Role of DNA topology in gene expression.

• Project Area: Chromatin potential for gene regulation
• Project/Area Number: 19H05261
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyoto University
• Principal Investigator: Canela Andres 京都大学, 白眉センター, 特定准教授 (90837585)
• Project Period (FY): 2019-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2020: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000); Fiscal Year 2019: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: DNA Topoisomerases / Transcription / DNA torsion / RNA polymerase II / Chromatin loop / DNA torsions / RNA polymerase 2

Outline of Research at the Start

How torsional tension in the chromatin impacts transcription? which steps are affected? To this end, I will set up a model to measure changes in the rates of RNA polymerase binding, pause release and transcriptional burst frequency with a combination of genomics and single-cell imaging.

Outline of Annual Research Achievements

During the fiscal year 2020, I evaluated the impact of torsional stress in transcription using cell lines deficient for DNA topoisomerase 2 (TOP2α and TOP2β) generated in the fiscal year 2019. Combining nascent RNA FISH with ChIP-seq for PolII I quantified how the torsional stress accumulated in absence of topoisomerase 2 activity affects transcription dynamics. I measured transcription bursting, intensity of transcription and rates of PollII binding and pause release

Research Progress Status

令和2年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和2年度が最終年度であるため、記入しない。

Research Products

• [Int'l Joint Research] National Institutes of Health(米国)
• [Journal Article] END-seq: An Unbiased, High-Resolution, and Genome-Wide Approach to Map DNA Double-Strand Breaks and Resection in Human Cells (2021)
  • Author(s): Wong N, John S, Nussenzweig A, Canela A.
  • Journal Title: Methods in Molecular Biology Volume: 2153 Pages: 9-31
  • DOI: 10.1007/978-1-0716-0644-5_2
  • ISBN: 9781071606438, 9781071606445
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Exonuclease VII repairs quinolone-induced damage by resolving DNA gyrase cleavage complexes (2021)
  • Author(s): Huang SN, Michaels SA, Mitchell BB, Majdalani N, Vanden Broeck A, Canela A, Tse-Dinh YC, Lamour V, Pommier Y.
  • Journal Title: Science Advances Volume: 7 Issue: 10
  • DOI: 10.1126/sciadv.abe0384
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Neuronal enhancers are hotspots for DNA single-strand break repair. (2021)
  • Author(s): Wu W, Hill SE, Nathan WJ, Paiano J, Callen E, Wang D, Shinoda K, van Wietmarschen N, Colon-Mercado JM, Zong D, De Pace R, Shih HY, Coon S, Parsadanian M, Pavani R, Hanzlikova H, Park S, Jung SK, McHugh PJ, Canela A, Chen C, Casellas R, Caldecott KW, Ward ME, Nussenzweig A.
  • Journal Title: Nature Volume: online Issue: 7859 Pages: 440-444
  • DOI: 10.1038/s41586-021-03468-5
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] 53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination. (2020)
  • Author(s): Callen E, Zong D, Wu W, Wong N, Stanlie A, Ishikawa M, Pavani R, Dumitrache LC, Byrum AK, Mendez-Dorantes C, Martinez P, Canela A, Maman Y, Day A, Kruhlak MJ, Blasco MA, Stark JM, Mosammaparast N, McKinnon PJ, Nussenzweig A
  • Journal Title: Molecular Cell Volume: 77 Issue: 1 Pages: 26-38
  • DOI: 10.1016/j.molcel.2019.09.024
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity. (2019)
  • Author(s): Canela A, Maman Y, Huang SN, Wutz G, Tang W, Zagnoli-Vieira G, Callen E, Wong N, Day A, Peters JM, Caldecott KW, Pommier Y, Nussenzweig A
  • Journal Title: Molecular Cell Volume: 75 Issue: 2 Pages: 252-266
  • DOI: 10.1016/j.molcel.2019.04.030
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Intra-V? Cluster Recombination Shapes the Ig Kappa Locus Repertoire (2019)
  • Author(s): Shinoda K, Maman Y, Canela A, Schatz DG, Livak F, Nussenzweig A
  • Journal Title: Cell Reports Volume: 29 Issue: 13 Pages: 4471-4481
  • DOI: 10.1016/j.celrep.2019.11.088
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] How to find breaks in the DNA and what they can tell us about genome organization (2020)
  • Author(s): Andres Canela
  • Organizer: Central Dogma Seminar. Graduate School of Biostudies. Kyoto University
  • Invited
• [Presentation] Topoisomerase II-induced chromosome breakage and translocation is determined by chromosome architecture and transcriptional activity. (2019)
  • Author(s): Andres Canela
  • Organizer: EMBO Workshop: Organization of bacterial and eukaryotic genomes by SMC complexes. Vienna, Austria
  • Int'l Joint Research / Invited
• [Presentation] Topoisomerase II-induced chromosome breakage and translocation is determined by chromosome architecture and transcriptional activity. (2019)
  • Author(s): Andres Canela
  • Organizer: EMBO Workshop: DNA topology and topoisomerases in genome dynamics. Les Diablerets, Switzerland
  • Int'l Joint Research
• [Presentation] Genome folding as a source of DNA damage and tumorigenesis (2019)
  • Author(s): Andres Canela
  • Organizer: 21st Symposium of Graduate School of Biostudies. Kyoto University
  • Invited