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RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity

Author

Listed:
  • Sumin Feng

    (Peking University)

  • Sai Ma

    (Peking University)

  • Kejiao Li

    (Peking University)

  • Shengxian Gao

    (Peking University)

  • Shaokai Ning

    (Peking University)

  • Jinfeng Shang

    (Peking University)

  • Ruiyuan Guo

    (Peking University)

  • Yingying Chen

    (Peking University)

  • Britny Blumenfeld

    (The Hebrew University)

  • Itamar Simon

    (The Hebrew University)

  • Qing Li

    (Peking University
    Peking University)

  • Rong Guo

    (Peking University)

  • Dongyi Xu

    (Peking University)

Abstract

The 53BP1-RIF1 pathway antagonizes resection of DNA broken ends and confers PARP inhibitor sensitivity on BRCA1-mutated tumors. However, it is unclear how this pathway suppresses initiation of resection. Here, we identify ASF1 as a partner of RIF1 via an interacting manner similar to its interactions with histone chaperones CAF-1 and HIRA. ASF1 is recruited to distal chromatin flanking DNA breaks by 53BP1-RIF1 and promotes non-homologous end joining (NHEJ) using its histone chaperone activity. Epistasis analysis shows that ASF1 acts in the same NHEJ pathway as RIF1, but via a parallel pathway with the shieldin complex, which suppresses resection after initiation. Moreover, defects in end resection and homologous recombination (HR) in BRCA1-deficient cells are largely suppressed by ASF1 deficiency. Mechanistically, ASF1 compacts adjacent chromatin by heterochromatinization to protect broken DNA ends from BRCA1-mediated resection. Taken together, our findings identify a RIF1-ASF1 histone chaperone complex that promotes changes in high-order chromatin structure to stimulate the NHEJ pathway for DSB repair.

Suggested Citation

  • Sumin Feng & Sai Ma & Kejiao Li & Shengxian Gao & Shaokai Ning & Jinfeng Shang & Ruiyuan Guo & Yingying Chen & Britny Blumenfeld & Itamar Simon & Qing Li & Rong Guo & Dongyi Xu, 2022. "RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28588-y
    DOI: 10.1038/s41467-022-28588-y
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    1. Shangda Yang & Ling Liu & Cheng Cao & Nan Song & Yuejiao Wang & Shuai Ma & Qi Zhang & Na Yu & Xiang Ding & Fuquan Yang & Shanshan Tian & Kai Zhang & Tao Sun & Jie Yang & Zhi Yao & Shaoyuan Wu & Lei Sh, 2018. "USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization," Nature Communications, Nature, vol. 9(1), pages 1-17, December.
    2. Vera Boersma & Nathalie Moatti & Sandra Segura-Bayona & Marieke H. Peuscher & Jaco van der Torre & Brigitte A. Wevers & Alexandre Orthwein & Daniel Durocher & Jacqueline J. L. Jacobs, 2015. "MAD2L2 controls DNA repair at telomeres and DNA breaks by inhibiting 5′ end resection," Nature, Nature, vol. 521(7553), pages 537-540, May.
    3. Guotai Xu & J. Ross Chapman & Inger Brandsma & Jingsong Yuan & Martin Mistrik & Peter Bouwman & Jirina Bartkova & Ewa Gogola & Daniël Warmerdam & Marco Barazas & Janneke E. Jaspers & Kenji Watanabe & , 2015. "REV7 counteracts DNA double-strand break resection and affects PARP inhibition," Nature, Nature, vol. 521(7553), pages 541-544, May.
    4. Craig J. Ceol & Yariv Houvras & Judit Jane-Valbuena & Steve Bilodeau & David A. Orlando & Valentine Battisti & Lauriane Fritsch & William M. Lin & Travis J. Hollmann & Fabrizio Ferré & Caitlin Bourque, 2011. "The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset," Nature, Nature, vol. 471(7339), pages 513-517, March.
    5. Chao Lu & Patrick S. Ward & Gurpreet S. Kapoor & Dan Rohle & Sevin Turcan & Omar Abdel-Wahab & Christopher R. Edwards & Raya Khanin & Maria E. Figueroa & Ari Melnick & Kathryn E. Wellen & Donald M. O’, 2012. "IDH mutation impairs histone demethylation and results in a block to cell differentiation," Nature, Nature, vol. 483(7390), pages 474-478, March.
    6. Shengxian Gao & Sumin Feng & Shaokai Ning & Jingyan Liu & Huayu Zhao & Yixi Xu & Jinfeng Shang & Kejiao Li & Qing Li & Rong Guo & Dongyi Xu, 2018. "An OB-fold complex controls the repair pathways for DNA double-strand breaks," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    7. Mengtan Xing & Mingrui Yang & Wei Huo & Feng Feng & Leizhen Wei & Wenxia Jiang & Shaokai Ning & Zhenxin Yan & Wen Li & Qingsong Wang & Mei Hou & Chunxia Dong & Rong Guo & Ge Gao & Jianguo Ji & Shan Zh, 2015. "Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway," Nature Communications, Nature, vol. 6(1), pages 1-12, May.
    8. Sylvie M. Noordermeer & Salomé Adam & Dheva Setiaputra & Marco Barazas & Stephen J. Pettitt & Alexanda K. Ling & Michele Olivieri & Alejandro Álvarez-Quilón & Nathalie Moatti & Michal Zimmermann & Ste, 2018. "The shieldin complex mediates 53BP1-dependent DNA repair," Nature, Nature, vol. 560(7716), pages 117-121, August.
    9. Hannah Farmer & Nuala McCabe & Christopher J. Lord & Andrew N. J. Tutt & Damian A. Johnson & Tobias B. Richardson & Manuela Santarosa & Krystyna J. Dillon & Ian Hickson & Charlotte Knights & Niall M. , 2005. "Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy," Nature, Nature, vol. 434(7035), pages 917-921, April.
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