哺乳類のDNA複製タイミング制御におけるゲノムとエピゲノムの機能的リンク

• Project/Area Number: 21K06129
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 43050:Genome biology-related
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: SHARIF JAFAR 国立研究開発法人理化学研究所, 生命医科学研究センター, 専任研究員 (00577968)
• Project Period (FY): 2021-04-01 – 2024-03-31
• Project Status: Completed (Fiscal Year 2023)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2023: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2022: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2021: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: 3D genome / Epigenome / Replication timing / Euchromatin / Heterochromatin / A/B compartments / Transcription / DNA replication / H2B monoubiquitination / RNF20 / Retrotransposon

Outline of Research at the Start

本研究では、哺乳類細胞における複製タイミング（RT）の分子メカニズムを解析する。RTの決定に、ゲノムDNA配列そのものが貢献し、さらにそれらの配列を読み取るエピゲノム修飾因子が寄与しているとの仮説を立てる。我々の予備実験から、RNA polymerase II (POL2)による転写伸長反応がRTの制御に重要な役割を持ち、さらにPOL2の下流に集積するH2Bモノユビキチン化（H2Bub）がDNA複製の決定に関与している可能性が示唆された。本研究では、ゲノムのDNA配列がPOL2やH2Bubを誘導することにより、どのようにしてRTの決定に貢献するのか、その分子機構に迫る。

Outline of Annual Research Achievements

The higher order mammalian genome is organized into euchromatin associated A, and heterochromatin associated B, compartments. In this project, I analyzed the mechanistic link between A/B compartments and early/late replication timing. By taking advantage of degron-based acute depletion of transcriptional machinery, I have found that transcriptional elongation functions as a molecular link to connect A/B compartments and early/late replication timing. Furthermore, by taking advantage of a conditional gene knockout strategy, I have been able to identify an epigenetic mechanism that functions directly downstream of transcriptional elongation to connect compartmentalization with replication timing.

Research Products

• [Journal Article] Bridging multiple dimensions: roles of transposable elements in higher-order genome regulation (2023)
  • Author(s): Jafar Sharif, Haruhiko Koseki, Nicholas F Parrish
  • Journal Title: Curr Opin Genet Dev . Volume: 80 Pages: 102035-102035
  • DOI: 10.1016/j.gde.2023.102035
  • Int'l Joint Research
• [Journal Article] PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment (2022)
  • Author(s): Takano J, Ito S, Dong Y, Sharif J, Nakajima-Takagi Y, Umeyama T, Han YW, Isono K, Kondo T, Iizuka Y, Miyai T, Koseki Y, Ikegaya M, Sakihara M, Nakayama M, Ohara O, Hasegawa Y, Hashimoto K, Arner E, Klose RJ, Iwama A, Koseki H, Ikawa T
  • Journal Title: Nat Commun. Volume: 13 (1) Issue: 1 Pages: 7159-7159
  • DOI: 10.1038/s41467-022-34856-8
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural basis for activation of DNMT1 (2022)
  • Author(s): Kikuchi A, Onoda H, Yamaguchi K, Kori S, Matsuzawa S, Chiba Y, Tanimoto S, Yoshimi S, Sato H, Yamagata A, Shirouzu M, Adachi N, Sharif J, Koseki H, Nishiyama A, Nakanishi M, Defossez PA, Arita K
  • Journal Title: Nat Commun. Volume: 13 (1) Issue: 1 Pages: 1-11
  • DOI: 10.1038/s41467-022-34779-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Efficient de novo assembly and modification of large DNA fragments (2022)
  • Author(s): Jiang S, Tang Y, Xiang L, Zhu X, Cai Z, Li L, Chen Y, Chen P, Feng Y, Lin X, Li G, Sharif J, Dai J
  • Journal Title: Sci China Life Sci. Volume: 65 (7) Issue: 7 Pages: 1445-1455
  • DOI: 10.1007/s11427-021-2029-0
  • Peer Reviewed / Int'l Joint Research