Researcher basic information

• Ph.D., The University of Tokyo, Mar. 2000

• https://researchmap.jp/3dgenome?lang=en

• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=202201001979670734
• https://orcid.org/0000-0002-5187-6788
• https://www.igm.hokudai.ac.jp/3dgenome/ja/

• https://orcid.org/0000-0002-5187-6788

• 202201001979670734

• ヒト細胞
• 分裂酵母
• 細胞老化
• 転写制御
• 染色体分配
• 染色体
• ゲノム構造
• ゲノム

• Life Science, Molecular biology
• Life Science, System genome science
• Life Science, Genome biology

Research activity information

• 2014, W.W. Smith Charitable Trust
• 2011, G. Harold & Leila Y. Mathers Foundation
• 2010, Edward Mallinckrodt, Jr. Foundation
• 2010, V Foundation for Cancer Research
• 2008, NIH Director’s New Innovator Award
• 2002, Newcomb Cleveland Prize of the American Association for the Advancement of Science (Breakthrough of the Year in Science Magazine)
• 2002, Leukemia & Lymphoma Society Fellow

• TRF-1 Mediates PRC2 Function at Ectopic Telomere Repeats in Neurospora crassa
  Colleen C. Mumford; Peregrine D. Painter; Kevin J. McNaught; Hideki Tanizawa; Nolan J. Smith; Shinji Honda; Osamu Iwasaki; Sanki Tashiro; Ken-ichi Noma; Eric U. Selker
  Molecular and Cellular Biology, 1, 15, Informa UK Limited, 17 Feb. 2026
  English, Scientific journal
• A role for condensin-mediator interaction in mitotic chromosome organization
  Osamu Iwasaki; Sanki Tashiro; Claire Yik-Lok Chung; Tomomi Hayashi; Hideki Tanizawa; Xuebing Wang; Shinya Ohta; Yuko Fujioka; Joseph Han; Gabrielle Tabor; Mikihiro Kawagoe; Ronen Marmorstein; Nobuo N. Noda; Ken-ichi Noma
  Nature Communications, 08 Feb. 2026, [International Magazine]
  English, Scientific journal, Condensin organizes eukaryotic genomes into three-dimensional (3D) chromosome architectures that support accurate chromosome segregation during mitosis. However, the molecular mechanisms underlying this organization remain unclear. Here, we identify a previously unrecognized interaction between the condensin subunit Cnd1 and the mediator subunit Pmc4 in fission yeast, Schizosaccharomyces pombe. We characterize a condensin mutation, cnd1-K658E, which disrupts this interaction and observe that it impairs the formation of condensin-mediated chromatin domains during mitosis, resulting in chromosome segregation defects. This condensin-mediator interaction facilitates condensin recruitment to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains. Moreover, 1,6-hexanediol treatment and Pmc4 mediator depletion impair expression of mitotically activated genes, diminish condensin enrichment at those boundary genes, and disrupt domain boundaries, suggesting that mediator contributes to mitotic gene expression and chromosome architecture via phase separation. Together, these results reveal a mechanism by which mitotic gene expression patterns shape condensin-mediated chromosome architecture to ensure faithful chromosome segregation.
• ChIA-PET Analysis for Investigating SMC-Mediated 3D Genomic Contacts
  Kyoung-Dong Kim; Ken-ichi Noma
  Methods in Molecular Biology, 2991, 247, 255, 2026, [International Magazine]
  English, Scientific journal, We present a detailed ChIA-PET benchwork protocol optimized for investigating cohesin- and condensin-mediated chromatin contacts. This method combines chromatin immunoprecipitation (ChIP), proximity ligation, EcoP15I digestion, and sequencing library construction to achieve high specificity in detecting SMC-dependent genomic contacts. Key quality control measures, including ChIP DNA validation, linker ligation strategies, and PCR cycle optimization, are outlined to enhance data reliability. By providing a genome-wide view of SMC-driven chromatin contacts, this method offers valuable insights into the fundamental principles of genome folding and maintenance.
• Integrative analysis of hi-C variance and multi-contact data identifies enhancer–promoter hub structures
  HidekiTanizawa; Claire Yik-Lok Chung; Ken-ichi Noma
  Briefings in Bioinformatics, 26, Supplement_1, i27, i27, Oxford University Press (OUP), 12 Dec. 2025
  Scientific journal, Abstract
  
  Enhancer–promoter (EP) interactions are essential for transcriptional regulation, yet the mechanisms underlying the simultaneous engagement of multiple enhancers with a single promoter (‘hub structures’) remain elusive. Here, we present a computational framework that integrates Hi-C variance analysis with multi-contact data to identify such structures. We statistically modeled replicate-to-replicate variability in Hi-C contact frequencies, enabling the extraction of dynamically flexible genomic regions that are not evident from averaged contact maps. This variance-based approach highlights loci with high interaction plasticity, which often coincide with regulatory elements. To further characterize these regions, we incorporated multi-contact information from Pore-C and active EP association signals from H3K27ac-HiChIP, allowing us to detect EP hubs and evaluate their molecular determinants. Our comparative analysis revealed distinct mechanisms: Condensin tends to recruit multiple enhancers to a promoter simultaneously via a diffusion capture–based process, whereas Cohesin predominantly mediates one-to-one interactions through loop extrusion. This difference suggests that Condensin contributes to cooperative enhancer activity, particularly in contexts where strong transcriptional upregulation is required. In this presentation, we will introduce the framework, demonstrate its application to yeast and human fibroblast datasets, and discuss its potential for dissecting dynamic features of genome architecture at scale.
• DeepSAHF: deep learning-based detection of senescence-associated chromatin features reveals nuclear heterogeneity
  Claire Yik-Lok Chung; Shinya Ohta; HidekiTanizawa; Ken-ichi Noma
  Briefings in Bioinformatics, 26, Supplement_1, i27, i27, Oxford University Press (OUP), 12 Dec. 2025
  Scientific journal, Abstract
  
  Senescence-associated heterochromatin foci (SAHF) are condensed chromatin domains that mark cellular aging. Manual microscopy-based counting of SAHF-positive nuclei is widely used but is labor-intensive, subjective, and limited by binary classification that overlooks nuclear heterogeneity, especially in intermediate senescence or under non-canonical chromatin features. Accurate automated detection remains challenging due to variability in nuclear morphology, fluorescence intensity, and imaging conditions, with current approaches relying on arbitrary thresholds that hinder reproducibility.
  
  We present DeepSAHF, a deep learning–based pipeline for robust and reproducible detection of senescence-specific chromatin states from fluorescence microscopy images. The workflow integrates image pre-processing, YOLO-based single nucleus segmentation, and chromatin pattern classification to identify SAHF-positive cells. An extension using a visual language model (VLM) systematically comments on nuclear shape and features, facilitating interpretability and filtering unsuitable nuclei (e.g., out-of-focus). DeepSAHF is trained and tested at 20× resolution on oncogene-induced senescence cells across multiple time points, using curated high-confidence images from literature and novel data to ensure generalization without manual thresholds.
  
  By enabling scalable, reproducible, and interpretable analysis of chromatin reorganization, DeepSAHF advances beyond traditional methods, opening avenues to explore nuclear heterogeneity in aging and stress responses, with broad applications in drug screening, regenerative medicine, and cancer biology.
• Acetic acid produced by Staphylococcus epidermidis remodels chromatin architecture and suppresses gene expression in Malassezia restricta
  Jae Min Lee; Hyun Oh Yang; Hideki Tanizawa; Ken-ichi Noma; Tae Kwon Lee; Won Hee Jung; Yong-Joon Cho; Kyoung-Dong Kim
  mBio, 16, 10, e0159225, 08 Oct. 2025, [International Magazine]
  English, Scientific journal, The skin microbiome is composed of diverse microbial communities that engage in interkingdom interactions, influencing host physiology and microbial balance. Although Malassezia restricta and Staphylococcus epidermidis are codominant members of the human skin microbiome, the molecular mechanisms underlying their interactions remain poorly understood. We aimed to investigate the mechanism by which S. epidermidis-derived acetic acid affects chromatin organization and gene expression in M. restricta. S. epidermidis modulated chromatin structure and transcriptional activity in M. restricta by secreting acetic acid (AcOH), a common skin-associated organic acid. Using in situ Hi-C, we established the first three-dimensional genome architecture map of M. restricta and identified putative centromeric loci based on inter-chromosomal association scores. Co-culture with S. epidermidis or direct treatment with AcOH induced large-scale chromatin decompaction and enhanced centromeric clustering, indicating significant reorganization of the nuclear architecture. Through chromatin immunoprecipitation (ChIP)-seq analysis, we observed that AcOH exposure led to a redistribution of histone acetylation from promoter regions to gene bodies. This chromatin remodeling was further associated with extensive transcriptional repression, particularly of genes involved in translation, metabolism, and virulence, as revealed by RNA-seq analysis. Of note, these changes were specific to AcOH and were not replicated under inorganic acid stress (HCl), indicating a metabolite-specific epigenetic response. This study reveals a novel form of interkingdom communication in the skin microbiome, in which S. epidermidis-derived AcOH acts as an epigenetic modulator in M. restricta. Our findings provide key mechanistic insights into how bacterial metabolites influence fungal chromatin architecture and transcription, with implications for microbial community dynamics and skin health.IMPORTANCEThis study provides essential insights into interkingdom interactions within the human skin microbiome, highlighting how microbial metabolites influence fungal biology at the chromatin level. Specifically, we identify acetic acid (AcOH), secreted by Staphylococcus epidermidis, as a key regulator that induces significant chromatin remodeling and transcriptional changes in Malassezia restricta. By presenting the first three-dimensional genome architecture map of M. restricta, our findings uncover metabolite-specific chromatin dynamics that cannot be replicated by inorganic acid stress. Additionally, the conservation of this chromatin response in other Malassezia species suggests broader implications for understanding microbial adaptation mechanisms in the skin environment. This work underscores the critical role of bacterial metabolites as modulators of microbial interactions and provides new avenues for investigating microbial community balance and potential therapeutic strategies for skin health.
• Novel role of zinc-finger protein 518 in heterochromatin formation on α-satellite DNA
  Shinya Ohta; Jun-Ichirou Ohzeki; Nobuko Sato; Hideki Tanizawa; Claire Yik-Lok Chung; Ken-Ichi Noma; Hiroshi Masumoto
  Nucleic Acids Research, 11 Jan. 2025, [Peer-reviewed]
  English, Scientific journal, Abstract
  Aneuploidy is caused by chromosomal missegregation and is frequently observed in cancers and hematological diseases. Therefore, it is important to understand the molecular mechanisms underlying chromosomal segregation. The centromere's intricate structure is crucial for proper chromosome segregation, with heterochromatin at the pericentromeric α-satellites playing a key role. However, the mechanism targeting heterochromatin to pericentromeres remains elusive. This study identifies a novel mechanism involving two homologous zinc-finger proteins ZNF518A and ZNF518B in human pericentric heterochromatin formation. Our investigation demonstrated that ZNF518s localize to the centromere via centromere protein B (CENP-B). Moreover, ZNF518s interact with heterochromatin protein 1 (HP1) and H3K9 methyltransferase G9A, recruiting the heterochromatin components to pericentromeres. We found that centromeric histone H3K9 trimethylation was diminished in the absence of ZNF518s when another H3K9 methyltransferase, SUV39H1, was depleted. In somatic cells, the ZNF518s-G9a axis is not the principal pathway for heterochromatin formation but plays a supplementary role. Furthermore, ZNF518s are involved in histone H3K9 trimethylation at ectopic sites, indicating their broad role in heterochromatin establishment. Consequently, we propose that ZNF518s participate in the mechanism underlying heterochromatin establishment at pericentromeres. Our findings shed light on the novel mechanism underlying pericentromeric heterochromatin formation, highlighting the central role of ZNF518 in this process.
• Senotherapeutic potential against xeroderma pigmentosum
  Wang, Xuebing; Nishida, Masako; Yoshioka, Ai; Chung, Claire Yik-Lok; Hashimoto, Shinya; Tanizawa, Hideki; Ohta, Shinya; Noma, Ken-ichi; Fukumoto, Takeshi
  bioRxiv, Cold Spring Harbor Laboratory, 23 May 2025
  Scientific journal, Abstract
  
  Xeroderma pigmentosum (XP) is an inherited photoaging syndrome caused by mutations in genes involved in the nucleotide excision repair (NER) pathway. XP patients exhibit hypersensitivity to ultraviolet (UV) radiation, leading to accelerated skin aging and requiring lifelong sun avoidance. Here, we demonstrate that UV-induced DNA damage triggers cellular senescence and up-regulates senescence-associated secretory phenotype (SASP) genes in melanocytes derived from an XP patient. To explore the potential therapeutics for XP, we developed a cisplatin-based drug screening system and identified JAK inhibitors and curcuminoids as promising senomorphic agents. In addition, two classes of senolytic agents, BCL-2-like protein inhibitors and HSP90 inhibitors, effectively eliminate senescent melanocytes. Further analysis demonstrates that senomorphic treatment effectively counteracts senescence and reduces SASP gene expression in XP-derived melanocytes. Moreover, genes in senescence-related pathways, including the JAK/STAT, Type I interferon (IFN-I), and PI3K/AKT pathways, which are activated by both UV irradiation and cisplatin treatment, are down-regulated by senomorphic treatment. This study highlights a potential senotherapeutic strategy for XP, which may help alleviate photoaging symptoms in XP patients.
• Step-by-Step Protocol to Generate Hi-C Contact Maps Using the rfy_hic2 Pipeline
  Hideki Tanizawa; Claire Yik-Lok Chung; Shun-ichiro Fuse; Tomomi Hayashi; Peter Weisel; Ken-ichi Noma
  Methods in Molecular Biology, 2856, 133, 155, 2025, [International Magazine]
  English, Scientific journal, The Hi-C method has emerged as an indispensable tool for analyzing the 3D organization of the genome, becoming increasingly accessible and frequently utilized in chromatin research. To effectively leverage 3D genomics data obtained through advanced technologies, it is crucial to understand what processes are undertaken and what aspects require special attention within the bioinformatics pipeline. This protocol aims to demystify the Hi-C data analysis process for field newcomers. In a step-by-step manner, we describe how to process Hi-C data, from the initial sequencing of the Hi-C library to the final visualization of Hi-C contact data as heatmaps. Each step of the analysis is clearly explained to ensure an understanding of the procedures and their objectives. By the end of this chapter, readers will be equipped with the knowledge to transform raw Hi-C reads into informative visual representations, facilitating a deeper comprehension of the spatial genomic structures critical to cellular functions.
• Chemo-Senolytic Therapeutic Potential against Angiosarcoma
  Xuebing Wang; Claire Yik-Lok Chung; Ai Yoshioka; Shinya Hashimoto; Haruki Jimbo; Hideki Tanizawa; Shinya Ohta; Takeshi Fukumoto; Ken-ichi Noma
  Journal of Investigative Dermatology, 144, 10, 2285, 2297, Oct. 2024, [International Magazine]
  English, Scientific journal, Angiosarcoma is an aggressive soft-tissue sarcoma with a poor prognosis. Chemotherapy for this cancer typically employs paclitaxel, a taxane (genotoxic drug), although it has a limited effect owing to chemoresistance to prolonged treatment. In this study, we examine an alternative angiosarcoma treatment approach that combines chemotherapeutic and senolytic agents. We find that the chemotherapeutic drugs cisplatin and paclitaxel efficiently induce senescence in angiosarcoma cells. Subsequent treatment with the senolytic agent ABT-263 eliminates senescent cells by activating the apoptotic pathway. In addition, expression analysis indicates that senescence-associated secretory phenotype genes are activated in senescent angiosarcoma cells and that ABT-263 treatment downregulates IFN-I pathway genes in senescent cells. Moreover, we show that cisplatin treatment alone requires high doses to remove angiosarcoma cells. In contrast, lower doses of cisplatin are sufficient to induce senescence, followed by the elimination of senescent cells by the senolytic treatment. This study sheds light on a potential therapeutic strategy against angiosarcoma by combining a relatively low dose of cisplatin with the ABT-263 senolytic agent, which can help ease the deleterious side effects of chemotherapy.
• A role for condensin-mediator interaction in mitotic chromosomal organization.
  Osamu Iwasaki; Sanki Tashiro; Claire Chung; Tomomi Hayashi; Hideki Tanizawa; Xuebing Wang; Shinya Ohta; Yuko Fujioka; Joseph Han; Gabrielle Tabor; Mikihiro Kawagoe; Ronen Marmorstein; Nobuo N Noda; Ken-Ichi Noma
  bioRxiv : the preprint server for biology, 28 Jun. 2024, [International Magazine]
  English, Scientific journal, Eukaryotic genomes are organized by condensin into 3D chromosomal architectures suitable for chromosomal segregation during mitosis. However, molecular mechanisms underlying the condensin-mediated chromosomal organization remain largely unclear. Here, we investigate the role of newly identified interaction between the Cnd1 condensin and Pmc4 mediator subunits in fission yeast, Schizosaccharomyces pombe. We develop a condensin mutation, cnd1-K658E, that impairs the condensin-mediator interaction and find that this mutation diminishes condensinmediated chromatin domains during mitosis and causes chromosomal segregation defects. The condensin-mediator interaction is involved in recruiting condensin to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains. Furthermore, this study predicts that mediator-driven transcription of mitotically activated genes contributes to forming domain boundaries via phase separation. This study provides a novel insight into how genome-wide gene expression during mitosis is transformed into the functional chromosomal architecture suitable for chromosomal segregation.
• METTL3-mediated chromatin contacts promote stress granule phase separation through metabolic reprogramming during senescence
  Chen Wang; Hideki Tanizawa; Connor Hill; Aaron Havas; Qiang Zhang; Liping Liao; Xue Hao; Xue Lei; Lu Wang; Hao Nie; Yuan Qi; Bin Tian; Alessandro Gardini; Andrew V. Kossenkov; Aaron Goldman; Shelley L. Berger; Ken-ichi Noma; Peter D. Adams; Rugang Zhang
  Nature Communications, 15, 1, 5410, 5410, 26 Jun. 2024, [International Magazine]
  English, Scientific journal, METTL3 is the catalytic subunit of the methyltransferase complex, which mediates m6A modification to regulate gene expression. In addition, METTL3 regulates transcription in an enzymatic activity-independent manner by driving changes in high-order chromatin structure. However, how these functions of the methyltransferase complex are coordinated remains unknown. Here we show that the methyltransferase complex coordinates its enzymatic activity-dependent and independent functions to regulate cellular senescence, a state of stable cell growth arrest. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 expression through the three-dimensional chromatin organization during senescence. Elevated Hexokinase 2 expression subsequently promotes liquid-liquid phase separation, manifesting as stress granule phase separation, by driving metabolic reprogramming. This correlates with an impairment of translation of cell-cycle related mRNAs harboring polymethylated m6A sites. In summary, our results report a coordination of m6A-dependent and -independent function of the methyltransferase complex in regulating senescence through phase separation driven by metabolic reprogramming.
• Therapeutic strategies targeting cellular senescence for cancer and other diseases
  Xuebing Wang; Takeshi Fukumoto; Ken-ichi Noma
  The Journal of Biochemistry, 175, 5, 525, 537, 29 Apr. 2024, [International Magazine]
  English, Scientific journal, Cellular senescence occurs in response to endogenous or exogenous stresses and is characterized by stable cell cycle arrest, alterations in nuclear morphology and secretion of proinflammatory factors, referred to as the senescence-associated secretory phenotype (SASP). An increase of senescent cells is associated with the development of several types of cancer and aging-related diseases. Therefore, senolytic agents that selectively remove senescent cells may offer opportunities for developing new therapeutic strategies against such cancers and aging-related diseases. This review outlines senescence inducers and the general characteristics of senescent cells. We also discuss the involvement of senescent cells in certain cancers and diseases. Finally, we describe a series of senolytic agents and their utilization in therapeutic strategies.
• Local chromatin decompaction shapes mitotic chromosome landscape
  Tashiro, Sanki; Tanizawa, Hideki; Noma, Ken-ichi
  bioRxiv, 2024
  Scientific journal
• Establishment of dsDNA-dsDNA interactions by the condensin complex.
  Tang M; Pobegalov G; Tanizawa H; Chen ZA; Rappsilber J; Molodtsov M; Noma KI; Uhlmann F
  Molecular cell, 83, 21, 3787, 3800, 10 Oct. 2023, [International Magazine]
  English, Scientific journal, Condensin is a structural maintenance of chromosomes (SMC) complex family member thought to build mitotic chromosomes by DNA loop extrusion. However, condensin variants unable to extrude loops, yet proficient in chromosome formation, were recently described. Here, we explore how condensin might alternatively build chromosomes. Using bulk biochemical and single-molecule experiments with purified fission yeast condensin, we observe that individual condensins sequentially and topologically entrap two double-stranded DNAs (dsDNAs). Condensin loading transitions through a state requiring DNA bending, as proposed for the related cohesin complex. While cohesin then favors the capture of a second single-stranded DNA (ssDNA), second dsDNA capture emerges as a defining feature of condensin. We provide complementary in vivo evidence for DNA-DNA capture in the form of condensin-dependent chromatin contacts within, as well as between, chromosomes. Our results support a "diffusion capture" model in which condensin acts in mitotic chromosome formation by sequential dsDNA-dsDNA capture.
• Rec8 Cohesin-mediated Axis-loop chromatin architecture is required for meiotic recombination.
  Sakuno T; Tashiro S; Tanizawa H; Iwasaki O; Ding DQ; Haraguchi T; Noma KI; Hiraoka Y
  Nucleic acids research, 50, 7, 3799, 3816, 01 Apr. 2022, [International Magazine]
  English, Scientific journal, During meiotic prophase, cohesin-dependent axial structures are formed in the synaptonemal complex (SC). However, the functional correlation between these structures and cohesion remains elusive. Here, we examined the formation of cohesin-dependent axial structures in the fission yeast Schizosaccharomyces pombe. This organism forms atypical SCs composed of linear elements (LinEs) resembling the lateral elements of SC but lacking the transverse filaments. Hi-C analysis using a highly synchronous population of meiotic S. pombe cells revealed that the axis-loop chromatin structure formed in meiotic prophase was dependent on the Rec8 cohesin complex. In contrast, the Rec8-mediated formation of the axis-loop structure occurred in cells lacking components of LinEs. To dissect the functions of Rec8, we identified a rec8-F204S mutant that lost the ability to assemble the axis-loop structure without losing cohesion of sister chromatids. This mutant showed defects in the formation of the axis-loop structure and LinE assembly and thus exhibited reduced meiotic recombination. Collectively, our results demonstrate that the Rec8-dependent axis-loop structure provides a structural platform essential for LinE assembly, facilitating meiotic recombination of homologous chromosomes, independently of its role in sister chromatid cohesion.
• Epigenetic specifications of host chromosome docking sites for latent Epstein-Barr virus.
  Kim KD; Tanizawa H; De Leo A; Vladimirova O; Kossenkov A; Lu F; Showe LC; Noma KI; Lieberman PM
  Nature communications, 11, 1, 877, 877, 13 Feb. 2020, [International Magazine]
  English, Scientific journal, Epstein-Barr virus (EBV) genomes persist in latently infected cells as extrachromosomal episomes that attach to host chromosomes through the tethering functions of EBNA1, a viral encoded sequence-specific DNA binding protein. Here we employ circular chromosome conformation capture (4C) analysis to identify genome-wide associations between EBV episomes and host chromosomes. We find that EBV episomes in Burkitt's lymphoma cells preferentially associate with cellular genomic sites containing EBNA1 binding sites enriched with B-cell factors EBF1 and RBP-jK, the repressive histone mark H3K9me3, and AT-rich flanking sequence. These attachment sites correspond to transcriptionally silenced genes with GO enrichment for neuronal function and protein kinase A pathways. Depletion of EBNA1 leads to a transcriptional de-repression of silenced genes and reduction in H3K9me3. EBV attachment sites in lymphoblastoid cells with different latency type show different correlations, suggesting that host chromosome attachment sites are functionally linked to latency type gene expression programs.
• Involvement of condensin in cellular senescence through gene regulation and compartmental reorganization.
  Iwasaki O; Tanizawa H; Kim KD; Kossenkov A; Nacarelli T; Tashiro S; Majumdar S; Showe LC; Zhang R; Noma KI
  Nature communications, 10, 1, 5688, 5688, 12 Dec. 2019, [International Magazine]
  English, Scientific journal, Senescence is induced by various stimuli such as oncogene expression and telomere shortening, referred to as oncogene-induced senescence (OIS) and replicative senescence (RS), respectively, and accompanied by global transcriptional alterations and 3D genome reorganization. Here, we demonstrate that the human condensin II complex participates in senescence via gene regulation and reorganization of euchromatic A and heterochromatic B compartments. Both OIS and RS are accompanied by A-to-B and B-to-A compartmental transitions, the latter of which occur more frequently and are undergone by 14% (430 Mb) of the human genome. Mechanistically, condensin is enriched in A compartments and implicated in B-to-A transitions. The full activation of senescence genes (SASP genes and p53 targets) requires condensin; its depletion impairs senescence markers. This study describes that condensin reinforces euchromatic A compartments and promotes B-to-A transitions, both of which are coupled to optimal expression of senescence genes, thereby allowing condensin to contribute to senescent processes.
• ARID1A spatially partitions interphase chromosomes.
  Wu S; Fatkhutdinov N; Rosin L; Luppino JM; Iwasaki O; Tanizawa H; Tang HY; Kossenkov AV; Gardini A; Noma KI; Speicher DW; Joyce EF; Zhang R
  Science advances, 5, 5, eaaw5294, 22 May 2019, [International Magazine]
  English, Scientific journal, ARID1A, a subunit of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex, localizes to both promoters and enhancers to influence transcription. However, the role of ARID1A in higher-order spatial chromosome partitioning and genome organization is unknown. Here, we show that ARID1A spatially partitions interphase chromosomes and regulates higher-order genome organization. The SWI/SNF complex interacts with condensin II, and they display significant colocalizations at enhancers. ARID1A knockout drives the redistribution of condensin II preferentially at enhancers, which positively correlates with changes in transcription. ARID1A and condensin II contribute to transcriptionally inactive B-compartment formation, while ARID1A weakens the border strength of topologically associated domains. Condensin II redistribution induced by ARID1A knockout positively correlates with chromosome sizes, which negatively correlates with interchromosomal interactions. ARID1A loss increases the trans interactions of small chromosomes, which was validated by three-dimensional interphase chromosome painting. These results demonstrate that ARID1A is important for large-scale genome folding and spatially partitions interphase chromosomes.
• NAD(+) metabolism governs the proinflammatory senescence-associated secretome.
  Nacarelli T; Lau L; Fukumoto T; Zundell J; Fatkhutdinov N; Wu S; Aird KM; Iwasaki O; Kossenkov AV; Schultz D; Noma KI; Baur JA; Schug Z; Tang HY; Speicher DW; David G; Zhang R
  Nature cell biology, 21, 3, 397, 407, 18 Feb. 2019, [International Magazine]
  English, Scientific journal, Cellular senescence is a stable growth arrest that is implicated in tissue ageing and cancer. Senescent cells are characterized by an upregulation of proinflammatory cytokines, which is termed the senescence-associated secretory phenotype (SASP). NAD+ metabolism influences both tissue ageing and cancer. However, the role of NAD+ metabolism in regulating the SASP is poorly understood. Here, we show that nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of the NAD+ salvage pathway, governs the proinflammatory SASP independent of senescence-associated growth arrest. NAMPT expression is regulated by high mobility group A (HMGA) proteins during senescence. The HMGA-NAMPT-NAD+ signalling axis promotes the proinflammatory SASP by enhancing glycolysis and mitochondrial respiration. HMGA proteins and NAMPT promote the proinflammatory SASP through NAD+-mediated suppression of AMPK kinase, which suppresses the p53-mediated inhibition of p38 MAPK to enhance NF-κB activity. We conclude that NAD+ metabolism governs the proinflammatory SASP. Given the tumour-promoting effects of the proinflammatory SASP, our results suggest that anti-ageing dietary NAD+ augmentation should be administered with precision.
• HMGB2 orchestrates the chromatin landscape of senescence-associated secretory phenotype gene loci.
  Aird KM; Iwasaki O; Kossenkov AV; Tanizawa H; Fatkhutdinov N; Bitler BG; Le L; Alicea G; Yang TL; Johnson FB; Noma KI; Zhang R
  The Journal of cell biology, 215, 3, 325, 334, 31 Oct. 2016, [International Magazine]
  English, Scientific journal, Cellular senescence is a stable cell growth arrest that is characterized by the silencing of proliferation-promoting genes through compaction of chromosomes into senescence-associated heterochromatin foci (SAHF). Paradoxically, senescence is also accompanied by increased transcription of certain genes encoding for secreted factors such as cytokines and chemokines, known as the senescence-associated secretory phenotype (SASP). How SASP genes are excluded from SAHF-mediated global gene silencing remains unclear. In this study, we report that high mobility group box 2 (HMGB2) orchestrates the chromatin landscape of SASP gene loci. HMGB2 preferentially localizes to SASP gene loci during senescence. Loss of HMGB2 during senescence blunts SASP gene expression by allowing for spreading of repressive heterochromatin into SASP gene loci. This correlates with incorporation of SASP gene loci into SAHF. Our results establish HMGB2 as a novel master regulator that orchestrates SASP through prevention of heterochromatin spreading to allow for exclusion of SASP gene loci from a global heterochromatin environment during senescence.
• An IF-FISH Approach for Covisualization of Gene Loci and Nuclear Architecture in Fission Yeast.
  Kim KD; Iwasaki O; Noma K
  Methods in enzymology, 01 Jun. 2016
  Scientific journal, Recent genomic studies have revealed that chromosomal structures are formed by a hierarchy of organizing processes ranging from gene associations, including interactions among enhancers and promoters, to topologically associating domain formations. Gene associations identified by these studies can be characterized by microscopic analyses. Fission yeast is a model organism, in which gene associations have been broadly mapped across the genome, although many of those associations have not been further examined by cell biological approaches. To address the technically challenging process of the visualization of associating gene loci in the fission yeast nuclei, we provide, in detail, an IF-FISH procedure that allows for covisualizing both gene loci and nuclear structural markers such as the nuclear membrane and nucleolus.
• Condensin-mediated chromosome organization in fission yeast.
  Iwasaki O; Noma KI
  Current genetics, 62, 4, 739, 743, 09 Apr. 2016, [International Magazine]
  English, Scientific journal, Genome/chromosome structures are formed by a hierarchy of organizing processes ranging from gene interactions to chromosome territory formation. The SMC complex, cohesin, mediates interactions among enhancers and promoters, thereby regulating transcription. Another SMC complex, condensin, also plays critical roles in genome organization, although the detailed mechanisms remain much less well understood. Here, we discuss our recent findings on how fission yeast condensin mediates interactions among genes and how condensin-dependent interactions play dual roles in the chromosome territory arrangement during interphase and in mitotic chromosome organization, which supports the fidelity of chromosome segregation. Our studies suggest that condensin serves as a functional ligature connecting gene interactions, chromosome territory arrangement, transcriptional regulation, and chromosome segregation.
• Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres.
  Gadaleta MC; Das MM; Tanizawa H; Chang YT; Noma K; Nakamura TM; Noguchi E
  PLoS genetics, 12, 3, e1005943, 18 Mar. 2016, [International Magazine]
  English, Scientific journal, Genomic instability associated with DNA replication stress is linked to cancer and genetic pathologies in humans. If not properly regulated, replication stress, such as fork stalling and collapse, can be induced at natural replication impediments present throughout the genome. The fork protection complex (FPC) is thought to play a critical role in stabilizing stalled replication forks at several known replication barriers including eukaryotic rDNA genes and the fission yeast mating-type locus. However, little is known about the role of the FPC at other natural impediments including telomeres. Telomeres are considered to be difficult to replicate due to the presence of repetitive GT-rich sequences and telomere-binding proteins. However, the regulatory mechanism that ensures telomere replication is not fully understood. Here, we report the role of the fission yeast Swi1(Timeless), a subunit of the FPC, in telomere replication. Loss of Swi1 causes telomere shortening in a telomerase-independent manner. Our epistasis analyses suggest that heterochromatin and telomere-binding proteins are not major impediments for telomere replication in the absence of Swi1. Instead, repetitive DNA sequences impair telomere integrity in swi1Δ mutant cells, leading to the loss of repeat DNA. In the absence of Swi1, telomere shortening is accompanied with an increased recruitment of Rad52 recombinase and more frequent amplification of telomere/subtelomeres, reminiscent of tumor cells that utilize the alternative lengthening of telomeres pathway (ALT) to maintain telomeres. These results suggest that Swi1 ensures telomere replication by suppressing recombination and repeat instability at telomeres. Our studies may also be relevant in understanding the potential role of Swi1(Timeless) in regulation of telomere stability in cancer cells.
• Involvement of condensin-directed gene associations in the organization and regulation of chromosome territories during the cell cycle.
  Iwasaki O; Corcoran CJ; Noma K
  Nucleic acids research, 44, 8, 3618, 28, 23 Dec. 2015, [International Magazine]
  English, Scientific journal, Chromosomes are not randomly disposed in the nucleus but instead occupy discrete sub-nuclear domains, referred to as chromosome territories. The molecular mechanisms that underlie the formation of chromosome territories and how they are regulated during the cell cycle remain largely unknown. Here, we have developed two different chromosome-painting approaches to address how chromosome territories are organized in the fission yeast model organism. We show that condensin frequently associates RNA polymerase III-transcribed genes (tRNA and 5S rRNA) that are present on the same chromosomes, and that the disruption of these associations by condensin mutations significantly compromises the chromosome territory arrangement. We also find that condensin-dependent intra-chromosomal gene associations and chromosome territories are co-regulated during the cell cycle. For example, condensin-directed gene associations occur to the least degree during S phase, with the chromosomal overlap becoming largest. In clear contrast, condensin-directed gene associations become tighter in other cell-cycle phases, especially during mitosis, with the overlap between the different chromosomes being smaller. This study suggests that condensin-driven intra-chromosomal gene associations contribute to the organization and regulation of chromosome territories during the cell cycle.
• Interaction between TBP and Condensin Drives the Organization and Faithful Segregation of Mitotic Chromosomes.
  Iwasaki O; Tanizawa H; Kim KD; Yokoyama Y; Corcoran CJ; Tanaka A; Skordalakes E; Showe LC; Noma K
  Molecular cell, 59, 5, 755, 67, 06 Aug. 2015, [International Magazine]
  English, Scientific journal, Genome/chromosome organization is highly ordered and controls various nuclear events, although the molecular mechanisms underlying the functional organization remain largely unknown. Here, we show that the TATA box-binding protein (TBP) interacts with the Cnd2 kleisin subunit of condensin to mediate interphase and mitotic chromosomal organization in fission yeast. TBP recruits condensin onto RNA polymerase III-transcribed (Pol III) genes and highly transcribed Pol II genes; condensin in turn associates these genes with centromeres. Inhibition of the Cnd2-TBP interaction disrupts condensin localization across the genome and the proper assembly of mitotic chromosomes, leading to severe defects in chromosome segregation and eventually causing cellular lethality. We propose that the Cnd2-TBP interaction coordinates transcription with chromosomal architecture by linking dispersed gene loci with centromeres. This chromosome arrangement can contribute to the efficient transmission of physical force at the kinetochore to chromosomal arms, thereby supporting the fidelity of chromosome segregation.
• Chromatin immunoprecipitation to detect DNA replication and repair factors.
  Gadaleta MC; Iwasaki O; Noguchi C; Noma K; Noguchi E
  Methods in molecular biology (Clifton, N.J.), 1300, 169, 86, 01 Jan. 2015, [International Magazine]
  English, Scientific journal, DNA replication is tightly coupled with DNA repair processes in order to preserve genomic integrity. During DNA replication, the replication fork encounters a variety of obstacles including DNA damage/adducts, secondary structures, and programmed fork-blocking sites, which are all difficult to replicate. The replication fork also collides with the transcription machinery, which shares the template DNA with the replisome complex. Under these conditions, replication forks stall, causing replication stress and/or fork collapse, ultimately leading to genomic instability. The mechanisms to overcome these replication problems remain elusive. Therefore, it is important to investigate how DNA repair and replication factors are recruited and coordinated at chromosomal regions that are difficult to replicate. In this chapter, we describe a chromatin immunoprecipitation method to locate proteins required for DNA repair during DNA replication in the fission yeast Schizosaccharomyces pombe. This method can also easily be adapted to study replisome components or chromatin-associated factors.
• A novel role for the condensin II complex in cellular senescence.
  Yokoyama Y; Zhu H; Zhang R; Noma K
  Cell cycle (Georgetown, Tex.), 14, 13, 2160, 70, 01 Jan. 2015, [International Magazine]
  English, Scientific journal, Although cellular senescence is accompanied by global alterations in genome architecture, how the genome is restructured during the senescent processes is not well understood. Here, we show that the hCAP-H2 subunit of the condensin II complex exists as either a full-length protein or an N-terminus truncated variant (ΔN). While the full-length hCAP-H2 associates with mitotic chromosomes, the ΔN variant exists as an insoluble nuclear structure. When overexpressed, both hCAP-H2 isoforms assemble this nuclear architecture and induce senescence-associated heterochromatic foci (SAHF). The hCAP-H2ΔN protein accumulates as cells approach senescence, and hCAP-H2 knockdown inhibits oncogene-induced senescence. This study identifies a novel mechanism whereby condensin drives senescence via nuclear/genomic reorganization.
• New vectors for epitope tagging and gene disruption in Schizosaccharomyces pombe.
  Gadaleta MC; Iwasaki O; Noguchi C; Noma K; Noguchi E
  BioTechniques, 55, 5, 257, 63, 01 Nov. 2013, [International Magazine]
  English, Scientific journal, We describe a series of new vectors for PCR-based epitope tagging and gene disruption in the fission yeast Schizosaccharomyces pombe, an exceptional model organism for the study of cellular processes. The vectors are designed for amplification of gene-targeting DNA cassettes and integration into specific genetic loci, allowing expression of proteins fused to 12 tandem copies of the Pk (V5) epitope or 5 tandem copies of the FLAG epitope with a glycine linker. These vectors are available with various antibiotic or nutritional markers and are useful for protein studies using biochemical and cell biological methods. We also describe new vectors for fluorescent protein-tagging and gene disruption using ura4MX6, LEU2MX6, and his3MX6 selection markers, allowing researchers in the S. pombe community to disrupt genes and manipulate genomic loci using primer sets already available for the widely used pFA6a-MX6 system. Our new vectors may also be useful for gene manipulation in Saccharomyces cerevisiae.
• Centromeric motion facilitates the mobility of interphase genomic regions in fission yeast.
  Kim KD; Tanizawa H; Iwasaki O; Corcoran CJ; Capizzi JR; Hayden JE; Noma K
  Journal of cell science, 126, Pt 22, 5271, 83, 28 Aug. 2013, [International Magazine]
  English, Scientific journal, Dispersed genetic elements, such as retrotransposons and Pol-III-transcribed genes, including tRNA and 5S rRNA, cluster and associate with centromeres in fission yeast through the function of condensin. However, the dynamics of these condensin-mediated genomic associations remains unknown. We have examined the 3D motions of genomic loci including the centromere, telomere, rDNA repeat locus, and the loci carrying Pol-III-transcribed genes or long-terminal repeat (LTR) retrotransposons in live cells at as short as 1.5-second intervals. Treatment with carbendazim (CBZ), a microtubule-destabilizing agent, not only prevents centromeric motion, but also reduces the mobility of the other genomic loci during interphase. Further analyses demonstrate that condensin-mediated associations between centromeres and the genomic loci are clonal, infrequent and transient. However, when associated, centromeres and the genomic loci migrate together in a coordinated fashion. In addition, a condensin mutation that disrupts associations between centromeres and the genomic loci results in a concomitant decrease in the mobility of the loci. Our study suggests that highly mobile centromeres pulled by microtubules in cytoplasm serve as 'genome mobility elements' by facilitating physical relocations of associating genomic regions.
• Mapping of Long-Range Associations throughout the Fission Yeast Genome Reveals Global Genome Organization Linked to Transcriptional Regulation
  Hideki Tanizawa; Osamu Iwasaki; Atsunari Tanaka; Joseph R. Capizzi; Priyankara Wickramasinghe; Mihee Lee; Zhiyan Fu; Ken-ichi Noma
  BIOPHYSICAL JOURNAL, 104, 2, 425A, 425A, Jan. 2013
  English
• Epigenetic regulation of condensin-mediated genome organization during the cell cycle and upon DNA damage through histone H3 lysine 56 acetylation.
  Tanaka A; Tanizawa H; Sriswasdi S; Iwasaki O; Chatterjee AG; Speicher DW; Levin HL; Noguchi E; Noma K
  Molecular cell, 48, 4, 532, 46, 18 Oct. 2012, [International Magazine]
  English, Scientific journal
• Evolutionary mechanisms of microbial genomes 2012.
  Nishida H; Kondo S; Nojiri H; Noma K; Oshima K
  International journal of evolutionary biology, 22 Aug. 2012
  Scientific journal
• Unravelling global genome organization by 3C-seq.
  Tanizawa H; Noma K
  Seminars in cell & developmental biology, 23, 2, 213, 21, 18 Nov. 2011, [International Magazine]
  English, Scientific journal, Eukaryotic genomes exist in the cell nucleus as an elaborate three-dimensional structure which reflects various nuclear processes such as transcription, DNA replication and repair. Next-generation sequencing (NGS) combined with chromosome conformation capture (3C), referred to as 3C-seq in this article, has recently been applied to the yeast and human genomes, revealing genome-wide views of functional associations among genes and their regulatory elements. Here, we compare the latest genomic approaches such as 3C-seq and ChIA-PET, and provide a condensed overview of how eukaryotic genomes are functionally organized in the nucleus.
• Conversion from senescent cells to pluripotent cells by modulating expression of Alu retroelements.
  Iwasaki O; Corcoran CJ; Noma K
  Cell cycle (Georgetown, Tex.), 10, 21, 3633, 4, 01 Nov. 2011, [International Magazine]
  English, Scientific journal
• Evolutionary mechanisms of microbial genomes.
  Nishida H; Kondo S; Nojiri H; Noma K; Oshima K
  International journal of evolutionary biology, 31 May 2011
  Scientific journal
• Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci.
  Yamane K; Mizuguchi T; Cui B; Zofall M; Noma K; Grewal SI
  Molecular cell, 41, 1, 56, 66, 01 Jan. 2011, [International Magazine]
  English, Scientific journal, Heterochromatin impacts various nuclear processes by providing a recruiting platform for diverse chromosomal proteins. In fission yeast, HP1 proteins Chp2 and Swi6, which bind to methylated histone H3 lysine 9, associate with SHREC (Snf2/HDAC repressor complex) and Clr6 histone deacetylases (HDACs) involved in heterochromatic silencing. However, heterochromatic silencing machinery is not fully defined. We describe a histone chaperone complex containing Asf1 and HIRA that spreads across silenced domains via its association with Swi6 to enforce transcriptional silencing. Asf1 functions in concert with a Clr6 HDAC complex to silence heterochromatic repeats, and it suppresses antisense transcription by promoting histone deacetylation. Furthermore, we demonstrate that Asf1 and SHREC facilitate nucleosome occupancy at heterochromatic regions but TFIIIC transcription factor binding sites within boundary elements are refractory to these factors. These analyses uncover a role for Asf1 in global histone deacetylation and suggest that HP1-associated histone chaperone promotes nucleosome occupancy to assemble repressive heterochromatin.
• Global genome organization mediated by RNA polymerase III-transcribed genes in fission yeast.
  Iwasaki O; Noma K
  Gene, 30 Dec. 2010
  Scientific journal, Eukaryotic genomes exist as an elaborate three-dimensional structure in the nucleus. Recent studies have shown that this higher-order organization of the chromatin fiber is coupled to various nuclear processes including transcription. In fission yeast, we demonstrated that RNA polymerase III (Pol III)-transcribed genes such as tRNA and 5S rRNA genes, dispersed throughout chromosomal arm regions, localize to centromeres in interphase. This centromeric association of Pol III genes, mediated by the condensin complex, becomes prominent during mitosis. Here, we discuss potential roles of the Pol III gene-mediated genome organization during interphase and mitosis, and hypothesize that the interphase genome structure serves as a scaffold for the efficient assembly of condensed mitotic chromosomes and that tethering of chromosomal arm regions to centromeres allows chromosomes to properly segregate along the spindle microtubules during anaphase.
• Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation.
  Tanizawa H; Iwasaki O; Tanaka A; Capizzi JR; Wickramasinghe P; Lee M; Fu Z; Noma K
  Nucleic acids research, 38, 22, 8164, 77, 28 Oct. 2010, [International Magazine]
  English, Scientific journal, We have comprehensively mapped long-range associations between chromosomal regions throughout the fission yeast genome using the latest genomics approach that combines next generation sequencing and chromosome conformation capture (3C). Our relatively simple approach, referred to as enrichment of ligation products (ELP), involves digestion of the 3C sample with a 4 bp cutter and self-ligation, achieving a resolution of 20 kb. It recaptures previously characterized genome organizations and also identifies new and important interactions. We have modeled the 3D structure of the entire fission yeast genome and have explored the functional relationships between the global genome organization and transcriptional regulation. We find significant associations among highly transcribed genes. Moreover, we demonstrate that genes co-regulated during the cell cycle tend to associate with one another when activated. Remarkably, functionally defined genes derived from particular gene ontology groups tend to associate in a statistically significant manner. Those significantly associating genes frequently contain the same DNA motifs at their promoter regions, suggesting that potential transcription factors binding to these motifs are involved in defining the associations among those genes. Our study suggests the presence of a global genome organization in fission yeast that is functionally similar to the recently proposed mammalian transcription factory.
• The human Pol III transcriptome and gene information flow.
  Noma K; Kamakaka RT
  Nature structural & molecular biology, 01 May 2010
  Scientific journal
• Centromeric localization of dispersed Pol III genes in fission yeast.
  Iwasaki O; Tanaka A; Tanizawa H; Grewal SI; Noma K
  Molecular biology of the cell, 21, 2, 254, 65, 12 Nov. 2009, [International Magazine]
  English, Scientific journal, The eukaryotic genome is a complex three-dimensional entity residing in the nucleus. We present evidence that Pol III-transcribed genes such as tRNA and 5S rRNA genes can localize to centromeres and contribute to a global genome organization. Furthermore, we find that ectopic insertion of Pol III genes into a non-Pol III gene locus results in the centromeric localization of the locus. We show that the centromeric localization of Pol III genes is mediated by condensin, which interacts with the Pol III transcription machinery, and that transcription levels of the Pol III genes are negatively correlated with the centromeric localization of Pol III genes. This centromeric localization of Pol III genes initially observed in interphase becomes prominent during mitosis, when chromosomes are condensed. Remarkably, defective mitotic chromosome condensation by a condensin mutation, cut3-477, which reduces the centromeric localization of Pol III genes, is suppressed by a mutation in the sfc3 gene encoding the Pol III transcription factor TFIIIC subunit, sfc3-1. The sfc3-1 mutation promotes the centromeric localization of Pol III genes. Our study suggests there are functional links between the process of the centromeric localization of dispersed Pol III genes, their transcription, and the assembly of condensed mitotic chromosomes.
• Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein.
  Wang Y; Reddy B; Thompson J; Wang H; Noma K; Yates JR 3rd; Jia S
  Molecular cell, 33, 4, 428, 37, 01 Feb. 2009, [International Magazine]
  English, Scientific journal, Methylation of histone H4 lysine 20 (H4K20me) is essential for recruiting checkpoint proteins 53BP1/Crb2 to DNA lesions and subsequent activation of a DNA-damage checkpoint. In fission yeast, Set9 (spKMT5) catalyzes mono-, di-, and trimethylation of H4K20. However, the mechanisms that regulate Set9 function are poorly understood. Here, we identified a PWWP domain protein Pdp1 as a Set9-associated factor. Pdp1 binds to histones and is required for Set9 chromatin localization. Yeast cells without Pdp1 were deficient in all three states of H4K20me, sensitive to genotoxic treatments, and impaired in Crb2 recruitment. The PWWP domain of Pdp1 binds to H4K20me, and mutations within the PWWP domain that abrogated this interaction in vitro reduced both the association of Set9 with chromatin and the extent of H4K20me in vivo. These results demonstrate that the PWWP domain is a new methyl-lysine recognition motif that plays important roles in epigenetic regulation.
• Chromatin domains organized by boundaries
  Ken-ichi Noma
  2007
• Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe.
  Morris SA; Shibata Y; Noma K; Tsukamoto Y; Warren E; Temple B; Grewal SI; Strahl BD
  Eukaryotic cell, 4, 8, 1446, 54, 01 Aug. 2005, [International Magazine]
  English, Scientific journal, Set2 methylation of histone H3 at lysine 36 (K36) has recently been shown to be associated with RNA polymerase II (Pol II) elongation in Saccharomyces cerevisiae. However, whether this modification is conserved and associated with transcription elongation in other organisms is not known. Here we report the identification and characterization of the Set2 ortholog responsible for K36 methylation in the fission yeast Schizosaccharomyces pombe. We find that similar to the budding yeast enzyme, S. pombe Set2 is also a robust nucleosome-selective H3 methyltransferase that is specific for K36. Deletion of the S. pombe set2+ gene results in complete abolishment of K36 methylation as well as a slow-growth phenotype on plates containing synthetic medium. These results indicate that Set2 is the sole enzyme responsible for this modification in fission yeast and is important for cell growth under stressed conditions. Using the chromatin immunoprecipitation assay, we demonstrate that K36 methylation in S. pombe is associated with the transcribed regions of Pol II-regulated genes and is devoid in regions that are not transcribed by Pol II. Consistent with a role for Set2 in transcription elongation, we find that S. pombe Set2 associates with the hyperphosphorylated form of Pol II and can fully rescue K36 methylation and Pol II interaction in budding yeast cells deleted for Set2. These results, along with our finding that K36 methylation is highly conserved among eukaryotes, imply a conserved role for this modification in the transcription elongation process.
• RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing.
  Noma K; Sugiyama T; Cam H; Verdel A; Zofall M; Jia S; Moazed D; Grewal SI
  Nature genetics, 36, 11, 1174, 80, 10 Oct. 2004, [International Magazine]
  English, Scientific journal, RNA interference is a conserved mechanism by which double-stranded RNA is processed into short interfering RNAs (siRNAs) that can trigger both post-transcriptional and transcriptional gene silencing. In fission yeast, the RNA-induced initiation of transcriptional gene silencing (RITS) complex contains Dicer-generated siRNAs and is required for heterochromatic silencing. Here we show that RITS components, including Argonaute protein, bind to all known heterochromatic loci. At the mating-type region, RITS is recruited to the centromere-homologous repeat cenH in a Dicer-dependent manner, whereas the spreading of RITS across the entire 20-kb silenced domain, as well as its subsequent maintenance, requires heterochromatin machinery including Swi6 and occurs even in the absence of Dicer. Furthermore, our analyses suggest that RNA interference machinery operates in cis as a stable component of heterochromatic domains with RITS tethered to silenced loci by methylation of histone H3 at Lys9. This tethering promotes the processing of transcripts and generation of additional siRNAs for heterochromatin maintenance.
• RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins.
  Jia S; Noma K; Grewal SI
  Science, 304, 5679, 1971, 6, 01 Jun. 2004, [International Magazine]
  English, Scientific journal, At the silent mating-type interval of fission yeast, the RNA interference (RNAi) machinery cooperates with cenH, a DNA element homologous to centromeric repeats, to initiate heterochromatin formation. However, in RNAi mutants, heterochromatin assembly can still occur at low efficiency. Here, we report that Atf1 and Pcr1, two ATF/CREB family proteins, act in a parallel mechanism to the RNAi pathway for heterochromatin nucleation. Deletion of atf1 or pcr1 alone has little effect on silencing at the mating-type region, but when combined with RNAi mutants, double mutants fail to nucleate heterochromatin assembly. Moreover, deletion of atf1 or pcr1 in combination with cenH deletion causes loss of silencing and heterochromatin formation. Furthermore, Atf1 and Pcr1 bind to the mating-type region and target histone H3 lysine-9 methylation and the Swi6 protein essential for heterochromatin assembly. These analyses link ATF/CREB family proteins, involved in cellular response to environmental stresses, to nucleation of constitutive heterochromatin.
• Alp13, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity.
  Nakayama J; Xiao G; Noma K; Malikzay A; Bjerling P; Ekwall K; Kobayashi R; Grewal SI
  The EMBO journal, 22, 11, 2776, 87, 01 Jun. 2003, [International Magazine]
  English, Scientific journal, The post-translational modifications of histones are key to the modulation of chromatin structure. Distinct patterns of modifications established by histone-modifying enzymes control diverse chromosomal processes. Here, we report the purification and molecular characterization of the fission yeast Clr6 histone deacetyl ase involved in higher order chromatin assembly. We show that a chromodomain protein Alp13, which belongs to the conserved MRG protein family linked to cellular senescence in humans, is associated with Clr6. In addition, Clr6 interacts with homologs of the mammalian transcriptional co-repressors Sin3, Pst1 and Pst2, and a WD40 repeat-containing protein, Prw1. Alp13, Pst2 and Prw1 form a stable complex with Clr6 in the nucleus. Deletion of any of these factors causes progressive loss of viability and sensitivity to DNA-damaging agents, and impairs condensation/resolution of chromosomes during mitosis. This is accompanied by hyperacetylation of histones and a reduction in histone H3 Ser10 phosphorylation, which correlates with chromosome condensation during mitosis. These results link the MRG family protein Alp13 to histone deacetylation, and suggest that Clr6 and its associated factors are essential for fundamental chromosomal events.
• A novel jmjC domain protein modulates heterochromatization in fission yeast.
  Ayoub N; Noma K; Isaac S; Kahan T; Grewal SI; Cohen A
  Molecular and cellular biology, 23, 12, 4356, 70, 01 Jun. 2003, [International Magazine]
  English, Scientific journal, The heterochromatin domain at the mat locus of Schizosaccharomyces pombe is bounded by the IR-L and IR-R barriers. A genetic screen for mutations that promote silencing beyond IR-L revealed a novel gene named epe1, encoding a conserved nuclear protein with a jmjC domain. Disruption of epe1 promotes continuous spreading of heterochromatin-associated histone modifications and Swi6 binding to chromatin across heterochromatic barriers. It also enhances position effect variegation at heterochromatic domains, suppresses mutations in silencing genes, and stabilizes the repressed epigenetic state at the mat locus. However, it does not enhance silencing establishment. Our analysis suggests that the jmjC domain is essential for Epe1 activity and that Epe1 counteracts transcriptional silencing by negatively affecting heterochromatin stability. Consistent with this proposition, the meiotic stability of established heterochromatin beyond IR-L is diminished by Epe1 activity, and overexpression of Epe1 disrupts heterochromatin through acetylation of H3-K9 and H3-K14 and methylation of H3-K4. Furthermore, overexpression of Epe1 elevates the rate of chromosome loss. We propose that Epe1 helps control chromatin organization by down-regulating the stability of epigenetic marks that govern heterochromatization.
• RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast.
  Hall IM; Noma K; Grewal SI
  Proceedings of the National Academy of Sciences of the United States of America, 100, 1, 193, 8, 30 Dec. 2002, [International Magazine]
  English, Scientific journal, The regulation of higher-order chromosome structure is central to cell division and sexual reproduction. Heterochromatin assembly at the centromeres facilitates both kinetochore formation and sister chromatid cohesion, and the formation of specialized chromatin structures at telomeres serves to maintain the length of telomeric repeats, to suppress recombination, and to aid in formation of a bouquet-like structure that facilitates homologous chromosome pairing during meiosis. In fission yeast, genes encoding the Argonaute, Dicer, and RNA-dependent RNA polymerase factors involved in RNA interference (RNAi) are required for heterochromatin formation at the centromeres and mating type region. In this study, we examine the effects of deletions of the fission yeast RNAi machinery on chromosome dynamics during mitosis and meiosis. We find that the RNAi machinery is required for the accurate segregation of chromosomes. Defects in mitotic chromosome segregation are correlated with loss of cohesin at centromeres. Although the telomeres of RNAi mutants maintain silencing, length, and localization of the heterochromatin protein Swi6, we discovered defects in the proper clustering of telomeres in interphase mitotic cells. Furthermore, a small proportion of RNAi mutant cells display aberrant telomere clustering during meiotic prophase. This study demonstrates that the fission yeast RNAi machinery is required for the proper regulation of chromosome architecture during mitosis and meiosis.
• Expression of Arabidopsis LINEs from two promoters.
  Ohta Y; Noma K; Tsuchimoto S; Ohtsubo E; Ohtsubo H
  The Plant journal, 01 Dec. 2002
  Scientific journal, Most Arabidopsis long interspersed elements (LINEs, called ATLNs) have two open reading frames, orf1 and orf2. In the 5' untranslated regions (UTRs) located upstream of orf1, the most proximal segments of tens of base pairs long are not homologous even in two ATLN members with almost identical sequences. In this study, we first show that RT-PCR products from ATLN39, a member of ATLN, can be detected only in total RNA from the hypomethylation mutant ddm1 or from suspension-cultured cells treated with a DNA methylation inhibitor 5-azacytidine, indicating that the expression of ATLN39 is negatively regulated by DNA methylation. We then show that orf1 fused in frame with the luciferase (luc) gene is expressed in suspension-cultured cells of A. thaliana when the 5' UTR is present in the region upstream of orf1. Analysis of deletion in the 5' UTR revealed that the 5' UTR has two promoters, designated here as P1 and P2. Analysis of transcripts by 5' RACE showed that their 5' ends were located at sites immediately upstream of the P1 region or at sites downstream of the P2 region. This observation and the fact that the P1 region contains no TATA sequence indicate that P1 is an internal promoter that initiates transcription from sites upstream of the promoter. A sequence containing GGCGA with a CpG methylatable site is conserved in the P1 regions in members closely related to ATLN39. The P2 region, however, contains the TATA sequence as well as another sequence with a CpG site. The TATA sequence is conserved in members closely related to ATLN39 but not in the other ATLN members, suggesting that P2 is the promoter uniquely present in the ATLN39-related members. Transcripts from promoter P1 can be used as templates to give new copies proficient in retroposition, but those from promoter P2 cannot because of the lack of the proximal half region of the 5' UTR sequence. Transcripts from promoter P2, as well as those from promoter P1 can, however, be used for the production of a sufficient amount of proteins for retroposition. Only a short sequence of the non-homologous region is present at the 5' ends of transcripts from promoter P1, thus suggesting that the non-homologous regions seen in the most proximal regions in ATLN elements are not generated in transcription.
• Establishment and maintenance of a heterochromatin domain.
  Hall IM; Shankaranarayana GD; Noma K; Ayoub N; Cohen A; Grewal SI
  Science, 297, 5590, 2232, 7, 05 Sep. 2002, [International Magazine]
  English, Scientific journal, The higher-order assembly of chromatin imposes structural organization on the genetic information of eukaryotes and is thought to be largely determined by posttranslational modification of histone tails. Here, we study a 20-kilobase silent domain at the mating-type region of fission yeast as a model for heterochromatin formation. We find that, although histone H3 methylated at lysine 9 (H3 Lys9) directly recruits heterochromatin protein Swi6/HP1, the critical determinant for H3 Lys9 methylation to spread in cis and to be inherited through mitosis and meiosis is Swi6 itself. We demonstrate that a centromere-homologous repeat (cenH) present at the silent mating-type region is sufficient for heterochromatin formation at an ectopic site, and that its repressive capacity is mediated by components of the RNA interference (RNAi) machinery. Moreover, cenH and the RNAi machinery cooperate to nucleate heterochromatin assembly at the endogenous mat locus but are dispensable for its subsequent inheritance. This work defines sequential requirements for the initiation and propagation of regional heterochromatic domains.
• Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast.
  Noma K; Grewal SI
  Proceedings of the National Academy of Sciences of the United States of America, 99 Suppl 4, 16438, 45, 22 Aug. 2002, [International Magazine]
  English, Scientific journal, Methylation of histone H3 at lysine 4 (H3 Lys-4) or lysine 9 (H3 Lys-9) is known to define active and silent chromosomal domains respectively from fission yeast to humans. However, in budding yeast, H3 Lys-4 methylation is also necessary for silent chromatin assembly at telomeres and ribosomal DNA. Here we demonstrate that deletion of set1, which encodes a protein containing an RNA recognition motif at its amino terminus and a SET domain at the carboxy terminus, abolishes H3 Lys-4 methylation in fission yeast. Unlike in budding yeast, Set1-mediated H3 Lys-4 methylation is not required for heterochromatin assembly at the silent mating-type region and centromeres in fission yeast. Our analysis suggests that H3 Lys-4 methylation is a stable histone modification present throughout the cell cycle, including mitosis. The loss of H3 Lys-4 methylation in set1Delta cells is correlated with a decrease in histone H3 acetylation levels, suggesting a mechanistic link between H3 Lys-4 methylation and acetylation of the H3 tail. We suggest that methylation of H3 Lys-4 primarily acts in the maintenance of transcriptionally poised euchromatic domains, and that this modification is dispensable for heterochromatin formation in fission yeast, which instead utilizes H3 Lys-9 methylation.
• A new class of LINEs (ATLN-L) from Arabidopsis thaliana with extraordinary structural features.
  Noma K; Ohtsubo H; Ohtsubo E
  DNA research, 01 Dec. 2001
  Scientific journal, The Arabidopsis thaliana genome has about 250 copies of LINEs (here called ATLNs). Of these, some, called ATLN-Ls, have an extra sequence of about 2 kb in the region downstream of two consecutive open reading frames, orf1 and orf2. Interestingly, the extra sequences in these ATLN-L members have another open reading frame, designated as orf3. Each member is flanked by direct repeats of a target site sequence, showing that ATLN-L members with the three open reading frames have retrotransposed as a unit. The ATLN-L members are also distinct from other ATLN members: orf1 terminates with TAA (or TAG) and is located in the same frame as orf2, and the ATG initiation codon of orf2 is not present in the proximal region. A sequence that may form a pseudoknot structure in ATLN-L mRNA was present in the proximal region of orf2, therefore the TAA (or TAG) termination codon of orf1 is assumed to be suppressed to produce an Orf1-Orf2 transframe protein during the translation of the ATLN-L mRNA. The region between orf2 and orf3 is several hundred bp long, suggesting that orf3 expression is independent of orfl-orf2. The amino acid sequences of the proteins Orf1 and Orf3 are highly homologous in their N-terminal half regions that have a retroviral zinc-finger motif for RNA binding. Orf3, however, has a leucine-zipper motif in addition to the zinc-finger motif. The C-terminal regions of the Orf1 and Orf3 proteins have poor homology, but seem to have nuclear localization signals, suggesting that these proteins are involved in the transfer of ATLN-L mRNA to nuclei. A phylogenetic tree shows that Orf3 proteins form a branch distinct from the branches of the Orf1 proteins encoded by ATLN-L members. This indicates that an ancestor element of ATLN-Ls has incorporated the orf1 frame carried by another ATLN member into its distal region to orf1-orf2 during evolution.
• Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries.
  Noma K; Allis CD; Grewal SI
  Science, 01 Aug. 2001
  Scientific journal, Eukaryotic genomes are organized into discrete structural and functional chromatin domains. Here, we show that distinct site-specific histone H3 methylation patterns define euchromatic and heterochromatic chromosomal domains within a 47-kilobase region of the mating-type locus in fission yeast. H3 methylated at lysine 9 (H3 Lys9), and its interacting Swi6 protein, are strictly localized to a 20-kilobase silent heterochromatic interval. In contrast, H3 methylated at lysine 4 (H3 Lys4) is specific to the surrounding euchromatic regions. Two inverted repeats flanking the silent interval serve as boundary elements to mark the borders between heterochromatin and euchromatin. Deletions of these boundary elements lead to spreading of H3 Lys9 methylation and Swi6 into neighboring sequences. Furthermore, the H3 Lys9 methylation and corresponding heterochromatin-associated complexes prevent H3 Lys4 methylation in the silent domain.
• Identification and structural analysis of SINE elements in the Arabidopsis thaliana genome.
  Myouga F; Tsuchimoto S; Noma K; Ohtsubo H; Ohtsubo E
  Genes & genetic systems, 01 Jun. 2001
  Scientific journal, An insertion sequence was found in a Mu homologue in the genome of Arabidopsis thaliana. The insertion sequence had poly(A) at the 3' end, and promoter motifs (A- and B-boxes) recognized by RNA polymerase III. The sequence was flanked by direct repeats of a 15-bp sequence of the Mu homologue, which appears to be a target-site sequence duplicated upon insertion. These findings indicate that the insertion sequence is a retroposon SINE, and it was therefore named AtSN (A. thaliana SINE). Many members of the AtSN family were identified through a computer-aided homology search of databases and classified into two subfamilies, AtSN1 and AtSN2, having consensus sequences 159 and 149 bp in length, respectively. These had no homology to SINEs in other organisms. About half of AtSN members were truncated through loss of a region at either end of the element. Most of them were truncated at the 5' end, and had a duplication of the target-site sequence. This suggests that the ones with 5' truncation retroposed by the same mechanism as those without truncation. Members of the AtSN1 or AtSN2 subfamilies had many base substitutions when compared with the consensus sequence. All of the members examined were present in three different ecotypes of A. thaliana (Columbia, Landsberg erecta, and Wassilewskija). These findings suggest that AtSN members had proliferatedbefore the A. thaliana ecotype strains diverged.
• ATLN elements, LINEs from Arabidopsis thaliana: identification and characterization.
  Noma K; Ohtsubo H; Ohtsubo E
  DNA research, 01 Oct. 2000
  Scientific journal, Non-LTR retrotransposons (LINEs) are ubiquitous elements in the plant kingdom. Two hundred and nineteen LINE homologues (named ATLN) were identified in the A. thaliana genome, about 90% of which have been sequenced by a computer-aided homology search. Of these, the structures of 62 were analyzed in detail. Most, including those truncated for the 5' regions, were flanked by direct repeats of a sequence of 7-21 bp long, the target site sequence duplicated upon retrotransposition of each member. Thirty ATLN members had two consecutive open reading frames, corresponding to orf1 and orf2 essential for retrotransposition. The phylogenetic tree constructed from the amino acid sequences of the endonuclease domains of the Orf2 proteins showed that the ATLN members were grouped in two families (I and II) and that the members of each family could be further divided into several subfamilies. The members of each subfamily had several unique structural features in common in the intergenic region between orf1 and orf2 as well as in the downstream regions of orf2. Interestingly, orf2 in almost all the ATLN members is located in the -1 frame relative to orf1, indicative of the existence of such translational control mechanisms as translational coupling or frameshifting to produce an amount of Orf2 protein appropriate to that of Orf1. Moreover, the most proximal sequences in the 5' untranslated regions were non-homologous, even in members with the highest homology, unlike the LINEs in animals. The non-homologous sequences in the 5' untranslated regions might be acquired at or after transcription during retrotransposition of the ATLN elements.
• Tnat1 and Tnat2 from Arabidopsis thaliana: novel transposable elements with tandem repeat sequences.
  Noma K; Ohtsubo E
  DNA research, 01 Feb. 2000
  Scientific journal, A computer-aided homology search of databases found that the nucleotide sequences flanking ATLN44, a non-LTR retrotransposon (LINE) from Arabidopsis thaliana, are repeated in the A. thaliana genome. These sequences are homologous to flanking sequences of 664 bp with terminal inverted repeat sequences of about 70 bp. The 664-bp sequence and most of the 14 homologues identified were flanked by direct repeat sequences of 9 bp. These findings indicate that the repeated sequence, named Tnat1, is a transposable element that duplicates a 9-bp sequence at the target site on transposition and that ATLN44 is inserted in one Tnat1 member. Interestingly, all of the Tnat1 members had tandem repeats comprised of several units of a 60-bp sequence, the number of repeats differing among Tnat1 members. Of the Tnat1 members identified, one was inserted into another sequence repeated in the A. thaliana genome: that sequence is about 770 bp long and has terminal inverted repeat sequences of about 110 bp. The sequence is flanked by direct repeats of a 9-bp sequence, indicating that it is another transposable element, named Tnat2, from A. thaliana. Moreover, Tnat2 members had a tandem repeat about 240 bp long. Tnat1 and Tnat2 with tandem repeats in their internal regions show no homology to each other or to any of the elements identified previously; therefore they appear to be novel transposable elements.
• Non-LTR retrotransposons (LINEs) as ubiquitous components of plant genomes.
  Noma K; Ohtsubo E; Ohtsubo H
  Molecular & general genetics : MGG, 01 Feb. 1999
  Scientific journal, During the course of work aimed at isolating a rice gene from Oryza australiensis by PCR, the oligonucleotide primers used were found to generate a fragment that showed sequence homology to the endonuclease (EN) region of the maize non-LTR retrotransposon (LINE) Cin4. We carried out further PCRs using oligonucleotide primers that hybridized to these sequences, and found that they amplified several fragments, each with homology to the EN regions, from Oryza sativa cv. Nipponbare as well as O. australiensis. We mapped the approximate locations of two rice LINE homologues by screening clones in a YAC library made from a rice (O. sativa) genome, and found that each homologue was present in a low copy number apparently at nonspecific regions on rice chromosomes. We then carried out PCR using degenerate oligonucleotide primers which hybridized to the rice LINE homologues and Cin4 to ascertain whether LINE homologues are present in a variety of members of the plant kingdom, including angiosperms, gymnosperms, bracken, horsetail and liverwort. Cloning and nucleotide sequencing revealed that 53 clones obtained from 27 out of 33 plant species contained LINE homologues. In addition to these homologues, we identified four homologues with EN regions in the Arabidopsis thaliana genome by a computer search of databases. The nucleotide sequences of almost all the LINE homologues were greatly diverged, but the derived amino acid sequences were well conserved, and all contained glutamic acid and tyrosine residues at almost the same relative positions as in the the active site regions of AP (apurinic/apyrimidinic)-endonucleases. The EN regions in the LINE homologues from closely related plant species show a closer phylogenetic relationship, indicating that sequence divergence during vertical transmission has been a major influence upon the evolution of plant LINEs.
• RIRE1, a retrotransposon from wild rice Oryza australiensis.
  Noma K; Nakajima R; Ohtsubo H; Ohtsubo E
  Genes & genetic systems, 01 Jun. 1997
  Scientific journal, RIRE1 is a retrotransposon present in wild rice Oryza australiensis in an extraordinary number of copies, and only a portion of the LTR sequence has been determined previously. Here, we isolated and sequenced DNA segments of various portions of RIRE1, revealing that the sequences of LTR and the internal region were 1523 and 5277 bp in length, respectively. The internal region shows homology with the pol region in copia, a Drosophila retrotransposon, indicating that RIRE1 is a copia-like retrotransposon. The internal region of RIRE1 contained an open reading frame coding for genes, gag, pro, int, rt and rh, like copia and retroelements related to it. A clone screened from a library of the O. australiensis genomic DNA contained solo LTR, which was flanked by direct repeats of a 5-bp sequence. This suggests that RIRE1 generates a duplication of the target sequence of 5 bp upon retroposition. We observed that many RIRE1 members were nested by another RIRE1 member. This indicates that these RIRE1 members have received another RIRE1 to make an extraordinary number of copies in the O. australiensis genome without giving a deleterious effect on the growth of rice cells.
• Identification and characterization of two tandem repeat sequences (TrsB and TrsC) and a retrotransposon (RIRE1) as genome-general sequences in rice.
  Nakajima R; Noma K; Ohtsubo H; Ohtsubo E
  Genes & genetic systems, 01 Dec. 1996
  Scientific journal, Three kinds of DNA sequences (here called TrsB, TrsC and RIRE1) have been previously reported to be those repeated in tandem specifically in the wild rice species with FF, CC or EE genome, respectively. To characterize these genome type-specific sequences, we carried out PCR using a pair of primers, which hybridize to a restricted region in the repeating unit sequence and prime DNA synthesis in both directions. Gel electrophoresis and DNA sequencing revealed that PCR using primers for TrsB (or TrsC) amplified the fragments with an integral series of a unit length not only from total DNA of the rice strain with FF (or CC) genome, but also from those of the rice strains with non-FF (or non-CC) genome. TrsB or TrsC was, however, found to be repeated in an extraordinary number of copies in the species with FF or CC genome, respectively, in which the TrsB (or TrsC) sequence has been originally identified. PCR using primers for RIRE1 produced various sizes of fragments from total DNA of the rice strains with EE genome. The fragments, however, showed no progression at interval of the unit length characteristic for tandem repeats. Nucleotide sequencing of the amplified fragments revealed that they were not the sequences repeated in tandem, but were those interspersed as an element having partial homology with the LTR sequences of retrotransposons, Wis-2-1A in wheat and BARE-1 in barley. RIRE1 was present in the rice species with any types of genomes, but in the species with EE genome in an extraordinary number of copies.

• Analysis of the mechanism for meiotic cohesion-mediated formation of higher-order chromosomal structures enabling reductional segregation at meiosis I
  SAKUNO Takeshi; TASSHIRO Sanki; IWASAKI Osamu; TANIZAWA Hideki; HARAGUCHI Tokuko; NOMA Ken-ichi; NOMA Ken-ichi; HIRAOAKA Yasushi, 日本分子生物学会年会プログラム・要旨集(Web), 44th, 2021
• Tidying Up the 3D Genome
  NOMA Ken-ichi; IWASAKI Osamu; TANIZAWA Hideki; KIM Kyoung-Dong, 日本遺伝学会大会プログラム・予稿集, 90th, 2018
• Architectural alterations of the fission yeast genome during the cell cycle.
  Tanizawa H; Kim KD; Iwasaki O; Noma KI, Nature structural & molecular biology, 24, 11, 965, 976, 09 Oct. 2017, [International Magazine]
  Eukaryotic genomes are highly ordered through various mechanisms, including topologically associating domain (TAD) organization. We employed an in situ Hi-C approach to follow the 3D organization of the fission yeast genome during the cell cycle. We demonstrate that during mitosis, large domains of 300 kb-1 Mb are formed by condensin. This mitotic domain organization does not suddenly dissolve, but gradually diminishes until the next mitosis. By contrast, small domains of 30-40 kb that are formed by cohesin are relatively stable across the cell cycle. Condensin and cohesin mediate long- and short-range contacts, respectively, by bridging their binding sites, thereby forming the large and small domains. These domains are inversely regulated during the cell cycle but assemble independently. Our study describes the chromosomal oscillation between the formation and decay phases of the large and small domains, and we predict that the condensin-mediated domains serve as chromosomal compaction units., English
• The Yeast Genomes in Three Dimensions: Mechanisms and Functions.
  Noma KI, Annual review of genetics, 51, 23, 44, 30 Aug. 2017, [International Magazine]
  The three-dimensional (3D) genome structure is highly ordered by a hierarchy of organizing events ranging from enhancer-promoter or gene-gene contacts to chromosomal territorial arrangement. It is becoming clear that the cohesin and condensin complexes are key molecular machines that organize the 3D genome structure. These complexes are highly conserved from simple systems, e.g., yeast cells, to the much more complex human system. Therefore, knowledge from the budding and fission yeast systems illuminates highly conserved molecular mechanisms of how cohesin and condensin establish the functional 3D genome structures. Here I discuss how these complexes are recruited across the yeast genomes, mediate distinct genome-organizing events such as gene contacts and topological domain formation, and participate in important nuclear activities including transcriptional regulation and chromosomal dynamics., English
• Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast.
  Kim KD; Tanizawa H; Iwasaki O; Noma K, Nature genetics, 48, 10, 1242, 52, 22 Aug. 2016, [International Magazine]
  It is becoming clear that structural-maintenance-of-chromosomes (SMC) complexes such as condensin and cohesin are involved in three-dimensional genome organization, yet their exact roles in functional organization remain unclear. We used chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) to comprehensively identify genome-wide associations mediated by condensin and cohesin in fission yeast. We found that although cohesin and condensin often bind to the same loci, they direct different association networks and generate small and larger chromatin domains, respectively. Cohesin mediates associations between loci positioned within 100 kb of each other; condensin can drive longer-range associations. Moreover, condensin, but not cohesin, connects cell cycle-regulated genes bound by mitotic transcription factors. This study describes the different functions of condensin and cohesin in genome organization and how specific transcription factors function in condensin loading, cell cycle-dependent genome organization and mitotic chromosome organization to support faithful chromosome segregation., English
• フレミングが夢見た染色体の核心 コンデンシンによるゲノムの組織化とエピジェネティクス
  野間健一, 実験医学, 31, 16, 2013
• Host genome surveillance for retrotransposons by transposon-derived proteins.
  Cam HP; Noma K; Ebina H; Levin HL; Grewal SI, Nature, 451, 7177, 431, 6, 19 Dec. 2007, [International Magazine]
  Transposable elements and their remnants constitute a substantial fraction of eukaryotic genomes. Host genomes have evolved defence mechanisms, including chromatin modifications and RNA interference, to regulate transposable elements. Here we describe a genome surveillance mechanism for retrotransposons by transposase-derived centromeric protein CENP-B homologues of the fission yeast Schizosaccharomyces pombe. CENP-B homologues of S. pombe localize at and recruit histone deacetylases to silence Tf2 retrotransposons. CENP-Bs also repress solo long terminal repeats (LTRs) and LTR-associated genes. Tf2 elements are clustered into 'Tf' bodies, the organization of which depends on CENP-Bs that display discrete nuclear structures. Furthermore, CENP-Bs prevent an 'extinct' Tf1 retrotransposon from re-entering the host genome by blocking its recombination with extant Tf2, and silence and immobilize a Tf1 integrant that becomes sequestered into Tf bodies. Our results reveal a probable ancient retrotransposon surveillance pathway important for host genome integrity, and highlight potential conflicts between DNA transposons and retrotransposons, major transposable elements believed to have greatly moulded the evolution of genomes., English
• SHREC, an effector complex for heterochromatic transcriptional silencing.
  Sugiyama T; Cam HP; Sugiyama R; Noma K; Zofall M; Kobayashi R; Grewal SI, Cell, 128, 3, 491, 504, 01 Feb. 2007, [International Magazine]
  Transcriptional gene silencing (TGS) is the mechanism generally thought by which heterochromatin effects silencing. However, recent discovery in fission yeast of a cis-acting posttranscriptional gene-silencing (cis-PTGS) pathway operated by the RNAi machinery at heterochromatin challenges the role of TGS in heterochromatic silencing. Here, we describe a multienzyme effector complex (termed SHREC) that mediates heterochromatic TGS in fission yeast. SHREC consists of a core quartet of proteins - Clr1, Clr2, Clr3, and Mit1 - which distribute throughout all major heterochromatin domains to effect TGS via distinct activities associated with the histone deacetylase Clr3 and the SNF2 chromatin-remodeling factor homolog Mit1. SHREC is also recruited to the telomeres by multiple independent mechanisms involving telomere binding protein Ccq1 cooperating with Taz1 and the RNAi machinery, and to euchromatic sites, via mechanism(s) distinct from its heterochromatin localization aided by Swi6/HP1. Our analyses suggest that SHREC regulates nucleosome positioning to assemble higher-order chromatin structures critical for heterochromatin functions., English
• ゲノム上を“動く遺伝子”トランスポゾン バウンダリーによるクロマチンドメイン形成
  野間健一, 実験医学, 25, 16, 2007
• A role for TFIIIC transcription factor complex in genome organization.
  Noma K; Cam HP; Maraia RJ; Grewal SI, Cell, 125, 5, 859, 72, 01 Jun. 2006, [International Magazine]
  Eukaryotic genome complexity necessitates boundary and insulator elements to partition genomic content into distinct domains. We show that inverted repeat (IR) boundary elements flanking the fission yeast mating-type heterochromatin domain contain B-box sequences, which prevent heterochromatin from spreading into neighboring euchromatic regions by recruiting transcription factor TFIIIC complex without RNA polymerase III (Pol III). Genome-wide analysis reveals TFIIIC with Pol III at all tRNA genes, many of which cluster at pericentromeric heterochromatin domain boundaries. However, a single tRNA(phe) gene with modest TFIIIC enrichment is insufficient to serve as boundary and requires RNAi-associated element to restrain heterochromatin spreading. Remarkably, we found TFIIIC localization without Pol III at many sites located between divergent promoters. These sites appear to act as chromosome-organizing clamps by tethering distant loci to the nuclear periphery, at which TFIIIC is concentrated into several distinct bodies. Our analyses uncover a general genome organization mechanism involving conserved TFIIIC complex., English
• RNAiを介したヘテロクロマチン形成におけるRITS複合体の役割
  野間健一, 実験医学, 23, 3, 2005
• Epigenetic control of establishment and maintenance of heterochromatin
  Ken-ichi Noma, 細胞工学, 22, 6, 2003
• シロイヌナズナのLINE(ATLN)の新規5′末端配列の獲得
  野間健一; 太田与志津; 大坪久子; 大坪栄一, 日本分子生物学会年会プログラム・講演要旨集, 23rd, 2000
• アラビドプシスに存在する多種多様なLINEの同定と構造解析
  野間健一; 大坪久子; 大坪栄一, 日本分子生物学会年会プログラム・講演要旨集, 22nd, 1999
• LINEの存在の有無による生態型の異なるシロイヌナズナの系統関係の解析
  野間健一; CHENG C; 大坪久子; 大坪栄一, 日本遺伝学会大会プログラム・予稿集, 71st, 1999
• Identification and characterization of LINE-like retroposons in rice.
  野間健一; 大坪栄一; 大坪久子, 日本分子生物学会年会プログラム・講演要旨集, 20th, 1997
• Molecular evolution science of retrovirus and retroposon. Diversification of retroelement and plant genome.
  大坪久子; 久米川宣一; 野間健一; 本橋令子; 大坪栄一, 日本遺伝学会大会プログラム・予稿集, 69th, 1997
• Retrotransposon RIRE1 of which multicopies exist in wild rice plant Oryza australiensis.
  野間健一; 大坪久子; 大坪栄一, 日本分子生物学会年会プログラム・講演要旨集, 19th, 1996

• 染色体分離と転写を結び付ける分子機構の解明
  科学研究費助成事業
  01 Apr. 2025 - 31 Mar. 2028
  野間 健一; 太田 信哉; 谷澤 英樹
  日本学術振興会, 基盤研究(B), 北海道大学, 25K02249
• 姉妹染色分体に特異的な遺伝子制御機構の解明
  科学研究費助成事業
  27 Sep. 2023 - 31 Mar. 2026
  野間 健一; HORVATH ATTILA
  日本学術振興会, 特別研究員奨励費, 北海道大学, 23KF0130
• 分裂酵母とヒトの３Ｄゲノム構造とその形成機構の解明
  科学研究費助成事業 国際共同研究加速基金(帰国発展研究)
  18 Feb. 2022 - 31 Mar. 2025
  野間 健一; 太田 信哉
  日本学術振興会, 国際共同研究加速基金(帰国発展研究), 北海道大学, 20K23376
• イネのLINE、RILN1の発現と転移メカニズムの解析
  科学研究費助成事業 特別研究員奨励費
  1999 - 2000
  野間 健一
  日本学術振興会, 特別研究員奨励費, 東京大学, 99J09756