Researcher Database

Yota Murakami
Faculty of Science Chemistry Organic and Biological Chemistry

Researcher Profile and Settings


  • Faculty of Science Chemistry Organic and Biological Chemistry

Job Title

  • Professor


  • Ph.D.


J-Global ID

Research Interests

  • chromosome replication   epigenetics   ヘテロクロマチン   セントロメア   染色体分配   クロマチン構造   Heterochromatin   Centromere   Chromosome segregation   Chromatin structure   Chromosomal replication   

Research Areas

  • Life sciences / Genetics / chromatin
  • Life sciences / Genetics / epigenetics

Academic & Professional Experience

  • 2009/04 - Today Faculty of Science, Hokkaido University Professor
  • 1993/10 - Today Associate Professor,
  • 1993/10 - 2009/03 Institute for Virus Research, Kyoto University Associate Professor
  • 1990/10 - 1993/10 米国スローン・ケタリング記念がんセンター
  • 1990/10 - 1993/10 Memorial Sloan-Keetering Cancer Center(USA),
  • 1987/10 - 1990/10 博士研究員京都大学ウィルス研究所
  • 1987/10 - 1990/10 Institute for Virus Research,
  • 博士研究員
  • Institute for Virus Research, Kyoto University
  • Postdoctoral Fellow
  • Postdoctoral Fellow


  •        -   Kyoto University  Faculty of Science
  •        -   京都大学理学研究科
  •        -   Kyoto University, Faculty of Science
  •        -   Kyoto University, Graduate School of Science

Association Memberships

  • エピジェネティクス研究会   JAPAN SOCIETY FOR CELL BIOLOGY   分子生物学会   The Molecular Biology Society of Japan   

Research Activities

Published Papers

  • Yuta Sato, Keiju Kamijo, Motosuke Tsutsumi, Yota Murakami, Masayuki Takahashi
    The Journal of Biochemistry 0021-924X 2019/10 [Refereed][Not invited]
  • Sorida M, Hirauchi T, Ishizaki H, Kaito W, Shimada A, Mori C, Chikashige Y, Hiraoka Y, Suzuki Y, Ohkawa Y, Kato H, Takahata S, Murakami Y
    PLoS genetics 15 (6) e1008129  1553-7390 2019/06 [Refereed][Not invited]
  • Sorida M, Hirauchi T, Ishizaki H, Kaito W, Shimada A, Mori C, Chikashige Y, Hiraoka Y, Suzuki Y, Ohkawa Y, Kato H, Takahata S, Murakami Y
    PLOS Genetics 15 (6) e1008129  1553-7404 2019/06 [Refereed][Not invited]
  • Differential contributions of nonmuscle myosin IIA and IIB to cytokinesis in human immortalized fibroblasts
    Kei Yamamoto, Kohei Otomo, Tomomi Nemoto, Seiichiro Ishihara, Hisashi Haga, Akira Nagasaki, Yota Murakami, Masayuki Takahashi
    Exp. Cell Res. 376 (1) 67 - 76 2019/03 [Refereed][Not invited]
  • Naoe Kotomura, Satoru Tsunemine, Masahiro Kuragano, Takahiro Asanuma, Hiromi Nakagawa, Katsunori Tanaka, Yota Murakami
    Genes to cells : devoted to molecular & cellular mechanisms 23 (9) 738 - 752 2018/09 [Refereed][Not invited]
    Abp1 is a fission yeast CENP-B homologue that contributes to centromere function, silencing at pericentromeric heterochromatin and silencing of retrotransposons. We identified the sfh1 gene, encoding a core subunit of the fission yeast chromatin remodeling complex RSC as an Abp1-interacting protein. Because sfh1 is essential for growth, we isolated temperature-sensitive sfh1 mutants. These mutants showed defects in centromere functions, reflected by sensitivity to an inhibitor of spindle formation and minichromosome instability. Sfh1 localized at both kinetochore and pericentromeric heterochromatin regions. Although sfh1 mutations had minor effect on silencing at these regions, they decreased the levels of cohesin on centromeric heterochromatin. Sfh1 also localized at a retrotransposon, Tf2, in a partly Abp1-dependent manner, and assisted in silencing of Tf2 by Abp1 probably in the same pathway as a histone chaperon, HIRA, which is also known to involve in Tf2 repression. Furthermore, sfh1 mutants were sensitive to several DNA-damaging treatments (HU, MMS, UV and X-ray). Increase in spontaneous foci of Rad22, a recombination Mediator protein Rad52 homologue, in sfh1 mutant suggests that RSC functions in homologous recombination repair of double-stranded break downstream of the Rad22 recruitment. These results indicate that RSC plays multiple roles in the maintenance of genome integrity.
  • Okazaki K, Kato H, Iida T, Shinmyozu K, Nakayama J, Murakami Y, Urano T
    Epigenetics & Chromatin Springer Nature 11 (1) 2018/06 [Refereed][Not invited]
    【H. Kato: Corresponding/2nd author】
  • Masahiro Kuragano, Taro Q P Uyeda, Keiju Kamijo, Yota Murakami, Masayuki Takahashi
    Molecular biology of the cell 29 (8) 911 - 922 1059-1524 2018/04/15 [Refereed][Not invited]
    We demonstrated that myosin IIA and IIB are essential for the formation of transverse arcs and ventral stress fibers, respectively. Furthermore, we illustrated the roles of both isoforms in lamellar flattening and also raised the possibility that actin filaments in ventral stress fibers are in a stretched conformation.
  • Masahiro Kuragano, Yota Murakami, Masayuki Takahashi
    Biochemical and biophysical research communications 498 (1) 25 - 31 0006-291X 2018/03/25 [Refereed][Not invited]
    Nonmuscle myosin II (NMII) plays an essential role in directional cell migration. In this study, we investigated the roles of NMII isoforms (NMIIA and NMIIB) in the migration of human embryonic lung fibroblasts, which exhibit directionally persistent migration in an intrinsic manner. NMIIA-knockdown (KD) cells migrated unsteadily, but their direction of migration was approximately maintained. By contrast, NMIIB-KD cells occasionally reversed their direction of migration. Lamellipodium-like protrusions formed in the posterior region of NMIIB-KD cells prior to reversal of the migration direction. Moreover, NMIIB KD led to elongation of the posterior region in migrating cells, probably due to the lack of load-bearing stress fibers in this area. These results suggest that NMIIA plays a role in steering migration by maintaining stable protrusions in the anterior region, whereas NMIIB plays a role in maintenance of front-rear polarity by preventing aberrant protrusion formation in the posterior region. These distinct functions of NMIIA and NMIIB might promote intrinsic and directed migration of normal human fibroblasts.
  • Hidetsugu Kohzaki, Maki Asano, Yota Murakami
    Frontiers in Bioscience - Landmark 23 (3) 493 - 505 1093-4715 2018/01/01 [Refereed][Not invited]
    In Drosophila, some factors involved in chromosome replication seem to be involved in gene amplification and endoreplication, which are actively utilized in particular tissue development, but direct evidence has not been shown. Therefore, we examined the effect of depletion of replication factors on these processes. First, we confirmed RNAi knockdown can be used for the depletion of replication factors by comparing the phenotypes of RNAi knockdown and deletion or point mutants of the components of DNA licensing factor, MCM2, MCM4 and Cdt1. Next, we found that tissue-specific RNAi knockdown of replication factors caused tissue-specific defects, probably due to defects in DNA replication. In particular, we found that depletion inhibited gene amplification of the chorion gene in follicle cells and endoreplication in salivary glands, showing that chromosomal DNA replication factors are required for these processes. Finally, using RNAi, we screened the genes for chromosomal DNA replication that affected tissue development. Interestingly, wing specific knockdown of Mcm10 induced wing formation defects. These results suggest that some components of chromosomal replication machinery are directly involved in tissue development.
  • Hidetsugu Kohzaki, Yota Murakami
    Frontiers in Bioscience - Landmark 23 (3) 506 - 511 1093-4715 2018/01/01 [Refereed][Not invited]
    Chromosomal DNA replication machinery is essential for growth of all cells in all organs in multicellular organisms. Its knockdown in several tissues of Drosophila led to rough eye phenotype and the loss of bristles in the eye. These results show that the DNA replication machinery contributes to the body development independent of growth.
  • Takuya Kajitani, Hiroaki Kato, Yuji Chikashige, Chihiro Tsutsumi, Yasushi Hiraoka, Hiroshi Kimura, Yasuyuki Ohkawa, Chikashi Obuse, Damien Hermand, Yota Murakami
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 (52) E11208 - E11217 0027-8424 2017/12 [Refereed][Not invited]
    Some long noncoding RNAs (ncRNAs) transcribed by RNA polymerase II (RNAPII) are retained on chromatin, where they regulate RNAi and chromatin structure. The molecular basis of this retention remains unknown. We show that in fission yeast serine 7 (Ser7) of the C-terminal domain (CTD) of RNAPII is required for efficient siRNA generation for RNAi-dependent heterochromatin formation. Surprisingly, Ser7 facilitates chromatin retention of nascent heterochromatic RNAs (hRNAs). Chromatin retention of hRNAs and siRNA generation requires both Ser7 and an RNA-binding activity of the chromodomain of Chp1, a subunit of the RNA-induced transcriptional silencing (RITS) complex. Furthermore, RITS associates with RNAPII in a Ser7-dependent manner. We propose that Ser7 promotes cotranscriptional chromatin retention of hRNA by recruiting the RNA-chromatin connector protein Chp1, which facilitates RNAi-dependent hetero-chromatin formation. Our findings reveal a function of the CTD code: linking ncRNA transcription to RNAi for heterochromatin formation.
  • Yuta Sato, Yota Murakami, Masayuki Takahashi
    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 488 (4) 614 - 620 0006-291X 2017/07 [Refereed][Not invited]
    A variety of biochemical fractionation methods are available for the quantification of cytoskeletal components. However, each method is designed to target only one cytoskeletal network, either the micro tubule (MT) or actin cytoskeleton, and non-targeted cytoskeletal networks are ignored. Considering the importance of MT actin crosstalk, the organization of both the targeted and non-targeted cytoskeletal networks must be retained intact during fractionation for the accurate analysis of cytoskeletal organization. In this study, we reveal that existing fractionation methods, represented by the MT sedimentation-method for MTs and the Triton X-100 solubility assay-method for actin cytoskeletons, disrupt the organizations of the non-targeted cytoskeletons. We demonstrate a novel fractionation method for the accurate analysis of the cytoskeletal organizations using a taxol-containing PEM-based permeabilization buffer, which we name "semi-retentive cytoskeletal fractionation (SERCYF)-method". The organizations of both MTs and actin cytoskeletons were retained intact even after permeabilization with this buffer. By using the SERCYF-method, we analyzed the effects of nocodazole on the cytoskeletal organizations biochemically and showed promotion of the actin cytoskeletal organization by MT depolymerization. (C) 2017 Elsevier Inc. All rights reserved.
  • Shota Suzuki, Yota Murakami, Shinya Takahata
    Transcription 8 (1) 26 - 31 2154-1272 2017/01/01 [Refereed][Not invited]
    Epigenetic marks determine cell fate via numerous reader proteins. H3K36 methylation is a common epigenetic mark that is thought to be associated with the activities of the RNA polymerase 2 C-terminal domain. We discuss a novel silencing mechanism regulated by Set2-dependent H3K36 methylation that involves exosome-dependent RNA processing.
  • Shota Suzuki, Hiroaki Kato, Yutaka Suzuki, Yuji Chikashige, Yasushi Hiraoka, Hiroshi Kimura, Koji Nagao, Chikashi Obuse, Shinya Takahata, Yota Murakami
    NUCLEIC ACIDS RESEARCH 44 (9) 4147 - 4162 0305-1048 2016/05 [Refereed][Not invited]
    In budding yeast, Set2 catalyzes di- and trimethylation of H3K36 (H3K36me2 and H3K36me3) via an interaction between its Set2-Rpb1 interaction (SRI) domain and C-terminal repeats of RNA polymerase II (Pol2) phosphorylated at Ser(2) and Ser(5) (CTD-S2,5-P). H3K36me2 is sufficient for recruitment of the Rpd3S histone deacetylase complex to repress cryptic transcription from transcribed regions. In fission yeast, Set2 is also responsible for H3K36 methylation, which represses a subset of RNAs including heterochromatic and subtelomeric RNAs, at least in part via recruitment of Clr6 complex II, a homolog of Rpd3S. Here, we show that CTD-S2P-dependent interaction of fission yeast Set2 with Pol2 via the SRI domain is required for formation of H3K36me3, but not H3K36me2. H3K36me3 silenced heterochromatic and subtelomeric transcripts mainly through post-transcriptional and transcriptional mechanisms, respectively, whereas H3K36me2 was not enough for silencing. Clr6 complex II appeared not to be responsible for heterochromatic silencing by H3K36me3. Our results demonstrate that H3K36 methylation has multiple outputs in fission yeast; these findings provide insights into the distinct roles of H3K36 methylation in metazoans, which have different enzymes for synthesis of H3K36me1/2 and H3K36me3.
  • Tange, Y., Chikashige, Y., Takahata, S., Kawakami, K., Higashi, M., Mori, C., Kojidani, T., Hirano, Y., Asakawa, H., Murakami, Y., Haraguchi, T., Hiraoka, Y.
    Genes to Cells 21 (8) 812 - 832 1356-9597 2016 [Refereed][Not invited]
  • Shota Suzuki, Koji Nagao, Chikashi Obuse, Yota Murakami, Shinya Takahata
    PROTEIN EXPRESSION AND PURIFICATION 97 44 - 49 1046-5928 2014/05 [Refereed][Not invited]
    Chromatin-associated proteins are heterogeneously and dynamically composed. To gain a complete understanding of DNA packaging and basic nuclear functions, it is important to generate a comprehensive inventory of these proteins. However, biochemical purification of chromatin-associated proteins is difficult and is accompanied by concerns over complex stability, protein solubility and yield. Here, we describe a new method for optimized purification of the endogenously expressed fission yeast Set2 complex, histone H3K36 methyltransferase. Using the standard centrifugation procedure for purification, approximately half of the Set2 protein separated into the insoluble chromatin pellet fraction, making it impossible to recover the large amounts of soluble Set2. To overcome this poor recovery, we developed a novel protein purification technique termed the filtration/immunoaffinity purification/mass spectrometry (FIM) method, which eliminates the need for centrifugation. Using the FIM method, in which whole cell lysates were filtered consecutively through eight different pore sizes (53-0.8 mu m), a high yield of soluble FLAG-tagged Set2 was obtained from fission yeast. The technique was suitable for affinity purification and produced a low background. A mass spectrometry analysis of anti-FLAG immunoprecipitated proteins revealed that Rpb1, Rpb2 and Rpb3, which have all been reported previously as components of the budding yeast Set2 complex, were isolated from fission yeast using the FIM method. In addition, other subunits of RNA polymerase II and its phosphatase were also identified. In conclusion, the FIM method is valid for the efficient purification of protein complexes that separate into the insoluble chromatin pellet fraction during centrifugation. (C) 2014 Elsevier Inc. All rights reserved.
  • Yota Murakami
    EMBO JOURNAL 32 (17) 2301 - 2303 0261-4189 2013/08 [Refereed][Not invited]
  • Eriko Oya, Hiroaki Kato, Yuji Chikashige, Chihiro Tsutsumi, Yasushi Hiraoka, Yota Murakami
    PLoS Genetics 9 (8) e1003677  1553-7390 2013/08 [Refereed][Not invited]
    Heterochromatin at the pericentromeric repeats in fission yeast is assembled and spread by an RNAi-dependent mechanism, which is coupled with the transcription of non-coding RNA from the repeats by RNA polymerase II. In addition, Rrp6, a component of the nuclear exosome, also contributes to heterochromatin assembly and is coupled with non-coding RNA transcription. The multi-subunit complex Mediator, which directs initiation of RNA polymerase II-dependent transcription, has recently been suggested to function after initiation in processes such as elongation of transcription and splicing. However, the role of Mediator in the regulation of chromatin structure is not well understood. We investigated the role of Mediator in pericentromeric heterochromatin formation and found that deletion of specific subunits of the head domain of Mediator compromised heterochromatin structure. The Mediator head domain was required for Rrp6-dependent heterochromatin nucleation at the pericentromere and for RNAi-dependent spreading of heterochromatin into the neighboring region. In the latter process, Mediator appeared to contribute to efficient processing of siRNA from transcribed non-coding RNA, which was required for efficient spreading of heterochromatin. Furthermore, the head domain directed efficient transcription in heterochromatin. These results reveal a pivotal role for Mediator in multiple steps of transcription-coupled formation of pericentromeric heterochromatin. This observation further extends the role of Mediator to co-transcriptional chromatin regulation. © 2013 Oya et al.
  • Takayuki Kiboku, Tsuyoshi Katoh, Akio Nakamura, Akira Kitamura, Masataka Kinjo, Yota Murakami, Masayuki Takahashi
    GENES TO CELLS 18 (2) 90 - 109 1356-9597 2013/02 [Refereed][Not invited]
    Nonmuscle myosin II forms a folded conformation (10S form) in the inactivated state; however, the physiological importance of the 10S form is still unclear. To investigate the role of 10S form, we generated a chimeric mutant of nonmuscle myosin IIB (IIB-SK1 center dot 2), in which S1462-R1490 and L1551-E1577 were replaced with the corresponding portions of skeletal muscle myosin heavy chain. The IIB-SK1 center dot 2 mutant did not fold into a 10S form under physiological condition in vitro. IIB-SK1 center dot 2 was less dynamic by stabilizing the filamentous form and accumulated in the posterior region of migrating cells. IIB-SK1 center dot 2 functioned properly in cytokinesis but altered migratory properties; the rate and directional persistence were increased by IIB-SK1 center dot 2 expression. Surprisingly, endogenous nonmuscle myosin IIA was excluded from the posterior region of migrating cells expressing IIB-SK1 center dot 2, which may underlie the change of the cellular migratory properties. These results suggest that the 10S form is necessary for maintaining nonmuscle myosin II in an unassembled state and for recruitment of nonmuscle myosin II to a specific region of the cell.
  • Hiroaki Kato, Kosuke Okazaki, Tetsushi Iida, Jun-Ichi Nakayama, Yota Murakami, Takeshi Urano
    Scientific Reports 3 2186  2045-2322 2013 [Refereed][Not invited]
    The tail of histone H3 is an ideal medium for storing epigenetic information because displacement of histone H3 is heavily restricted during transcription. To maintain the locus-specific modifications of histone H3, histone molecules should be retained locally at the original position through multiple rounds of transcription. Here, we found that fission yeast Spt6, a highly conserved RNA polymerase II-interacting histone H3-H4 chaperone, is essential for the maintenance of Lys-4 and Lys-9 methylation of histone H3 in euchromatin and heterochromatin, respectively. In euchromatin, loss of Lys-4 methylated histone H3 and deposition of newly synthesized Lys-56 acetylated histone H3 induced by Spt6 inactivation were coupled with transcription. While in heterochromatin, Spt6 prevents histone turnover and cryptic transcription in parallel with Clr3 histone deacetylase. We propose that Spt6 retains posttranslationally modified histone H3 during transcription to maintain epigenome integrity.
  • Hirotsugu Hino, Kana Arimoto, Michio Yazawa, Yota Murakami, Akiko Nakatomi
    MARINE BIOTECHNOLOGY 14 (4) 479 - 490 1436-2228 2012/08 [Refereed][Not invited]
    Calcineurin is a calcium/calmodulin-dependent protein phosphatase that plays important roles in the transduction of calcium signals in a variety of tissues. In addition, calcineurin has been implicated in the process of spermatogenesis. A novel calcineurin-binding protein, CaNBP75, has been identified in scallop testis. The C-terminal region of CaNBP75 is homologous to the C-terminal region of RanBP3, a Ran-binding domain-containing protein. A small G protein Ran has been involved in spermiogenesis by virtue of the fact that its localization in spermatids changes during spermiogenesis. The current study was performed to investigate the functions of Ran and CaNBP75 in the regulation of calcineurin in testis to further understand the basic functions of calcineurin during spermatogenesis. First, cloning and sequencing of a scallop Ran cDNA isolated from testis revealed that scallop Ran is well-conserved at the amino acid level. Secondly, direct binding of Ran to CaNBP75 was demonstrated in an in vitro pull-down assay. Thirdly, analysis of the tissue distribution of Ran, CaNBP75, and calcineurin showed that these proteins are abundantly expressed in testis. Fourthly, comparison of the expression profiles of Ran and CaNBP75 with that of calcineurin in scallop testis during the maturation cycle revealed that Ran and CaNBP75 mRNA levels increase during meiosis and spermiogenesis, similar to calcineurin. Finally, co-immunoprecipitation analysis suggests that Ran, CaNBP75, and calcineurin interact in scallop testis during maturation. These results suggest that Ran, CaNBP75, and calcineurin may act in a coordinated manner to regulate spermatogenesis.
  • Kei Kawakami, Aki Hayashi, Jun-ichi Nakayama, Yota Murakami
    GENES & DEVELOPMENT 26 (16) 1811 - 1824 0890-9369 2012/08 [Refereed][Not invited]
    In fission yeast, siRNA is generated from pericentromeric noncoding RNA by the RNAi machinery. siRNA synthesis and heterochromatin formation are interdependent, forming a self-reinforcing loop on chromatin. In this system, siRNA is amplified by the RNA-dependent RNA polymerase complex (RDRC) and the endoribonuclease Dcr1, which synthesizes dsRNA and processes the dsRNA, respectively. The amplification is essential for stable heterochromatin formation. Here, a novel gene, dsh1(+) (defect of the gene silencing at centromeric heterochromatin), is identified as an essential component of RNAi-directed heterochromatin assembly. Loss of dsh1(+) abolishes normal RNAi function and heterochromatic gene silencing at pericentromeres. Dsh1 interacts with Dcr1 and RDRC and couples the reactions of both proteins to the effective production of siRNA in vivo. Dsh1 binds to heterochromatin in the absence of RDRC, while RDRC requires Dsh1 for its chromatin-binding activity, suggesting that Dsh1 recruits RDRC to chromatin. Immunofluorescence analysis shows that Dsh1 forms foci at the nuclear periphery, and some Dsh1 foci colocalize with Dcr1 and RDRC. Dsh1 is required for the colocalization of Dcr1 and RDRC. Moreover, loss of the nuclear periphery localization of Dsh1 abolishes Dsh1 function. Taken together, these results suggest that Dsh1 assembles the RNAi machinery on heterochromatin and forms a perinuclear compartment for amplification of heterochromatic siRNA.
  • Aki Hayashi, Mayumi Ishida, Rika Kawaguchi, Takeshi Urano, Yota Murakami, Jun-ichi Nakayama
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 109 (16) 6159 - 6164 0027-8424 2012/04 [Refereed][Not invited]
    In fission yeast, the RNAi pathway is required for centromeric heterochromatin assembly. siRNAs derived from centromeric transcripts are incorporated into the RNA-induced transcriptional silencing (RITS) complex and direct it to nascent homologous transcripts. The RNA-induced transcriptional silencing-bound nascent transcripts further recruit the RNA-directed RNA polymerase complex (RDRC) to promote dsRNA synthesis and siRNA production. Heterochromatin coated with Swi6/Heterochromain Protein 1 is then formed following recruitment of chromatin modification machinery. Swi6 is also required for the upstream production of siRNA, although the mechanism for this has remained obscure. Here, we demonstrate that Swi6 recruits RDRC to heterochromatin through Ers1, an RNAi factor intermediate. An ers1(+) mutant allele (ers1-C62) was identified in a genetic screen for mutants that alleviate centromeric silencing, and this phenotype was suppressed by overexpression of either the Hrr1 RDRC subunit or Clr4 histone H3-K9 methyltransferase. Ers1 physically interacts with Hrr1, and loss of Ers1 impairs RDRC centromeric localization. Although Ers1 failed to bind Clr4, a direct interaction with Swi6 was detected, and centromeric localization of Swi6 was enhanced by Clr4 overexpression in ers1-C62 cells. Consistent with this, deletion of swi6(+) reduced centromeric localization of Ers1 and RDRC. Moreover, tethering of Ers1 or Hrr1 to centromeric heterochromatin partially bypassed Swi6 function. These findings demonstrate an alternative mechanism for RDRC recruitment and explain the essential role of Swi6/Heterochromain Protein 1 in RNAi-directed heterochromatin assembly.
  • Mina Nakama, Kei Kawakami, Takuya Kajitani, Takeshi Urano, Yota Murakami
    GENES TO CELLS 17 (3) 218 - 233 1356-9597 2012/03 [Refereed][Not invited]
    Certain noncoding RNAs (ncRNAs) implicated in the regulation of chromatin structure associate with chromatin. During the formation of RNAi-directed heterochromatin in fission yeast, ncRNAs transcribed from heterochromatin are thought to recruit the RNAi machinery to chromatin for the formation of heterochromatin; however, the molecular details of this association are not clear. Here, using RNA immunoprecipitation assay, we showed that the heterochromatic ncRNA was associated with chromatin via the formation of a DNARNA hybrid and bound to the RNA-induced transcriptional silencing (RITS) complex. The presence of DNARNA hybrid in the cell was also confirmed by immunofluorescence analysis using anti-DNARNA hybrid antibody. Over-expression and depletion of RNase H in vivo decreased and increased the amount of DNARNA hybrid formed, respectively, and both disturbed heterochromatin. Moreover, DNARNA hybrid was formed on, and over-expression of RNase H inhibited the formation of, artificial heterochromatin induced by tethering of RITS to mRNA. These results indicate that heterochromatic ncRNAs are retained on chromatin via the formation of DNARNA hybrids and provide a platform for the RNAi-directed heterochromatin assembly and suggest that DNARNA hybrid formation plays a role in chromatic ncRNA function.
  • Chihiro Kitagawa, Akiko Nakatomi, Dasol Hwang, Issey Osaka, Hiroki Fujimori, Hideya Kawasaki, Ryuichi Arakawa, Yota Murakami, Shinya Ohki
    Biophysics 7 35 - 49 1349-2942 2011 [Refereed][Not invited]
    Electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy, flow dialysis, and bioactivity measurements were employed to investigate the roles of the C-terminal residues of calmodulin (CaM). In the present study, we prepared a series of truncated mutants of chicken CaM that lack four (CCMΔ4) to eight (CCMΔ8) residues at the C-terminal end. It was found that CCMΔ4, lacking the last four residues (M145 to K148), binds four Ca2+ ions. Further deletion gradually decreased the ability to bind the fourth Ca2+ ion, and CCMΔ8 completely lost the ability. Interestingly, both lobes of Ca2+-sturated CCMΔ5 showed instability in the conformation, although limited part in the C-lobe of Ca2+-saturated CCMΔ4 was instable. Moreover, unlike CCMΔ4, structure of the C-lobe in CCMΔ5 bound to the target displayed dissimilarity to that of CaM, suggesting that deletion of M144 changes the binding manner. Deletion of the last five residues (M144 to K148) and further truncation of the C-terminal region decreased apparent capacity for target activation. Little contribution of the last four residues including M145 was observed for structural stability, Ca2+-binding, and target activation. Although both M144 and M145 have been recognized as key residues for the function, the present data suggest that M144 is a more important residue to attain Ca2+ induced conformational change and to form a proper Ca2+-saturated conformation. © THE BIOPHYSICAL SOCIETY OF JAPAN.
  • Atsushi Shimada, Yota Murakami
    EPIGENETICS 5 (1) 30 - 33 1559-2294 2010/01 [Refereed][Not invited]
    Heterochromatin is characterized by methylation of histone H3 at lysine 9, which is recognized by well-conserved HP1-family proteins. Heterochromatin participates in various chromosome functions, which include transcriptional gene silencing and sister-chromatid cohesion. These heterochromatic functions are carried out by various effector proteins that associate with HP1-family proteins; however, the regulation of this association with the effectors is not well understood. Recently, we showed that phosphorylation of the fission-yeast HP1 homolog Swi6 regulates the association of the transcriptional regulators differentially and changes the transcriptional activity of heterochromatin, without affecting sister-chromatid cohesion. This study, together with another study performed using other systems, indicates that phosphorylation of HP1/Swi6 provides a dynamic pathway for the differential regulation of heterochromatin in response to inter-and intracellular signals.
  • Murakami Y
    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 54 (4 Suppl) 488 - 495 0039-9450 2009/03 [Refereed][Not invited]
  • Atsushi Shimada, Kohei Dohke, Mahito Sadaie, Kaori Shinmyozu, Jun-Ichi Nakayama, Takeshi Urano, Yota Murakami
    GENES & DEVELOPMENT 23 (1) 18 - 23 0890-9369 2009/01 [Refereed][Not invited]
    Heterochromatin protein 1 (HP1) recruits various effectors to heterochromatin for multiple functions, but its regulation is unclear. In fission yeast, a HP1 homolog Swi6 recruits SHREC, Epe1, and cohesin, which are involved in transcriptional gene silencing (TGS), transcriptional activation, and sister chromatid cohesion, respectively. We found that casein kinase II (CK2) phosphorylated Swi6. Loss of CK2-dependent Swi6 phosphorylation alleviated heterochromatic TGS without affecting heterochromatin structure. This was due to the inhibited recruitment of SHREC to heterochromatin, accompanied by an increase in Epe1. Interestingly, loss of phosphorylation did not affect cohesion. These results indicate that CK2-dependent Swi6 phosphorylation specifically controls TGS in heterochromatin.
  • Kohei Dohke, Shota Miyazaki, Katsunori Tanaka, Takeshi Urano, Shiv I. S. Grewal, Yota Murakami
    GENES TO CELLS 13 (10) 1027 - 1043 1356-9597 2008/10 [Refereed][Not invited]
    Chromatin assembly factor-1 (CAF1) is a well-conserved histone chaperone that loads the histone H3-H4 complex onto newly synthesized DNA in vitro through interaction with the replication factor PCNA. CAF1 is considered to be involved in heterochromatin maintenance in several organisms, but the evidence is circumstantial and functional details have not been established. We identified fission yeast CAF-1 (spCAF1), which interacts with PCNA in S phase. Depletion of spCAF1 caused defects in silencing at centromeric and mating locus heterochromatin, accompanied with a decrease in Swi6, the fission yeast HP1 homologue. Loss of spCAF1 destabilized both the silent and active states of chromatin at the meta-stable heterochromatic region, with a more pronounced effect on the silent state, indicating that spCAF1 is involved in the maintenance of heterochromatin. Swi6 dissociated from heterochromatin during G1/S phase appears to associate with spCAF1. In early S phase, spCAF1 localized to replicating heterochromatin as well as euchromatin and remained associated with Swi6, and Swi6 then bound to heterochromatin. Taken together, we propose that spCAF1 functions in heterochromatin maintenance by recruiting dislocated Swi6 during replication to replicated heterochromatin at the replication fork.
  • Kato H, Matsunaga F, Miyazaki S, Yin L, D'Urso G, Tanaka K, Murakami Y
    Cell cycle (Georgetown, Tex.) 7 (8) 1085 - 1096 1538-4101 2008/04 [Refereed][Not invited]
  • Mika Yokoyama, Hirokazu Inoue, Chizu Ishii, Yota Murakami
    DNA REPAIR 6 (6) 770 - 780 1568-7864 2007/06 [Refereed][Not invited]
    The progression of replication forks is often impeded by obstacles that cause them to stall or collapse, and appropriate responses to replication- associated DNA damage are important for genome integrity. Here we identified a new gene, mus7(+), that is involved in the repair of replication- associated DNA damage in the fission yeast Schizosaccharomyces pombe. The Delta mus7 mutant shows enhanced sensitivity to methyl methanesulfonate (MMS), camptothecin, and hydroxyurea, agents that cause replication fork stalling or collapse, but not to ultraviolet light or X-rays. Epistasis analysis of MMS sensitivity indicates that Mus7 functions in the same pathway as Mus81, a subunit of the Mus81-Eme1 structure -specific endonuclease, which has been implicated in the repair of the replication-associated DNA damage. In Delta mus7 and Delta mus81 cells, the repair of MMS-induced DNA double-strand breaks (DSBs) is severely impaired. Moreover, some cells with either mutation are hyper-elongated or enlarged, and most of these cells accumulate in late G2 phase. Spontaneous Rad22 (recombination mediator protein RAD52 homolog) foci increase in S phase to late G2 phase in Delta mus7 and Delta mus81 cells. These results suggest that replication-associated DSBs accumulate in these cells and that Rad22 foci form in the absence of Mus7 or Mus81. We also found that the rate of spontaneous conversion-type recombination is reduced in mitotic Delta mus7 cells, suggesting that Rhp51- (RAD51 homolog) dependent homologous recombination is disturbed in this mutant. From these data, we propose that Mus7 functions in the repair of replication- associated DSBs by promoting RAD51-dependent conversion-type recombination downstream of Rad22 and Mus81. (c) 2007 Elsevier B.V All rights reserved.
  • Kohzaki H, Murakami Y
    Seikagaku. The Journal of Japanese Biochemical Society 79 (5) 458 - 462 0037-1017 2007/05 [Refereed][Not invited]
  • Yota Murakami, Ling-Feng Chen, Noriyuki Sanechika, Hidetsugu Kohzaki, Yoshiaki Ito
    JOURNAL OF CELLULAR BIOCHEMISTRY 100 (5) 1313 - 1323 0730-2312 2007/04 [Refereed][Not invited]
    Eukaryotic DNA replication takes place in the replication factories, where replication proteins are properly assembled to form replication forks. Thus, recruitment of DNA replication origins to the replication factories must be the key step for the regulation of DNA replication. The transcription factor Runx1 associates with the nuclear matrix, the putative substructure of DNA replication factories. An earlier report from our laboratory showed that Runx1 activates polyomavirus DNA replication, and that this requires its nuclear matrix-binding activity. Here, we show that Runx1 activates polyomavirus DNA replication by stimulating the binding of the viral-encoded replication initiator/helicase, large T antigen, to its replication origin. We found that newly replicated polyomavirus DNA is associated with the nuclear matrix and that large T antigen is targeted to replication factories, suggesting that polyomavirus is replicated in replication factories on the nuclear matrix. Although Runx1 did not co-localize with large T antigen-containing foci by itself, it co-localized with large T antigen-containing replication factories during Runx1-dependent polyomavirus DNA replication. These observations together suggest that Runx1 recruits the polyomavirus replication origin to the replication factory on the nuclear matrix, and that this requires the nuclear matrix-binding activity of Runx1.
  • Hidetsugu Kohzaki, Yota Murakami
    PROTEOMICS 7 (1) 10 - 14 1615-9853 2007/01 [Refereed][Not invited]
    Chromatin immunoprecipitation (ChIP) assays are widely used to investigate where chromatin-binding proteins bind to the genome. The standard assay is very time consuming. We have developed a rapid ChIP assay in which the immunoprecipitates serve directly as PCR templates. This assay eliminates the step to reverse the crosslinking, shortening the assay by 1 day. It also requires a less immunoprecipitating antibody, permits many samples to be tested simultaneously, and is more sensitive than the standard ChIP assay.
  • Murakami Y
    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 51 (16 Suppl) 2456 - 2462 0039-9450 2006/12 [Refereed][Not invited]
  • Hiromitsu Yamamoto, Kosei Ito, Mariko Kawai, Yota Murakami, Kazuhisa Bessho, Yoshiaki Ito
    Anatomical Record - Part A Discoveries in Molecular, Cellular, and Evolutionary Biology 288 (7) 695 - 699 0003-276X 2006/07 [Refereed][Not invited]
    Studies of molecular mechanisms underlying the development of the mammalian oral mucosa have revealed a major involvement of transforming growth factor β (TGF-β) and bone morphologic protein (BMP) signaling pathways. Here, we examined the expression of a downstream target of TGF-β and BMPs, Runx3, in oral mucosa. Runx3 is a runt-related transcription factor that acts as a gastric tumor suppressor and regulator of growth and differentiation in mammalian gastric epithelial cells. Another member of the Runx family in C. elegans, run, is involved in the development of a functional hypodermis and gut. In this report, we examined Runx3 expression using reverse transcription- polymerase chain reaction, immnunohistochemistry, and in situ hybridization and found that Runx3 is expressed in the tongue and palate epithelium of mouse embryos from embryonic day 12.5 to 16.5. The functional relationship between Runx3 and TGF-β/BMPs signaling in tongue and palate development is discussed. © 2006 Wiley-Liss, Inc.
  • Hiromitsu Yamamoto, Kosei Ito, Mariko Kawai, Yota Murakami, Kazuhisa Bessho, Yoshiaki Ito
    Studies of molecular mechanisms underlying the development of the mammalian oral mucosa have revealed a major involvement of transforming growth factor beta (TGF-beta) and bone morphologic protein (BMP) signaling pathways. Here, we examined the expression of a downstream target of TGF-beta and BMPs, Runx3, in oral mucosa. Runx3 is a runt-related transcription factor that acts as a gastric tumor suppressor and regulator of growth and differentiation in mammalian gastric epithelial cells. Another member of the Runx family in C. elegans, run, is invoflved in the development of a functional hypodermis and gut. In this report, we examined Runx3 expression using reverse transcription-polymerase chain reaction, immnunohistochemistry, and in situ hybridization and found that Runx3 is expressed in the tongue and palate epithelium of mouse embryos from embryonic day 12.5 to 16.5. The functional relationship between Runx3 and TGF-beta/BMPs signaling in tongue and palate development is discussed.
  • MA Marchetti, M Weinberger, Y Murakami, WC Burhans, JA Huberman
    JOURNAL OF CELL SCIENCE 119 (1) 124 - 131 0021-9533 2006/01 [Refereed][Not invited]
    Previous studies have indicated that replication stress can trigger apoptosis-like cell death, accompanied (where tested) by production of reactive oxygen species (ROS), in mammalian cells and budding yeast (Saccharomyces cerevisiae). In mammalian cells, inappropriate entry into mitosis also leads to cell death. Here, we report similar responses in fission yeast (Schizosaccharomyces pombe). We used ROS- and death-specific fluorescent stains to measure the effects of mutations in replication initiation and checkpoint genes in fission yeast on the frequencies of ROS production and cell death. We found that certain mutant alleles of each of the four tested replication initiation genes caused elevated ROS and cell death. Where tested, these effects were not enhanced by checkpoint-gene mutations. Instead, when cells competent for replication but defective in both the replication and damage checkpoints were treated with hydroxyurea, which slows replication fork movement, the frequencies of ROS production and cell death were greatly increased. This was a consequence of elevated CDK activity, which permitted inappropriate entry into mitosis. Thus, studies in fission yeast are likely to prove helpful in understanding the pathways that lead from replication stress and inappropriate mitosis to cell death in mammalian cells.
  • Murakami Y
    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 51 (1) 54 - 60 0039-9450 2006/01 [Refereed][Not invited]
  • Alexandra M. Locovei, Maria-Grazia Spiga, Katsunori Tanaka, Yota Murakami, Gennaro D'Urso
    CELL DIVISION 1 27  1747-1028 2006 [Refereed][Not invited]
    Abp1, and the closely related Cbh1 and Cbh2 are homologous to the human centromere-binding protein CENP-B that has been implicated in the assembly of centromeric heterochromatin. Fission yeast cells lacking Abp1 show an increase in mini-chromosome instability suggesting that Abp1 is important for chromosome segregation and/or DNA synthesis. Here we show that Abp1 interacts with the DNA replication protein Cdc23 (MCM10) in a two-hybrid assay, and that the Delta abp1 mutant displays a synthetic phenotype with a cdc23 temperature-sensitive mutant. Moreover, genetic interactions were also observed between abp1(+) and four additional DNA replication initiation genes cdc18(+), cdc21(+), orc1(+), and orc2(+). Interestingly, we find that S phase is delayed in cells deleted for abp1(+) when released from a G1 block. However, no delay is observed when cells are released from an early S phase arrest induced by hydroxyurea suggesting that Abp1 functions prior to, or coincident with, the initiation of DNA replication.
  • H Kohzaki, Y Murakami
    BIOESSAYS 27 (11) 1107 - 1116 0265-9247 2005/11 [Refereed][Not invited]
    tThe chromosomes of eukaryotic cells possess many potential DNA replication origins, of which a subset is selected in response to the cellular environment, such as the developmental stage, to act as active replication start sites. The mechanism of origin selection is not yet fully understood. In this review, we summarize recent observations regarding replication origins and initiator proteins in various organisms. These studies suggest that the DNA-binding specificities of the initiator proteins that bind to the replication origins and promote DNA replication are primarily responsible for origin selection. We particularly focus on the importance of transcription factors in the origin selection process. We propose that transcription factors are general regulators of the formation of functional complexes on the chromosome, including the replication initiation complex. We discuss the possible mechanisms by which transcription factors influence the selection of particular origins. (c) 2005 Wiley Periodicals, Inc.
  • H Kato, DB Goto, RA Martienssen, T Urano, K Furukawa, Y Murakami
    SCIENCE 309 (5733) 467 - 469 0036-8075 2005/07 [Refereed][Not invited]
    In Schizosaccharomyces pombe, the RNA interference (RNAi) machinery con. verts pericentromeric transcripts into small interfering RNAs (siRNAs) and is, required for the assembly of pericentromeric heterochromatin. Here we describe a. mutation in the second largest subunit of RNA polymerase II (RNAPII). Both wild-type and mutant RNAPII localized to the pericentromere. However, the mutation resulted in the loss of heterochromatic histone modifications and in the accumulation of pericentromeric transcripts, accompanied by the loss of siRNAs. This phenotype resembles mutants in RNAi and suggests that RNAPII couples pericentromeric transcription with siRNA processing and heterochromatin assembly.
  • Kato H, Murakami Y
    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 49 (12) 1990 - 1997 0039-9450 2004/09 [Refereed][Not invited]
  • M Ueno, T Murase, T Kibe, N Ohashi, K Tomita, Y Murakami, M Uritani, T Ushimaru, M Harata
    NUCLEIC ACIDS RESEARCH 32 (2) 736 - 741 0305-1048 2004/01 [Refereed][Not invited]
    The actin-related proteins (Arps), which are subdivided into at least eight subfamilies, are conserved from yeast to humans. A member of the Arp6 subfamily in Drosophila, Arp4/Arp6, co-localizes with heterochromatin protein 1 (HP1) in pericentric heterochromatin. Fission yeast Schizosaccharomyces pombe possesses both an HP1 homolog and an Arp6 homolog. However, the function of S.pombe Arp6 has not been characterized yet. We found that deletion of arp6(+) impaired telomere silencing, but did not affect centromere silencing. Chromatin immunoprecipitation assays revealed that Arp6 bound to the telomere region. However, unlike Drosophila Arp4/Arp6, S.pombe Arp6 was distributed throughout nuclei. The binding of Arp6 to telomere DNA was not affected by deletion of swi6(+). Moreover, the binding of Swi6 to telomere ends was not affected by deletion of arp6(+). These results suggest that Arp6 and Swi6 function independently at telomere ends. We propose that the Arp6-mediated repression mechanism works side by side with Swi6-based telomere silencing in S.pombe.
  • J Kikuchi, J Iwahara, T Kigawa, Y Murakami, T Okazaki, S Yokoyama
    JOURNAL OF BIOMOLECULAR NMR 22 (4) 333 - 347 0925-2738 2002/04 [Refereed][Not invited]
    We have solved the solution structure of the N-terminal region of the fission yeast centromere protein, Abp1, bound to a 21-base pair DNA fragment bearing its recognition site (Mw = 30 kDa). Although the two DNA-binding domains in the Abp1 protein were defined well by a conventional NOE-based NMR methodology, the overall structure of the Abp1 protein was poorly defined, due to the lack of interdomain distance restraints. Therefore, we additionally used residual dipolar couplings measured in a weakly aligned state, and rotational diffusion anisotropies. Neither the NH residual dipolar couplings nor the backbone (1)5N T-1/T-2 data were sufficient to determine the overall structure of the Abp1 protein, due to spectral overlap. We used a combination of these two orientational restraints (residual dipolar coupling and rotational diffusion anisotropy), which significantly improved the convergence of the overall structures. The range of the observed T-1/T-2 ratios was wider (20-50 for the secondary structure regions of Abp1) than the previously reported data for several globular proteins, indicating that the overall shape of the Abp1.DNA complex is ellipsoid. This extended form would facilitate the recognition of the two separate sites in the relatively long DNA sequence by the DNA-binding domains of Apb1.
  • Chen LF, Ito K, Murakami Y, Ito Y
    Molecular and cellular biology 18 (7) 4165 - 4176 0270-7306 1998/07 [Refereed][Not invited]
  • Y Murakami, JA Huberman, J Hurwitz
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 93 (1) 502 - 507 0027-8424 1996/01 [Refereed][Not invited]
    Autonomously replicating sequence (ARS) elements of the fission yeast Schizosaccharomyces pombe contain multiple imperfect copies of the consensus sequence reported by Maundrell et al. [Maundrell K,, Hutchison, A, & Shall, S, (1988) EMBO J. 7, 2203-2209]. When cell free extracts of S, pombe were incubated with a dimer or tetramer of an oligonucleotide containing the ARS consensus sequence, several complexes were detected using a gel mobility-shift assay. The proteins forming these complexes also bind ars3002, which is the most active origin in the ura4 region of chromosome III of S, pombe. One protein, partly responsible for the binding activity observed with crude extracts, was purified to near homogeneity, It is a 60-kDa protein and was named ARS-binding protein 1 (Abp1). Abp1 preferentially binds to multiple sites in ARS 3002 and to the DNA polymer poly[d(A . T)]. The cloning and sequence of the gene coding for Abp1 revealed that it encodes a protein of 59.8 kDa (522 amino acids), Abp1 has significant homology (25% identity, 50% similarity) to the N-terminal region (approximate to 300 amino acids) of the human and mouse centromere DNA-binding protein CENP-B. Because centromeres of S. pombe contain a high density of ARS elements, Abp1 may play a role connecting DNA replication and chromosome segregation.


Research Grants & Projects

  • 真核細胞の染色体複製制御機構の解析
    Date (from‐to) : 1996 -2006
  • 真核細胞の染色体機能におけるクロマチン・核の高次構造の役割の解明
    Date (from‐to) : 2000
  • Structure and Funtion of higher order chromatin structure in the nuclei
  • Regulation of eukariotic chromosome replication

Educational Activities

Teaching Experience

  • 総合化学特別研究第二
    開講年度 : 2019
    課程区分 : 博士後期課程
    開講学部 : 総合化学院
  • 化学研究先端講義
    開講年度 : 2019
    課程区分 : 修士課程
    開講学部 : 総合化学院

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