IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-40843-4.html
   My bibliography  Save this article

Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair

Author

Listed:
  • Nikolaos Parisis

    (IGMM, CNRS, INSERM, University of Montpellier
    Equipe labellisée Ligue contre le Cancer
    University of Montpellier
    University Paris Diderot)

  • Pablo D. Dans

    (IRB Barcelona, BIST
    Institute Pasteur of Montevideo
    University of the Republic (UdelaR))

  • Muhammad Jbara

    (Schulich Faculty of Chemistry, Technion Israel Institute of Technology
    Tel Aviv University)

  • Balveer Singh

    (IGDR, CNRS, University of Rennes)

  • Diane Schausi-Tiffoche

    (IGDR, CNRS, University of Rennes)

  • Diego Molina-Serrano

    (IGDR, CNRS, University of Rennes)

  • Isabelle Brun-Heath

    (IRB Barcelona, BIST)

  • Denisa Hendrychová

    (IGMM, CNRS, INSERM, University of Montpellier
    Equipe labellisée Ligue contre le Cancer
    Palacký University Olomouc)

  • Suman Kumar Maity

    (Schulich Faculty of Chemistry, Technion Israel Institute of Technology)

  • Diana Buitrago

    (IRB Barcelona, BIST)

  • Rafael Lema

    (IRB Barcelona, BIST)

  • Thiziri Nait Achour

    (IGMM, CNRS, INSERM, University of Montpellier
    Equipe labellisée Ligue contre le Cancer)

  • Simona Giunta

    (The Rockefeller University
    Laboratory of Genome Evolution, Department of Biology and Biotechnology “Charles Darwin”, University of Rome Sapienza)

  • Michael Girardot

    (IGMM, CNRS, INSERM, University of Montpellier)

  • Nicolas Talarek

    (IGMM, CNRS, INSERM, University of Montpellier)

  • Valérie Rofidal

    (University of Montpellier)

  • Katerina Danezi

    (IGMM, CNRS, INSERM, University of Montpellier
    Equipe labellisée Ligue contre le Cancer)

  • Damien Coudreuse

    (IGDR, CNRS, University of Rennes
    University of Bordeaux)

  • Marie-Noëlle Prioleau

    (University Paris Diderot)

  • Robert Feil

    (IGMM, CNRS, INSERM, University of Montpellier)

  • Modesto Orozco

    (IRB Barcelona, BIST)

  • Ashraf Brik

    (Schulich Faculty of Chemistry, Technion Israel Institute of Technology)

  • Pei-Yun Jenny Wu

    (IGDR, CNRS, University of Rennes
    University of Bordeaux)

  • Liliana Krasinska

    (IGMM, CNRS, INSERM, University of Montpellier
    Equipe labellisée Ligue contre le Cancer)

  • Daniel Fisher

    (IGMM, CNRS, INSERM, University of Montpellier
    Equipe labellisée Ligue contre le Cancer)

Abstract

Histone post-translational modifications promote a chromatin environment that controls transcription, DNA replication and repair, but surprisingly few phosphorylations have been documented. We report the discovery of histone H3 serine-57 phosphorylation (H3S57ph) and show that it is implicated in different DNA repair pathways from fungi to vertebrates. We identified CHK1 as a major human H3S57 kinase, and disrupting or constitutively mimicking H3S57ph had opposing effects on rate of recovery from replication stress, 53BP1 chromatin binding, and dependency on RAD52. In fission yeast, mutation of all H3 alleles to S57A abrogated DNA repair by both non-homologous end-joining and homologous recombination, while cells with phospho-mimicking S57D alleles were partly compromised for both repair pathways, presented aberrant Rad52 foci and were strongly sensitised to replication stress. Mechanistically, H3S57ph loosens DNA-histone contacts, increasing nucleosome mobility, and interacts with H3K56. Our results suggest that dynamic phosphorylation of H3S57 is required for DNA repair and recovery from replication stress, opening avenues for investigating the role of this modification in other DNA-related processes.

Suggested Citation

  • Nikolaos Parisis & Pablo D. Dans & Muhammad Jbara & Balveer Singh & Diane Schausi-Tiffoche & Diego Molina-Serrano & Isabelle Brun-Heath & Denisa Hendrychová & Suman Kumar Maity & Diana Buitrago & Rafa, 2023. "Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40843-4
    DOI: 10.1038/s41467-023-40843-4
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-40843-4
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-40843-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Jordan R. Becker & Gillian Clifford & Clara Bonnet & Anja Groth & Marcus D. Wilson & J. Ross Chapman, 2021. "BARD1 reads H2A lysine 15 ubiquitination to direct homologous recombination," Nature, Nature, vol. 596(7872), pages 433-437, August.
    2. Toyoko Tsukuda & Alastair B. Fleming & Jac A. Nickoloff & Mary Ann Osley, 2005. "Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae," Nature, Nature, vol. 438(7066), pages 379-383, November.
    3. Amélie Fradet-Turcotte & Marella D. Canny & Cristina Escribano-Díaz & Alexandre Orthwein & Charles C. Y. Leung & Hao Huang & Marie-Claude Landry & Julianne Kitevski-LeBlanc & Sylvie M. Noordermeer & F, 2013. "53BP1 is a reader of the DNA-damage-induced H2A Lys 15 ubiquitin mark," Nature, Nature, vol. 499(7456), pages 50-54, July.
    4. Rebecca A. Burrell & Sarah E. McClelland & David Endesfelder & Petra Groth & Marie-Christine Weller & Nadeem Shaikh & Enric Domingo & Nnennaya Kanu & Sally M. Dewhurst & Eva Gronroos & Su Kit Chew & A, 2013. "Replication stress links structural and numerical cancer chromosomal instability," Nature, Nature, vol. 494(7438), pages 492-496, February.
    5. 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.
    6. Hiroshi Masumoto & David Hawke & Ryuji Kobayashi & Alain Verreault, 2005. "A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response," Nature, Nature, vol. 436(7048), pages 294-298, July.
    7. Arnab Ray Chaudhuri & Elsa Callen & Xia Ding & Ewa Gogola & Alexandra A. Duarte & Ji-Eun Lee & Nancy Wong & Vanessa Lafarga & Jennifer A. Calvo & Nicholas J. Panzarino & Sam John & Amanda Day & Anna V, 2016. "Replication fork stability confers chemoresistance in BRCA-deficient cells," Nature, Nature, vol. 535(7612), pages 382-387, July.
    8. Rebecca A. Burrell & Sarah E. McClelland & David Endesfelder & Petra Groth & Marie-Christine Weller & Nadeem Shaikh & Enric Domingo & Nnennaya Kanu & Sally M. Dewhurst & Eva Gronroos & Su Kit Chew & A, 2013. "Correction: Corrigendum: Replication stress links structural and numerical cancer chromosomal instability," Nature, Nature, vol. 500(7463), pages 490-490, August.
    9. Pedro A. Mateos-Gomez & Fade Gong & Nidhi Nair & Kyle M. Miller & Eros Lazzerini-Denchi & Agnel Sfeir, 2015. "Mammalian polymerase θ promotes alternative NHEJ and suppresses recombination," Nature, Nature, vol. 518(7538), pages 254-257, February.
    10. Arnab Ray Chaudhuri & Elsa Callen & Xia Ding & Ewa Gogola & Alexandra A. Duarte & Ji-Eun Lee & Nancy Wong & Vanessa Lafarga & Jennifer A. Calvo & Nicholas J. Panzarino & Sam John & Amanda Day & Anna V, 2016. "Erratum: Replication fork stability confers chemoresistance in BRCA-deficient cells," Nature, Nature, vol. 539(7629), pages 456-456, November.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Inés Paniagua & Zainab Tayeh & Mattia Falcone & Santiago Hernández Pérez & Aurora Cerutti & Jacqueline J. L. Jacobs, 2022. "MAD2L2 promotes replication fork protection and recovery in a shieldin-independent and REV3L-dependent manner," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Jian Ma & Yingke Zhou & Penglin Pan & Haixin Yu & Zixi Wang & Lei Lily Li & Bing Wang & Yuqian Yan & Yunqian Pan & Qi Ye & Tianjie Liu & Xiaoyu Feng & Shan Xu & Ke Wang & Xinyang Wang & Yanlin Jian & , 2023. "TRABID overexpression enables synthetic lethality to PARP inhibitor via prolonging 53BP1 retention at double-strand breaks," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Arindam Datta & Kajal Biswas & Joshua A. Sommers & Haley Thompson & Sanket Awate & Claudia M. Nicolae & Tanay Thakar & George-Lucian Moldovan & Robert H. Shoemaker & Shyam K. Sharan & Robert M. Brosh, 2021. "WRN helicase safeguards deprotected replication forks in BRCA2-mutated cancer cells," Nature Communications, Nature, vol. 12(1), pages 1-22, December.
    4. Anastasia Hale & Ashna Dhoonmoon & Joshua Straka & Claudia M. Nicolae & George-Lucian Moldovan, 2023. "Multi-step processing of replication stress-derived nascent strand DNA gaps by MRE11 and EXO1 nucleases," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    5. Cuige Zhu & Mari Iwase & Ziqian Li & Faliang Wang & Annabel Quinet & Alessandro Vindigni & Jieya Shao, 2022. "Profilin-1 regulates DNA replication forks in a context-dependent fashion by interacting with SNF2H and BOD1L," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    6. Antonios Revythis & Anu Limbu & Christos Mikropoulos & Aruni Ghose & Elisabet Sanchez & Matin Sheriff & Stergios Boussios, 2022. "Recent Insights into PARP and Immuno-Checkpoint Inhibitors in Epithelial Ovarian Cancer," IJERPH, MDPI, vol. 19(14), pages 1-19, July.
    7. Ramona N. Moro & Uddipta Biswas & Suhas S. Kharat & Filip D. Duzanic & Prosun Das & Maria Stavrou & Maria C. Raso & Raimundo Freire & Arnab Ray Chaudhuri & Shyam K. Sharan & Lorenza Penengo, 2023. "Interferon restores replication fork stability and cell viability in BRCA-defective cells via ISG15," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    8. Vera M. Kissling & Giordano Reginato & Eliana Bianco & Kristina Kasaciunaite & Janny Tilma & Gea Cereghetti & Natalie Schindler & Sung Sik Lee & Raphaël Guérois & Brian Luke & Ralf Seidel & Petr Cejka, 2022. "Mre11-Rad50 oligomerization promotes DNA double-strand break repair," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    9. Nagham Ghaddar & Yves Corda & Pierre Luciano & Martina Galli & Ylli Doksani & Vincent Géli, 2023. "The COMPASS subunit Spp1 protects nascent DNA at the Tus/Ter replication fork barrier by limiting DNA availability to nucleases," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    10. Anne Margriet Heijink & Colin Stok & David Porubsky & Eleni Maria Manolika & Jurrian K. Kanter & Yannick P. Kok & Marieke Everts & H. Rudolf Boer & Anastasia Audrey & Femke J. Bakker & Elles Wierenga , 2022. "Sister chromatid exchanges induced by perturbed replication can form independently of BRCA1, BRCA2 and RAD51," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    11. Lorenza Garribba & Giuseppina De Feudis & Valentino Martis & Martina Galli & Marie Dumont & Yonatan Eliezer & René Wardenaar & Marica Rosaria Ippolito & Divya Ramalingam Iyer & Andréa E. Tijhuis & Dia, 2023. "Short-term molecular consequences of chromosome mis-segregation for genome stability," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    12. Ivo A. Hendriks & Sara C. Buch-Larsen & Evgeniia Prokhorova & Jonas D. Elsborg & Alexandra K.L.F.S. Rebak & Kang Zhu & Dragana Ahel & Claudia Lukas & Ivan Ahel & Michael L. Nielsen, 2021. "The regulatory landscape of the human HPF1- and ARH3-dependent ADP-ribosylome," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    13. Zu Ye & Shengfeng Xu & Yin Shi & Xueqian Cheng & Yuan Zhang & Sunetra Roy & Sarita Namjoshi & Michael A. Longo & Todd M. Link & Katharina Schlacher & Guang Peng & Dihua Yu & Bin Wang & John A. Tainer , 2024. "GRB2 stabilizes RAD51 at reversed replication forks suppressing genomic instability and innate immunity against cancer," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    14. Matthew Day & Bilal Tetik & Milena Parlak & Yasser Almeida-Hernández & Markus Räschle & Farnusch Kaschani & Heike Siegert & Anika Marko & Elsa Sanchez-Garcia & Markus Kaiser & Isabel A. Barker & Laure, 2024. "TopBP1 utilises a bipartite GINS binding mode to support genome replication," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    15. Maria Dilia Palumbieri & Chiara Merigliano & Daniel González-Acosta & Danina Kuster & Jana Krietsch & Henriette Stoy & Thomas Känel & Svenja Ulferts & Bettina Welter & Joël Frey & Cyril Doerdelmann & , 2023. "Nuclear actin polymerization rapidly mediates replication fork remodeling upon stress by limiting PrimPol activity," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    16. Kate E. Coleman & Yandong Yin & Sarah Kit Leng Lui & Sarah Keegan & David Fenyo & Duncan J. Smith & Eli Rothenberg & Tony T. Huang, 2022. "USP1-trapping lesions as a source of DNA replication stress and genomic instability," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    17. Sijia Cui & Nicholas McGranahan & Jing Gao & Peng Chen & Wei Jiang & Lingrong Yang & Li Ma & Junfang Liao & Tian Xie & Congying Xie & Tariq Enver & Shixiu Wu, 2023. "Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    18. John J. Krais & David J. Glass & Ilse Chudoba & Yifan Wang & Wanjuan Feng & Dennis Simpson & Pooja Patel & Zemin Liu & Ryan Neumann-Domer & Robert G. Betsch & Andrea J. Bernhardy & Alice M. Bradbury &, 2023. "Genetic separation of Brca1 functions reveal mutation-dependent Polθ vulnerabilities," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    19. Gaofeng Cui & Maria Victoria Botuyan & Pascal Drané & Qi Hu & Benoît Bragantini & James R. Thompson & David J. Schuller & Alexandre Detappe & Michael T. Perfetti & Lindsey I. James & Stephen V. Frye &, 2023. "An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    20. Ashna Dhoonmoon & Claudia M. Nicolae & George-Lucian Moldovan, 2022. "The KU-PARP14 axis differentially regulates DNA resection at stalled replication forks by MRE11 and EXO1," Nature Communications, Nature, vol. 13(1), pages 1-18, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40843-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.