したpiRNA成熟のためのエクソヌクレアーゼTrimmerや、その前段階ではたらくエンドヌクレアーゼZucchiniを含めてごく少数に限られている。我々は、アメリカの研究室との共同研究と独自の生化学系の利用によって、GTSF1 (Gametocyte Specific Factor 1)と呼ばれる因子が、PIWIタンパク質と相互作用し、その標的RNA切断活性を大きく向上させる機能を持っているということを見いだした。さらに、別のアメリカの研究室との共同研究により、RNase κ と呼ばれるミトコンドリアに局在するヌクレアーゼが、piRNAの効率的な生産に重要であることを発見した。また、piRNA関連の新規因子を探索する解析を通じて、カイコが持つ2つのPIWIタンパク質、SiwiとBmAgo3のうち、BmAgo3をノックダウンした時だけ、Siwiと特異的に相互作用する機能未知の新規因子を発見した。さらには、次世代シーケンサーを駆使することにより、カイコBmN4細胞ゲノムの中に存在する最も代表的なpiRNAクラスターであるtorimochiの配列および性状解析を進めた。また、piRNA経路と同様に、トランスポゾンやウイルスなどの遺伝的侵略者からゲノムを守る役割を果たしているsiRNA経路については、その生合成において重要な働き果たすDicer(ショウジョウバエ由来のDicer-2)が長い二本鎖RNAを切断しながらsiRNAを次々と産生してゆく過程を一分子レベルで観察することに成功し、従来提案されていたモデルに修正を与えることとなった。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (S), The University of Tokyo, 18H05271
• Functional analyses of novel lncRNAs using reverse genetics
  Grants-in-Aid for Scientific Research
  01 Apr. 2017 - 31 Mar. 2022
  Nakagawa Shinichi
  Large numbers of non-protein-coding RNAs are transcribed from the genomes of higher organisms including human and mouse. In this study, we aimed to systematically select functional lncRNA candidate genes and to establish an efficient method for functional analyses. We found that functional lncRNAs that form tight complexes with proteins can be predicted based on the amount of RNAs recovered from the aqueous phase after UV irradiation. We also established a method to efficiently generate mutant mice lacking lncRNA function using the iGONAD method, a recently developed method that enables a low-cost, high-efficient genome editing.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 17H03604
• Support activities to promote international collaboration to accomplish the research on noncoding RNA neo-taxonomy
  Grants-in-Aid for Scientific Research
  06 Nov. 2015 - 31 Mar. 2019
  Hirose Tetsuro
  To support active interaction with foreign researchers, three main activities including enhancement of international collaboration, travel support for visiting the foreign research institutes and invitation of prominent foreign scientists were promoted. The international collaboration using ncRNA knockout mice were particularly supported. Also the travel fee for short term stay of young researchers in the foreign research institutes were particularly supported. These activities linked to multiple international collaboration with the group members that eventually achieve publication of 34 research articles.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Hokkaido University, 15K21720
• Functional analyses of physiological function of ncRNA according to the neo-taxonomy
  Grants-in-Aid for Scientific Research
  10 Jul. 2014 - 31 Mar. 2019
  Nakagawa Shinichi
  A number of noncoding RNAs that do not encode proteins are transcribed from the genome. The ncRNAs can be divided into two large groups: "small RNA", which are involved in RNA silencing, and "Long noncoding RNA (lncRNA)", which are more than 200 bases long. It is not clear how many of the lncRNAs actually have physiological functions. We have developed a method to identify novel functional lncRNA candidate genes using the property that known functional lncRNAs are highly efficiently cross-linked to proteins by mild UV irradiation. We also established a technique to analyze the fine structure formed by lncRNA using a super-resolution microscope.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 26113005
• Functional machinery for non-coding RNAs
  Grants-in-Aid for Scientific Research
  23 Jul. 2009 - 31 Mar. 2014
  TOMARI Yukihide; KAGEYAMA Yuji; SUZUKI Takeo; TEI Kumiko; NAKAZAWA Takanobu; WADA Takeshi; SADO Takashi; SIOMI Mikiko; MIYAGAWA Satomi; NAKAGAWA Shinichi; TAKESHITA Fumitaka; ODA Takeaki; YAMASHITA Akio; NISHIMURA Yukiko
  H21～25年度の新学術領域研究「非コードRNA作用マシナリー」領域からは非コードRNA動作原理に関する優れた研究成果が多数生み出され、本領域はホームページや雑誌企画、ワークショップ、一般向けのプレスリリースなど、外部に対して積極的に情報を発信し、得られた研究成果を社会に還元するように努めてきた。これまで、当該分野で顕著な成果を上げている海外の研究者と共に国際シンポジウムを開催することで、国際的にもこの分野を牽引する日本の非コードRNA研究を世界に向けて発信してきた。平成26年度の本研究取りまとめにおいては、過去の実績を踏まえ、本領域の研究期間である５年間を通して得られた研究成果を取りまとめ、その全体像を当該学問領域のみならず、一般国民に分かりやすく還元すると共に情報の発信を継続することを目的として下記の計画を遂行した。
  ①本分野をリードする著名な海外の研究者を第37回日本分子生物学会年会シンポジウムおよびワークショップに招聘するとともに、本領域主催の「非コードRNA作用マシナリー」をテーマとした国際シンポジウムの開催し、領域の研究成果を国内外に発信すると共に海外の研究者との情報交換を強化した。②領域の研究成果を広く社会・国民に発信するためのアウトリーチ活動の一環として、領域班員がRNA関連研究を伝える活動を地域の教育・研究機関で行った。③領域の研究成果や上記イベント等を広報するために、引き続きncrna.jpドメインを維持し、ホームページやブログを継続公開・更新した。④研究成果をわかりやすくまとめた成果報告書を作成し、本領域外の科学分野面にも広く配布した。
  以上のように、本領域の研究成果を当該分野のみならず、広く一般国民に還元することができたと考える。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), The University of Tokyo, 21115001
• Elucidation of molecular mechanisms controlling localization and metabolism of mRNAs via retrotransposon insertions
  Grants-in-Aid for Scientific Research
  2012 - 2012
  NAKAGAWA Shinichi
  To elucidate functions of retrotransposon sequences inserted in the untranslated region of mRNAs, we performed a series of analyses on an abundant nuclear noncoding RNA called 4.5SH, which is highly homologous to retrotransposon SINE B1. 4.5SH formed double-stranded RNA duplex with mRNAs containing antisense insertions of SINE B1, which were retained in the nucleus. The nuclear-retained mRNAs with antisense SINE B1 insertions were released into cytoplasm upon knockdown of 4.5SH. The nuclear retention via 4.5SH was regulated by a double-stranded RNA binding protein called NF110. These results revealed a novel mechanism that controls sub-cellular localization of mRNAs through the intra-molecular formation of the double stranded RNA structures.
  Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, The Institute of Physical and Chemical Research, Principal investigator, Competitive research funding, 24657123
• Analysis of regulatory mechanisms of epigenetic gene regulation by a complex of nuclear matrix protein and noncoding RNA
  Grants-in-Aid for Scientific Research
  2011 - 2012
  NAKAGAWA Shinichi
  In the human and mouse, vast majority of the genome is transcribed into RNAs, producing a huge number of non protein-coding RNAs. These noncoding RNAs associate with chromatin-modifying complexes, and are assumed to regulate epigenetic gene expression. In this study, we have performed functional analysis of a nuclear matrix protein hnRNP U that regulate chromosomal localization of Xist, a renowned noncoding RNA involved in the X chromosome inactivation. We found that hnRNP U also regulates the chromosomal localization and function of noncoding RNAs such as Kcnq1ot1 and Airn, and the allele-specific expression of the imprinted loci were impaired upon depletion of hnRNP U. We also performed genome-wide gene expression analysis of the hnRNP U depleted cells, and found that multiple allele-specific expression were also disturbed. We found a novel noncoding RNA expressed from the allele-specific locus, and its transcripts were also associated with the chromosome in a mono-allelic manner.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), The Institute of Physical and Chemical Research, Principal investigator, Competitive research funding, 23370093
• Chemical Genetics on Novel Functions of Splicing Factors
  Grants-in-Aid for Scientific Research
  2009 - 2012
  YOSHIDA Minoru; NAKAGAWA Shinichi; FURUMAI Ryohei
  Spliceostatin A (SSA) is a chemically stable derivative of anticancer natural product FR901464, which we identified as the first splicing inhibitor that binds the splicing factor SF3b. SSA provides a unique opportunity to analyze novel function of splicing factors and introns. This project aims to elucidate unknown roles of splicing factors by analyzing the mechanisms by which SSA induces a variety of phenotypes. In consequence, we demonstrated that splicing factors targeted by SSA are involved in the regulation of pre-mRNA nuclear retention, transcriptional elongation, polyadenylation, and subcellular localization of nuclear non-coding RNAs.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (S), The Institute of Physical and Chemical Research, Coinvestigator not use grants, Competitive research funding, 21228003
• Genetic approaches to physiological functions of long noncoding RNA machinery
  Grants-in-Aid for Scientific Research
  2009 - 2012
  KAGEYAMA Yuji; NAKAGAWA Shinichi
  Current research project demonstrates biological importance of long noncoding RNA by genetic approaches using fruit flies and mice. Mutational studies showed that 1) high-molecular weight long noncoding RNA plays an impotent role in formation of neural circuits in the adult fly brain and 2) RNA binding protein hnRNP U, which carries both an RNA binding domain and a chromatin binding domain, is essential for localization of Xist RNA, an essential component in dosage compensation in mammals. In the course of study, we found that some of the putative long noncoding RNA include short ORFs that encodes extremely small peptides and those peptides, at least in some cases, regulate gene expression in transcriptional network.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 大学共同利用機関法人自然科学研究機構(共通施設)->神戸大学, Coinvestigator not use grants, Competitive research funding, 21115007
• 核内mRNA型ノンコーディングRNAが関わる新規細胞内プロセスの解明
  2008 - 2011
  中川 真一
  高等真核細胞で発現しているmRNA型ノンコーディングRNAのなかには、転写産物が細胞質に運ばれず核内に蓄積するという非常にユニークな性質を示すものがいくつか知られています。本研究ではこれら核内mRNA型ノンコーディングRNAという新しいカテゴリーの分子群に注目し、その生理的な機能を明らかにすることで、これまでに知られていなかったような新規の核内プロセスを解明することを目指します。
  科学技術振興機構, 戦略的な研究開発の推進/戦略的創造研究推進事業/さきがけ, 08062810
• Elucidation of molecular mechanism that controls the maintenance of retinal stem cells
  Grants-in-Aid for Scientific Research(基盤研究(C))
  2007 - 2009
  Shinichi NAKAGAWA
  The marginal region of the retina contains retinal stem cells that continue to proliferate and remain undifferentiated for a long period. We have previously identified a signaling molecule Wnt2b as a retinal stem cell factor that maintains undifferentiated state of the retinal stem cells. In this research project, we investigated downstream pathway of the Wnt signaling, especially focusing on transcription factors. We have found that Wnt activates multiple transcription factors including c-myc, which in turn cooperatively activate a transcriptional repressor c-hairy1. We have also revealed ...
  Ministry of Education, Culture, Sports, Science and Technology, 基盤研究(C), 独立行政法人理化学研究所, Principal investigator, Competitive research funding, 19570216
• 網膜の予定神経節細胞の核に局在するノンコーディングRNAの機能解析
  科学研究費補助金(特定領域研究)
  2005 - 2006
  中川 真一
  我々は、中枢神経系の層構造の形成時に細胞タイプ特異的な振る舞いを制御する遺伝子を同定するために、それぞれの細胞タイプで特異的に発現している遺伝子を単一細胞サブトラクション法を用いて同定して来た。その過程で、通常のmRNAと異なり転写産物が核マトリクスに多数のスポットとして観察される、全長9kbのユニークなmRNA型ノンコーディングRNAを同定し、その特徴的な核内局在からこの遺伝子をGomafu(胡麻斑)と名付けた。本年度はGomafuの性質についてより詳細な解析を行なった。まず、GomafuをHelaやNeuro2Aなどの培養細胞に強制発現したところ、それらの細胞でも生体内と同様に核内に局在する事が分かった。また、これらの細胞を、Gomafuを発現していない親株と融合させてヘテロカリオンを作製したところ、Gomafu RNAはトランスフェクタント由来の核でのみ観察された事から、Gomafu RNAは転写後細胞質に輸送される事なく核内に保持されている事が分かった。また、これまでに知られているXist、Air、Evflなどの核内に局在するmRNA型ノンコーディングRNAと局在を比較したところ、GomafUはユニークな場所に局在する事が分かった。また、興味深い事に、Gomafu RNAは熱処理や翻訳阻害などのストレスによって消失する事が分かった。熱処理によっても新規タンパク質の合成...
  文部科学省, 特定領域研究, 独立行政法人理化学研究所, Principal investigator, Competitive research funding, 17026040
• Investigation of the mechanisms controlling formation of the laminated structures in the central nervous system
  Grants-in-Aid for Scientific Research(基盤研究(C))
  2004 - 2006
  Shinichi NAKAGAWA
  During the histogenesis of the central nervous system, an enormous number of processes must be precisely executed according to the genetic program controlled by both cell-intrinsic and extrinsic factors. We have investigated the molecular mechanisms controlling laminated structures in the central nervous system using retina as a model system. Previously we have shown ; 1) Wnt2b, a secreted signaling molecule, can induce correct laminar formation from singly dissociated retinal progenitor cells in a rotation culture condition. 2) Wnt2b control proliferation and differentiation of the retina ...
  Ministry of Education, Culture, Sports, Science and Technology, 基盤研究(C), 独立行政法人理化学研究所, Principal investigator, Competitive research funding, 16570184
• 中枢神経系の層形成時に細胞タイプ特異的に発現する新規遺伝子の機能解析
  科学研究費補助金(特定領域研究)
  2005 - 2005
  中川 真一
  中枢神経系の層形成の過程において、それぞれの細胞がどのようにして細胞タイプに応じた特定の層へ移動してゆくのかを調べるために、これまでに網膜をモデルシステムとして用いて、発生期に細胞タイプ特異的な発現を示す遺伝子を複数同定して来た。本年度はそれらの候補遺伝子を網膜全体に強制発現させ、それぞれの細胞の振る舞いに変化が起きるかを調べたが、顕著な異常を観察する事は出来なかった。一方、網膜への遺伝子導入技術を改良している過程で、時期特異的、かつ細胞タイプ特異的に遺伝子を発現する系を立ち上げる事に成功した。この技術を用いて網膜の水平細胞をEGFPでラベルしたところ、樹状突起の形態および軸索の有無から明確に区別出来る3種類の水平細胞が存在する事を見出した。さらに、これらの樹状突起の形態形成を制御する分子メカニズムを明らかにするために、神経系における主要な細胞間接着分子の一つであるカドヘリンの機能阻害実験を試みた。その結果、カドヘリンの機能を阻害すると、樹状突起の伸展が大きく阻害される事が分かった。しかしながら、短いながらもそれぞれの樹状突起の末端は適切な視細胞の末端に投射していた。ただし、そこでのシナプスマーカーの集積は阻害されていた。これらの事から、カドヘリンは樹状突起の伸展、および最終的なシナプス形成の過程を制御しているが、局所的な標的認識過程には関与していない事が明らかとなった。
  文部科学省, 特定領域研究, 独立行政法人理化学研究所, Principal investigator, Competitive research funding, 17023053
• 中枢神経系の層形成過程においてニューロンが特定の層を認識する分子メカニズムの研究
  科学研究費補助金(特定領域研究)
  2003 - 2004
  中川 真一
  中枢神経系の様々な領域で、特定の機能を持ったニューロンおよびグリア細胞が決められた位置に一列に並んだような、規則的な層構造が見られる。この層構造が形成される過程でそれぞれの細胞が細胞タイプに応じた目的地をどのように認識しそこへ移動してゆくのかを調べるために、我々は網膜をモデルシステムとして研究を進めてきた。網膜の神経節細胞と錐体光受容細胞は発生の初期、ほぼ同じ時期におなじ神経上皮のアピカル側で最終分裂を行うが、その後生み出された細胞は正反対の方向へ移動してゆく。すなわち神経節細胞は基底膜側に移動してゆくのに対し、錐体光受容細胞はアピカル側に戻ってきてそこで細胞層を形成する。我々はこのような振る舞いの違いはそれぞれの細胞タイプで特異的に発現している遺伝子によって制御されていると考え、以下のような実験を行った。まず、これらの細胞が移動をしているような時期のマウスの網膜を単一の細胞に解離し、それぞれの細胞からPCRによるバイアスを抑えるような条件のもとでcDNAを合成した。次にサザンプロット上でマーカー遺伝子の発現を調べることで、それぞれのcDNAがどの細胞タイプに由来するものかを遡及的に同定した。このようにして選んだ神経節細胞由来のcDNAと錐体光受容細胞由来のcDNAを用いてサブトラクションライブラリーを作製し、それぞれの細胞由来のプローブでディファレンシャルスクリーニングを行...
  文部科学省, 特定領域研究, 特殊法人理化学研究所->独立行政法人理化学研究所, Principal investigator, Competitive research funding, 15029262
• Analysis of the laminated structures in the central nervous system
  Grants-in-Aid for Scientific Research(基盤研究(C))
  2001 - 2003
  Sinichi NAKAGAWA
  To study cortical neuron patterning, we utilized reaggregation cultures of dissociated retinal cells prepared from chicken embryos. Singly dissociated retinal cells can reaggregate and undergo a certain level of histogenesis, including cell type-specific segregation of cells, but they have never been found to reform into laminated structures. Instead, they form rosetted cell layers within the aggregates. However, it is known that conditioned media (CM) prepared from some cell cultures can induce laminated structures in the reaggregates. We hypothesized that the CM should contain important r...
  Ministry of Education, Culture, Sports, Science and Technology, 基盤研究(C), 京都大学->特殊法人理化学研究所->独立行政法人理化学研究所, Principal investigator, Competitive research funding, 13680804