Concerted regulation of DNA replication, transcription, and repair by the conserved nuclear factor Rif1.

• Project/Area Number: 26251004
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Molecular biology
• Research Institution: Tokyo Metropolitan Institute of Medical Science
• Principal Investigator: MASAI Hisao 公益財団法人東京都医学総合研究所, ゲノム医科学研究分野, 副所長 (40229349)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥40,430,000 (Direct Cost: ¥31,100,000、Indirect Cost: ¥9,330,000); Fiscal Year 2016: ¥13,650,000 (Direct Cost: ¥10,500,000、Indirect Cost: ¥3,150,000); Fiscal Year 2015: ¥14,040,000 (Direct Cost: ¥10,800,000、Indirect Cost: ¥3,240,000); Fiscal Year 2014: ¥12,740,000 (Direct Cost: ¥9,800,000、Indirect Cost: ¥2,940,000)
• Keywords: 複製タイミング / グアニン４重鎖 / クロマチンループ / 染色体高次構造 / 非相同末端結合 / Rif1タンパク質 / ES細胞 / 転写 / 組換え修復 / グアニン４重鎖DNA / G4 DNA / 染色体 / 核 / DNA複製 / 組換え / 修復 / DNA結合

Outline of Final Research Achievements

Rif1 is a conserved chromatin factor that regulates DNA replication, DNA repair and transcription. It may be involved in chromatin loop formation at nuclear periphery. We have determined genome-wide Rif1 bindings sites (Rif1BS) in fission yeast and identified a G-rich consensus sequence (Rif1CS). We then demonstrated the essential role of Rif1CS in chromatin binding of Rif1 and subsequent repression of DNA replication over a 100kb segment. Footprinting with DMS or various nucleases, polymerase stop assays as well as the effect of 7-deaza dGTP demonstrated that Rif1BS adopts G-quadruplex like structures. Purified fission yeast and mammalian Rif1 proteins specifically bind to this structure. Rif1 can simultaneously bind to multiple molecules of G4 through oligomerization, providing potential basis for its ability to tether multiple chromatin fibers to generate chromatin compartment that may coordinately regulate replication, transcription or repair.

Research Products

• [Journal Article] Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex. (2016)
  • Author(s): You Z, Ode KL, Shindo M, Takisawa H, Masai H.
  • Journal Title: Cell Cycle. Volume: 15 Issue: 9 Pages: 1213-1226
  • DOI: 10.1080/15384101.2015.1106652
  • Peer Reviewed / Open Access
• [Journal Article] Fork restart protein, PriA, binds around oriC after depletion of nucleotide precursors: Replication fork arrest near the replication origin. (2016)
  • Author(s): Tanaka T, Nishito Y, *Masai H.
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 470 Issue: 3 Pages: 546-551
  • DOI: 10.1016/j.bbrc.2016.01.108
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Epigenetic Regulation of the Blimp-1 Gene (Prdm1) in B Cells Involves Bach2 and Histone Deacetylase 3* (2016)
  • Author(s): Tanaka H
  • Journal Title: JBC Volume: 291 Issue: 12 Pages: 6316-6330
  • DOI: 10.1074/jbc.m116.713842
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Phosphorylation of TAR DNA-binding Protein of 43 kDa (TDP-43) by Truncated Casein Kinase 1δ Triggers Mislocalization and Accumulation of TDP-43. (2016)
  • Author(s): Nonaka T, Suzuki G, Tanaka Y, Kametani F, Hirai S, Okado H, Miyashita T, Saitoe M, Akiyama H, Masai H, Hasegawa M.
  • Journal Title: The journal of Biological Chemistry Volume: 291 Issue: 11 Pages: 5473-83
  • DOI: 10.1074/jbc.m115.695379
  • Peer Reviewed / Open Access
• [Journal Article] Overexpression of eIF5 or its protein mimic 5MP perturbs eIF2 function and induces ATF4 translation through delayed re-initiation. (2016)
  • Author(s): Kozel C, Thompson B, Hustak S, Moore C, Nakashima A, Singh CR, Reid M, Cox C, Papadopoulos E, Luna RE, Anderson A, Tagami H, Hiraishi H, Slone EA, Yoshino KI, Asano M, Gillaspie S, Nietfeld J, Perchellet JP, Rothenburg S, Masai H, Wagner G, Beeser A, Kikkawa U, Fleming SD, Asano K.
  • Journal Title: Nucleic Acids Res. Volume: 44 Issue: 18 Pages: 8704-8713
  • DOI: 10.1093/nar/gkw559
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Claspin recruits Cdc7 kinase for initiation of DNA replication in human cells. (2016)
  • Author(s): Yang CC, Suzuki M, Yamakawa S, Uno S, Ishii A, Yamazaki S, Fukatsu R, Fujisawa R, Sakimura K, Tsurimoto T, Masai H.
  • Journal Title: Nat Commun. Volume: 7 Issue: 1 Pages: 12135-12135
  • DOI: 10.1038/ncomms12135
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex. (2016)
  • Author(s): Zhiying You, Koji L. Ode, Haruhiko Takisawa, and *Hisao Masai
  • Journal Title: Cell Cycle Volume: 3
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Claspin recruits Cdc7 kinase for initiation of DNA replication in human cells. (2016)
  • Author(s): Chi-Chun Yang, Masahiro Suzuki, Shiori Yamakawa, Syuzi Uno, Ai Ishii, Satoshi Yamazaki, Rino Fukatsu, Ryo Fujisawa, Kenji Sakimura3, Toshiki Tsurimoto, *Hisao Masai
  • Journal Title: Nature Communications Volume: TBA
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Rif1はグアニン４重鎖構造を介して染色体に結合し、広範囲に複製を抑制する (2016)
  • Author(s): 加納 豊、松本 清治、正井 久雄
  • Journal Title: 実験医学 Volume: 34-no.3 Pages: 458-461
• [Journal Article] CDC28 phosphorylates Cac1p and regulates the association of Chromatin Assembly Factor I with chromatin. (2015)
  • Author(s): Jeffery, D., Kakusho, N., You, Z., Gharib, M., Wyse, B., Drury, E., Weinreich, M., Thibault, P. Verreault, A., Masai, H. and *Yankulov, K.
  • Journal Title: Cell Cycle Volume: 14 Issue: 1 Pages: 74-85
  • DOI: 10.4161/15384101.2014.973745
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Definition of the transcription factor TdIF1 consensus binding sequence through genome-wide mapping of its binding sites. (2015)
  • Author(s): Kotaro Koiwai, Takashi Kubota, Nobuhisa Watanabe, Katsutoshi Hori, Osamu Koiwai and Hisao Masai
  • Journal Title: Genes to Cells Volume: 20 Issue: 3 Pages: 242-254
  • DOI: 10.1111/gtc.12216
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The DNA-Binding Domain of S. pombe Mrc1 (Claspin) Acts to Enhance Stalling at Replication Barriers. (2015)
  • Author(s): Zech, J., Godfrey, E.L., Masai, H., Hartsuiker, E. and *Dalgaard, J.Z.
  • Journal Title: PLoS One Volume: 10 Issue: 7 Pages: e0132595-e0132595
  • DOI: 10.1371/journal.pone.0132595
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] BTB-ZF Protein Znf131 Regulates Cell Growth of Developing and Mature T Cells. (2015)
  • Author(s): Iguchi T, Aoki K, Ikawa T, Taoka M, Taya C, Yoshitani H, Toma-Hirano M, Koiwai O, Isobe T, Kawamoto H, Masai H, Miyatake S.
  • Journal Title: The Journal of Immunology Volume: 195 Issue: 3 Pages: 982-93
  • DOI: 10.4049/jimmunol.1500602
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Rif1 binds to G-quadruplexes and suppresses replication over long distances. (2015)
  • Author(s): Yutaka Kanoh, Seiji Matsumoto, Rino Fukatsu, Naoko Kakusho, Nobuaki Kono, Claire Renard-Guillet, Koji Masuda, Keisuke Iida, Kazuo Nagasawa, Katsuhiko Shirahige, and *Hisao Masai
  • Journal Title: Nature Struct. Mol. Biol. Volume: 22 Issue: 11 Pages: 889-897
  • DOI: 10.1038/nsmb.3102
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Building up the machinery for DNA replication. (2015)
  • Author(s): *Masai, H.
  • Journal Title: Cell Cycle Volume: 14 Issue: 19 Pages: 3011-3012
  • DOI: 10.1080/15384101.2015.1084195
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Rif1はグアニン4重鎖構造を形成するDNAを介して染色体へ結合し複製の開始を広範囲にわたり抑制する (2015)
  • Author(s): 加納 豊・松本清治・正井久雄
  • Journal Title: ライフサイエンス 新着論文レビュー Volume: -
  • Open Access
• [Journal Article] NCOA4 Transcriptional Coactivator Inhibits Activation of DNA Replication Origins. (2014)
  • Author(s): Bellelli, R., Castellone, M.D., Guida, T., Limongello, R., Dathan, N.A., Merolla, F., Cirafici, A.M., Affuso, A., Masai, H., Costanzo, V., Grieco, D., Fusco, A., Santoro, M., and Carlomagno, F.
  • Journal Title: Mol. Cell Volume: 55 Issue: 1 Pages: 123-137
  • DOI: 10.1016/j.molcel.2014.04.031
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Cell cycle synchronization and flow cytometry analysis of mammalian cell. (2014)
  • Author(s): Yoshizawa-Sugata, N. and Masai, H.
  • Journal Title: Methods in Molecular Biology Volume: 1170 Pages: 279-293
  • DOI: 10.1007/978-1-4939-0888-2_13
  • ISBN: 9781493908875, 9781493908882
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] ATM in prevention of genomic instability. (2014)
  • Author(s): Hisao Masai
  • Journal Title: Cell Cycle Volume: 13 Issue: 6 Pages: 882-883
  • DOI: 10.4161/cc.28216
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Temporal and spatial regulation of eukaryotic DNA replication: from regulated initiation to genome-scale timing program. (2014)
  • Author(s): Renard-Guillet, C., Kanoh, Y., Shirahige, K., and Masai, H.
  • Journal Title: Seminars in Cell & Developmental Biology, Volume: 30 Pages: 110-120
  • DOI: 10.1016/j.semcdb.2014.04.014
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Regulation and roles of Cdc7 kinase under replication stress. (2014)
  • Author(s): Yamada, M., Masai, H., and *Bartek, J.
  • Journal Title: Cell Cycle Volume: 13 Pages: 1859-1866
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Presentation] Interaction with G-quadruplex structures forms a basis for Rif1-mediated regulation of DNA replication, transcription and chromatin architecture (2016)
  • Author(s): Masai, H., (他8名)
  • Organizer: Cold Spring Harbor Asia conference on DNA Metabolism, Genomic Stability and Human Disease
  • Int'l Joint Research / Invited
• [Presentation] Biological roles of G-quadruplex structures (2016)
  • Author(s): Masai, H.
  • Organizer: 14th IGAKUKEN International Symposium IGAKUKEN Summit for Japan and Korea Science Leaders 2016
  • Int'l Joint Research
• [Presentation] グアニン４重鎖構造の生物学的意義Molecular basis of chromosome and genome instability in cancer (2016)
  • Author(s): Masai, H.
  • Organizer: HiHA 第 6 回 Workshop Hiroshima Research Center for Healthy Aging
  • Invited
• [Presentation] 大腸菌の第二の複製システムから考える複製システムの進化 (2016)
  • Author(s): 正井 久雄
  • Organizer: 日本進化学会 第18回東京大会、シンポジウム
  • Invited
• [Presentation] 大腸菌染色体の第二の複製システム (2016)
  • Author(s): 田中 卓、関 由美香、正井 久雄
  • Organizer: 第88回日本遺伝学会大会
  • Invited
• [Presentation] グアニン４重鎖の形成と、その認識タンパク質との相互作用 (2016)
  • Author(s): 正井 久雄, (他5名)
  • Organizer: 第89回 日本生化学会大会
• [Presentation] グアニン４重鎖構造の生物学的意義 Biological Roles of G-quadruplex (2016)
  • Author(s): 正井 久雄
  • Organizer: 第75回日本癌学会学術総会
  • Invited
• [Presentation] グアニン４重鎖構造の普遍的生物学的意義の解明に向けて (2016)
  • Author(s): 正井 久雄、(他14名)
  • Organizer: 第39回日本分子生物学会年会
  • Invited
• [Presentation] Interaction with G-quadruplex structures forms a basis for Rif1-mediated regulation of DNA replication, transcription and chromatin architecture (2015)
  • Author(s): 正井 久雄、加納 豊、松本 清治、覺正 直子、深津 理乃、森山 賢治、河野 暢明、飯田 啓介、長澤 和夫、増田 晃士、Claire Renard-Guillet、白髭 克彦、山崎 聡志、吉沢 直子
  • Organizer: BMB2015
  • Place of Presentation: 神戸国際会議場（兵庫県神戸市）
  • Year and Date: 2015-12-01
  • Int'l Joint Research / Invited
• [Presentation] Roles of G-quadruplex structures in regulation of DNA replication. (2015)
  • Author(s): Hisao Masai, Yutaka Kanoh, Taku Tanaka, Kenji Moriyama, Yumika Seki, Seiji Matsumoto, Rino Fukatsu, Naoko Kakusho, Satoshi Yamazaki, Yumeka Matsushima, Naoko Yoshizawa, Keisuke Iida, Kazuo Nagasawa
  • Organizer: Cold Spring Harbor Meeting EUKARYOTIC DNA REPLICATION & GENOME MAINTENANCE
  • Place of Presentation: Cold Spring Harbor, New York,USA
  • Year and Date: 2015-09-01
  • Int'l Joint Research / Invited
• [Presentation] Interaction of Rif1 and G-quadruplex forms a basis of Rif1-mediated chromatin regulation. (2015)
  • Author(s): Hisao Masai, Rino Fukatsu, Naoko Kakusho, Yutaka Kanoh, Kenji Moriyama
  • Organizer: The 8th international fission yeast meeting (Pombe2015)
  • Place of Presentation: 神戸国際会議場（兵庫県神戸市）
  • Year and Date: 2015-06-21
  • Int'l Joint Research / Invited
• [Presentation] ゲノムDNA複製制御のメカニズム：生物種を超えた統一像と多様性 (Conserved mechanisms and diversity of genome DNA replication: from bacteria to human) (2014)
  • Author(s): 正井 久雄
  • Organizer: 第37回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
  • Year and Date: 2014-11-25
  • Invited
• [Presentation] Regulation of mammalian Mcm helicase complexes (2014)
  • Author(s): Hisao Masai, You Zhiying, Koji L. Ode, Naoko Kakusho, Rino Fukatsu, and Haruhiko Takisawa
  • Organizer: 第87回日本生化学会大会 シンポジウム
  • Place of Presentation: 国立京都国際会館（京都府京都市）
  • Year and Date: 2014-10-15
  • Invited
• [Presentation] ゲノムを支えるDNAヘリカーゼの動態を探求する新たな研究展開 (2014)
  • Author(s): 正井 久雄
  • Organizer: 第87回日本生化学会大会シンポジウム
  • Place of Presentation: 国立京都国際会館（京都府京都市）
  • Year and Date: 2014-10-15
• [Presentation] 染色体DNA複製プログラムの制御機構 (2014)
  • Author(s): 正井 久雄
  • Organizer: 大阪大学蛋白質研究所セミナー「染色体伝承の分子背景：複製から染色体分離まで」
  • Place of Presentation: 大阪大学（大阪府豊中市）
  • Year and Date: 2014-09-25
  • Invited
• [Book] The Initiation of DNA Replication in Eukaryotes "Rif1, a conserved chromatin factor regulating DNA replication, DNA repair and transcription." (2015)
  • Author(s): Naoko Yoshizawa, Satoshi Yamazaki, and *Hisao Masai
  • Total Pages: 623
  • Publisher: Springer
• [Book] DNA Replication, Recombination, and Repair "DNA Replication Timing: Temporal and Spatial Regulation of Eukaryotic DNA Replication." (2015)
  • Author(s): Hayano, M., Matsumoto, S. and *Masai, H.
  • Total Pages: 555
  • Publisher: Springer
• [Remarks] 公益財団法人東京都医学総合研究所ゲノム動態プロジェクト
  • URL: http://www.igakuken.or.jp/genome/