Mechanism for repairing of double-strand breaks in heterochromatin

• Project/Area Number: 19H03156
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 43010:Molecular biology-related
• Research Institution: Osaka University
• Principal Investigator: Obuse Chikashi 大阪大学, 大学院理学研究科, 教授 (00273855)
• Project Period (FY): 2019-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000); Fiscal Year 2021: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000); Fiscal Year 2020: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000); Fiscal Year 2019: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
• Keywords: DNA損傷修復 / DNA二重鎖切断修復 / 相同組替え / 非相同末端結合 / ヘテロクロマチン / 二重鎖切断 / 相同組換え / 修復

Outline of Research at the Start

繰り返し配列上に形成されるヘテロクロマチンにおいてDNA二重鎖切断(DSB)が生じると、相同性のある繰り返し配列間で誤った結合や欠失が生じ、染色体異常が引き起こされる可能性があり、それを克服するためのメカニズムの存在が想像される。本課題では、私たちがこれまで見出したヘテロクロマチンタンパク質と修復因子との相互作用を基軸に、ヘテロクロマチンにおけるDSB修復反応の特殊性のメカニズムを明らかにする。

Outline of Final Research Achievements

Two pathways are known to repair double-strand breaks caused by radiation and other factors on heterochromatin: non-homologous end joining repair (NHEJ) and homologous recombination repair (HR). The choice between these is important from the perspective of preventing chromosome translocations and deletions when there are repeated sequences or similar base sequences where heterochromatin is formed. In this pathway selection, it is known that a protein called RIF1 inhibits the trimming of damage sites necessary for HR and promotes NHEJ. Through this project, we found that PP1 binds to RIF1, and the enzymatic activity that trims the damage sites is inhibited by the activity of this PP1, shedding light on part of the mechanism of DNA damage repair pathway selection.

Academic Significance and Societal Importance of the Research Achievements

DNA損傷修復に関わる遺伝子の変異はさまざまな疾患の原因となることが知られている。例えば、RIF1は、乳がん、卵巣がんの原因遺伝子であるBRCA1と深い関わりがある。RIF1の機能に問題があると、NHEJによる修復への誘導が起こらないため、BRCA1がない状態でも異常なHR経路が発動され、抗がん剤耐性細胞になることが実験的に証明されている。今回発見したRIF1と結合しているPP1の働きは、シールディンとともにRIF1のDNA損傷修復における機能そのものであるため、抗がん剤耐性細胞が出現する仕組みや、解決への糸口になると考えられる。

Research Products

• [Int'l Joint Research] University of Aberdeen(英国)
• [Int'l Joint Research] The Children's Hospital of Philadelphia(米国)
• [Int'l Joint Research] Institut Curie(フランス)
• [Int'l Joint Research] EMBL, Directors' research unit(ドイツ)
• [Int'l Joint Research] Leiden University Medical Center(オランダ)
• [Int'l Joint Research] University of Aberdeen(英国)
• [Int'l Joint Research] University of Aberdeen(英国)
• [Journal Article] Dominant-negative variants in CBX1 cause a neurodevelopmental disorder (2023)
  • Author(s): Kuroda, Y.、Nagao, K、Isobe, S-Y.、Nishibuchi, G.、Obuse, C.、Roscioli, T.、Izumi, K.他
  • Journal Title: Genetics in Medicine Volume: X Issue: 7 Pages: 100861-100861
  • DOI: 10.1016/j.gim.2023.100861
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Inner nuclear membrane proteins Lem2 and Bqt4 interact with different lipid synthesis enzymes in fission yeast (2023)
  • Author(s): Hirano Yasuhiro、Kinugasa Yasuha、Kubota Yoshino、Obuse Chikashi、Haraguchi Tokuko、Hiraoka Yasushi
  • Journal Title: The Journal of Biochemistry Volume: online Issue: 1 Pages: 33-46
  • DOI: 10.1093/jb/mvad017
  • Peer Reviewed / Open Access
• [Journal Article] Polycomb repressive complexes 1 and 2 are each essential for maintenance of X inactivation in extra-embryonic lineages (2023)
  • Author(s): Masui Osamu、Corbel Catherine、Nagao Koji、Endo Takaho A.、Kezuka Fuyuko、Diabangouaya Patricia、Nakayama Manabu、Kumon Mami、Koseki Yoko、Obuse Chikashi、Koseki Haruhiko、Heard Edith
  • Journal Title: Nature Cell Biology Volume: 25 Issue: 1 Pages: 134-144
  • DOI: 10.1038/s41556-022-01047-y
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] RNaseH2A downregulation drives inflammatory gene expression via genomic DNA fragmentation in senescent and cancer cells (2022)
  • Author(s): Sugawara S, Okada R, Loo TM, Tanaka H, Miyata K, Chiba M, Kawasaki H, Katoh K, Kaji S, Maezawa Y, Yokote K, Nakayama M, Oshima M, Nagao K, Obuse C, Nagayama S, Takubo K, Nakanishi A, Kanemaki MT, Hara E, Takahashi A.
  • Journal Title: Commun Biol Volume: 5 Issue: 1 Pages: 1420-1420
  • DOI: 10.1038/s42003-022-04369-7
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice (2022)
  • Author(s): Ichihara Saya、Nagao Koji、Sakaguchi Takehisa、Obuse Chikashi、Sado Takashi
  • Journal Title: Development Volume: 149 Issue: 15
  • DOI: 10.1242/dev.200864
  • Peer Reviewed / Open Access
• [Journal Article] Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry. (2021)
  • Author(s): Hayashi-Takanaka Y, Hayashi Y, Hirano Y, Miyawaki-Kuwakado A, Ohkawa Y, Obuse C, Kimura H, Haraguchi T, Hiraoka Y.
  • Journal Title: Nucleic Acids Res. Volume: 49 Issue: 21 Pages: 12152-12166
  • DOI: 10.1093/nar/gkab1068
  • Peer Reviewed / Open Access
• [Journal Article] Protein phosphatase 1 acts as a RIF1 effector to suppress DSB resection prior to Shieldin action (2021)
  • Author(s): Isobe Shin-Ya、Hiraga Shin-ichiro、Nagao Koji、Sasanuma Hiroyuki、Donaldson Anne D.、Obuse Chikashi
  • Journal Title: Cell Reports Volume: 36 Issue: 2 Pages: 109383-109383
  • DOI: 10.1016/j.celrep.2021.109383
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Homozygous nonsense variant in LRIF1 associated with facioscapulohumeral muscular dystrophy (2020)
  • Author(s): Hamanaka Kohei、Sikrova Darina、Mitsuhashi Satomi、Masuda Hiroki、Sekiguchi Yukari、Sugiyama Atsuhiko、Shibuya Kazumoto、Lemmers Richard J.L.F.、Goossens Remko、Ogawa Megumu、Nagao Koji、Obuse Chikashi、Noguchi Satoru、Hayashi Yukiko K.、Kuwabara Satoshi、Balog Judit、Nishino Ichizo、van der Maarel Silvere M.
  • Journal Title: Neurology Volume: 94 Issue: 23
  • DOI: 10.1212/wnl.0000000000009617
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Rare variant of the epigenetic regulator SMCHD1 in a patient with pituitary hormone deficiency. (2020)
  • Author(s): Kinjo K, Nagasaki K, Muroya K, Suzuki E, Ishiwata K, Nakabayashi K, Hattori A, Nagao K, Nozawa R-S, Obuse C, Miyado K, Ogata T, Fukami M and Miyado M.
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 10985-10985
  • DOI: 10.1038/s41598-020-67715-x
  • Peer Reviewed / Open Access
• [Journal Article] Regulation of an adaptor protein STING by Hsp90β to enhance innate immune responses against microbial infections (2020)
  • Author(s): Seiichi Sato, Kai Li, Nozomi Sakurai, Mei Hashizume, Sunanda Baidya, Hirotaka Nonaka, Koki Noguchi, Kozo Ishikawa, Chikashi Obuse, Akinori Takaoka
  • Journal Title: Cellular Immunology Volume: 356 Pages: 104188-104188
  • DOI: 10.1016/j.cellimm.2020.104188
  • Peer Reviewed / Open Access
• [Journal Article] Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing (2020)
  • Author(s): Miura Hisashi、Takahashi Saori、Shibata Takahiro、Nagao Koji、Obuse Chikashi、Okumura Katsuzumi、Ogata Masato、Hiratani Ichiro、Takebayashi Shin-ichiro
  • Journal Title: Nature Protocols Volume: 15 Issue: 12 Pages: 4058-4100
  • DOI: 10.1038/s41596-020-0378-5
  • Peer Reviewed / Open Access
• [Journal Article] Subacute cutaneous lupus erythematosus with melanocyte elimination induced by pembrolizumab. (2020)
  • Author(s): Ogawa-Momohara M, Muro Y, Goto K, Obuse C, Satoh M, Kono M, Akiyama M.
  • Journal Title: J. Dermatol. Volume: 47 Issue: 6
  • DOI: 10.1111/1346-8138.15316
  • NAID: 120006884960
  • Peer Reviewed
• [Journal Article] KDM2A-dependent reduction of rRNA transcription on glucose starvation requires HP1 in cells, including triple-negative breast cancer cells (2019)
  • Author(s): Okamoto Kengo、Tanaka Yuji、Ogasawara Sachiko、Obuse Chikashi、Nakayama Jun-ichi、Yano Hirohisa、Tsuneoka Makoto
  • Journal Title: Oncotarget Volume: 10 Issue: 46 Pages: 4743-4760
  • DOI: 10.18632/oncotarget.27092
  • Peer Reviewed / Open Access
• [Journal Article] Asymmetrical localization of Nup107-160 subcomplex components within the nuclear pore complex in fission yeast (2019)
  • Author(s): Asakawa Haruhiko、Kojidani Tomoko、Yang Hui-Ju、Ohtsuki Chizuru、Osakada Hiroko、Matsuda Atsushi、Iwamoto Masaaki、Chikashige Yuji、Nagao Koji、Obuse Chikashi、Hiraoka Yasushi、Haraguchi Tokuko
  • Journal Title: PLOS Genetics Volume: 15 Issue: 6 Pages: 008061-1008061
  • DOI: 10.1371/journal.pgen.1008061
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] RNA polymerase II Ser7リン酸化は、転写と共役したヌクレオソーム弛緩・再構築を促進して転写一時停止を安定化する (2022)
  • Author(s): 梶谷卓也, 加藤太陽, 沖昌也, 木村宏, 大川恭行, 小布施力史, Hermand Damien, Lis John, 村上洋太
  • Organizer: 第45回日本分子生物学会年会
• [Presentation] エピゲノムとヘテロクロマチン構造構築に働きかけるHP1結合タンパク質 (2022)
  • Author(s): 小布施力史, 磯部真也, 佐渡敬, 長尾恒治
  • Organizer: 第45回日本分子生物学会年会
  • Invited
• [Presentation] Replication dynamics identifies the folding principles of the inactive X chromosome (2022)
  • Author(s): Rawin Poonperm, Saya Ichihara, Hisashi Miura, Akie Tanigawa, Koji Nagao, Chikashi Obuse, Takashi Sado, Ichiro Hiratani
  • Organizer: 第45回日本分子生物学会年会
• [Presentation] ポリコーム複合体PRC1とPRC2はマウス胚体外組織におけるＸ染色体不活性化の維持に必須である (2022)
  • Author(s): 増井修, Corbel Catherine, 長尾恒治, 遠藤高帆, 毛塚芙由子, 小布施力史, Heard Edith, 古関明彦
  • Organizer: 第45回日本分子生物学会年会
• [Presentation] PCGF6-PRC1 は着床後胚においてＸ染色体不活性化を安定に保つ役割を持つ (2022)
  • Author(s): 増井修, 長尾恒治, 信賀順, 遠藤高帆, 毛塚芙由子, 小布施力史, 古関明
  • Organizer: 第45回日本分子生物学会年会
• [Presentation] PHIP/ICEN4 regulates centromere via CENP-B (2022)
  • Author(s): Marinela Perpelescu, Chikashi Obuse, Hiroshi Masumoto, Masato Kanemaki, Hiroshi Kimura
  • Organizer: 第45回日本分子生物学会年会
• [Presentation] ヒストン修飾とヘテロクロマチン構造に働きかけるHP1結合タンパク質 (2022)
  • Author(s): 小布施力史
  • Organizer: 令和４年度遺伝研研究会
  • Invited
• [Presentation] PP1はRIF1のエフェクターとして、Shieldinに先立って相同組換え修復の制御を行う (2021)
  • Author(s): 磯部真也、平賀信一朗、長尾恒治、笹沼博之、Donaldson D. Anne、小布施力史
  • Organizer: 第26回 DNA複製・組換え・修復ワークショップ
• [Presentation] PP1はRIF1のエフェクターとして、Shieldinに先立って相同組換え修復の制御を行う (2021)
  • Author(s): 磯部真也、平賀信一朗、長尾恒治、笹沼博之、Donaldson D. Anne、小布施力史
  • Organizer: 第39回染色体ワークショップ・第20回核ダイナミクス研究会
• [Presentation] PP1はRIF1のエフェクターとして、Shieldinに先立って相同組換え修復の制御を行う (2021)
  • Author(s): 磯部真也、平賀信一朗、長尾恒治、笹沼博之、Donaldson D. Anne、小布施力史
  • Organizer: 第44回日本分子生物学会年会
• [Presentation] ヘテロクロマチンの構造と機能の理解 (2021)
  • Author(s): 小布施力史
  • Organizer: 第1回新学術領域「非ゲノム情報複製」Webセミナー
  • Invited
• [Presentation] Protein Phosphatase 1 acts as a RIF1 effector to suppress DSB resection prior to Shieldin action (2021)
  • Author(s): 磯部 真也, 平賀 信一朗, 長尾 恒治, 笹沼 博之 , Donaldson D Anne, 小布施 力史
  • Organizer: 第 38 回 染色体ワークショップ 第 19 回 核ダイナミクス研究会
• [Presentation] PP1, another RIF1 effector to shieldin, suppresses resection of damaged DNA ends as a barrier against HDR (2020)
  • Author(s): 磯部 真也, 平賀 信一朗, 長尾 恒治, 野崎 直仁, Donaldson D Anne, 小布施 力史
  • Organizer: 第43回 日本分子生物学会年会
• [Presentation] ヘテロクロマチンの構造と機 (2019)
  • Author(s): 小布施力史
  • Organizer: 第13回エピジェネティクス研究会年会
  • Invited
• [Presentation] Elucidation of the molecular basis of heterochromatin body formation. (2019)
  • Author(s): Obuse C.
  • Organizer: Chromosome Dynamics 2019
  • Int'l Joint Research / Invited
• [Remarks] 切断されたDNAをつなぎ直す、細胞の初動対応を解明
  • URL: https://resou.osaka-u.ac.jp/ja/research/2021/20210714_1
• [Remarks] The path less traveled in DNA DSB repair
  • URL: https://www.eurekalert.org/news-releases/478166
• [Remarks] 染色体構造機能学研究室
  • URL: https://www.bio.sci.osaka-u.ac.jp/dbs01/re-paper-temp.php?id=98
• [Remarks] 染色体構造機能学研究室
  • URL: http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/obuse/