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

2022 Fiscal Year Research-status Report

• Project/Area Number: 21K06129
• 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
• Keywords: Euchromatin / Heterochromatin / Replication timing / A/B compartments / Transcription

Outline of Annual Research Achievements

The eukaryotic genome is organized into eu- or hetero-chromatin domains, the former is gene-rich and transcriptionally active, while the latter is gene-poor and transcriptionally inactive. Eu- or hetero-chromatin are also analogous to A or B compartments, calculated from the PC1 (primary component 1) value of the eigenvector of the Hi-C (a method for chromatin conformation capture) matrix. During S phase, A compartments replicate early while B compartments replicate late. It is, however, not understood if A/B compartmentalization and early/late replication timing is mechanistically linked.

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

The aim of this project is to determine if A/B compartments and early/late replication timing are mechanistically linked. 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. Finally, via genomics-based screening and genetic knock-in experiments, I have determined specific genetic sequences that play a key role in connecting A/B compartments with early/late replication timing.

Strategy for Future Research Activity

My research reveals that in addition to regulating gene expression, transcription possesses distinct roles to regulate 3D genome and replication timing. Intriguingly, this role of transcription appears to be mediated by distinct epigenetic mechanisms that are deposited downstream of transcriptional elongation. In this project, I have focused on one such epigenetic mechanism that is enriched in A compartments and promotes early replication. By research, however, has unveiled several other epigenetic pathways that may also take part in regulation of the 3D genome and replication timing. Some of these epigenetic mechanisms are expected to be involved in regulation of B compartments and/or late replication timing. Further exploration of these mechanisms is my future goal.

Causes of Carryover

The incurring amount will be used to perform additional experiments in next fiscal year.

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: Epub
  • 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) Pages: Online
  • DOI: 10.1038/s41467-022-34856-8
  • Peer Reviewed / 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) Pages: Online
  • DOI: 10.1038/s41467-022-34779-4
  • Peer Reviewed / 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) Pages: 1445-1455
  • DOI: 10.1007/s11427-021-2029-0
  • Peer Reviewed / Int'l Joint Research