IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-024-55144-7.html
   My bibliography  Save this article

H3K56 acetylation regulates chromatin maturation following DNA replication

Author

Listed:
  • Shoufu Duan

    (Columbia University Irving Medical Center
    Chinese Academy of Sciences)

  • Ilana M. Nodelman

    (Johns Hopkins University)

  • Hui Zhou

    (Columbia University Irving Medical Center)

  • Toshio Tsukiyama

    (Fred Hutchinson Cancer Center)

  • Gregory D. Bowman

    (Johns Hopkins University)

  • Zhiguo Zhang

    (Columbia University Irving Medical Center)

Abstract

Following DNA replication, the newly reassembled chromatin is disorganized and must mature to its steady state to maintain both genome and epigenome integrity. However, the regulatory mechanisms governing this critical process remain poorly understood. Here, we show that histone H3K56 acetylation (H3K56ac), a mark on newly-synthesized H3, facilitates the remodeling of disorganized nucleosomes in nascent chromatin, and its removal at the subsequent G2/M phase of the cell cycle marks the completion of chromatin maturation. In vitro, H3K56ac enhances the activity of ISWI chromatin remodelers, including yeast ISW1 and its human equivalent SNF2h. In vivo, a deficiency of H3K56ac in nascent chromatin results in the formation of closely packed di-nucleosomes and/or tetra-nucleosomes. In contrast, abnormally high H3K56ac levels disrupt chromatin maturation, leading to genome instability. These findings establish a central role of H3K56ac in chromatin maturation and reveal a mechanism regulating this critical aspect of chromosome replication.

Suggested Citation

  • Shoufu Duan & Ilana M. Nodelman & Hui Zhou & Toshio Tsukiyama & Gregory D. Bowman & Zhiguo Zhang, 2025. "H3K56 acetylation regulates chromatin maturation following DNA replication," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-024-55144-7
    DOI: 10.1038/s41467-024-55144-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-55144-7
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-55144-7?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. Giulia Saredi & Hongda Huang & Colin M. Hammond & Constance Alabert & Simon Bekker-Jensen & Ignasi Forne & Nazaret Reverón-Gómez & Benjamin M. Foster & Lucie Mlejnkova & Till Bartke & Petr Cejka & Nie, 2016. "H4K20me0 marks post-replicative chromatin and recruits the TONSL–MMS22L DNA repair complex," Nature, Nature, vol. 534(7609), pages 714-718, June.
    2. Marilyn G. Pray-Grant & Jeremy A. Daniel & David Schieltz & John R. Yates & Patrick A. Grant, 2005. "Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation," Nature, Nature, vol. 433(7024), pages 434-438, January.
    3. Karolin Luger & Armin W. Mäder & Robin K. Richmond & David F. Sargent & Timothy J. Richmond, 1997. "Crystal structure of the nucleosome core particle at 2.8 Å resolution," Nature, Nature, vol. 389(6648), pages 251-260, September.
    4. Kristin Brogaard & Liqun Xi & Ji-Ping Wang & Jonathan Widom, 2012. "A map of nucleosome positions in yeast at base-pair resolution," Nature, Nature, vol. 486(7404), pages 496-501, June.
    5. John F. Flanagan & Li-Zhi Mi & Maksymilian Chruszcz & Marcin Cymborowski & Katrina L. Clines & Youngchang Kim & Wladek Minor & Fraydoon Rastinejad & Sepideh Khorasanizadeh, 2005. "Double chromodomains cooperate to recognize the methylated histone H3 tail," Nature, Nature, vol. 438(7071), pages 1181-1185, December.
    6. Sean R. Collins & Kyle M. Miller & Nancy L. Maas & Assen Roguev & Jeffrey Fillingham & Clement S. Chu & Maya Schuldiner & Marinella Gebbia & Judith Recht & Michael Shales & Huiming Ding & Hong Xu & Ju, 2007. "Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map," Nature, Nature, vol. 446(7137), pages 806-810, April.
    7. Darko Barisic & Michael B. Stadler & Mario Iurlaro & Dirk Schübeler, 2019. "Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors," Nature, Nature, vol. 569(7754), pages 136-140, May.
    8. Geoffrey P. Dann & Glen P. Liszczak & John D. Bagert & Manuel M. Müller & Uyen T. T. Nguyen & Felix Wojcik & Zachary Z. Brown & Jeffrey Bos & Tatyana Panchenko & Rasmus Pihl & Samuel B. Pollock & Kath, 2017. "ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference," Nature, Nature, vol. 548(7669), pages 607-611, August.
    9. Erika Chacin & Karl-Uwe Reusswig & Jessica Furtmeier & Priyanka Bansal & Leonhard A. Karl & Boris Pfander & Tobias Straub & Philipp Korber & Christoph F. Kurat, 2023. "Establishment and function of chromatin organization at replication origins," Nature, Nature, vol. 616(7958), pages 836-842, April.
    10. V. Parreno & V. Loubiere & B. Schuettengruber & L. Fritsch & C. C. Rawal & M. Erokhin & B. Győrffy & D. Normanno & M. Stefano & J. Moreaux & N. L. Butova & I. Chiolo & D. Chetverina & A.-M. Martinez &, 2024. "Transient loss of Polycomb components induces an epigenetic cancer fate," Nature, Nature, vol. 629(8012), pages 688-696, May.
    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. Marko Dunjić & Felix Jonas & Gilad Yaakov & Roye More & Yoav Mayshar & Yoach Rais & Ayelet-Hashahar Orenbuch & Saifeng Cheng & Naama Barkai & Yonatan Stelzer, 2023. "Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    2. Ke Chen & Li Wang & Zishuo Yu & Jiali Yu & Yulei Ren & Qianmin Wang & Yanhui Xu, 2024. "Structure of the human TIP60 complex," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Corina Maritz & Reihaneh Khaleghi & Michelle N. Yancoskie & Sarah Diethelm & Sonja Brülisauer & Natalia Santos Ferreira & Yang Jiang & Shana J. Sturla & Hanspeter Naegeli, 2023. "ASH1L-MRG15 methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Yichen Zhong & Hakimeh Moghaddas Sani & Bishnu P. Paudel & Jason K. K. Low & Ana P. G. Silva & Stefan Mueller & Chandrika Deshpande & Santosh Panjikar & Xavier J. Reid & Max J. Bedward & Antoine M. Oi, 2022. "The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    5. Namrata Kumar & Arjan F. Theil & Vera Roginskaya & Yasmin Ali & Michael Calderon & Simon C. Watkins & Ryan P. Barnes & Patricia L. Opresko & Alex Pines & Hannes Lans & Wim Vermeulen & Bennett Houten, 2022. "Global and transcription-coupled repair of 8-oxoG is initiated by nucleotide excision repair proteins," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    6. Susan Kilgas & Aleem Syed & Patrick Toolan-Kerr & Michelle L. Swift & Shrabasti Roychoudhury & Aniruddha Sarkar & Sarah Wilkins & Mikayla Quigley & Anna R. Poetsch & Maria Victoria Botuyan & Gaofeng C, 2024. "NEAT1 modulates the TIRR/53BP1 complex to maintain genome integrity," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    7. Xinhao Hou & Mingjing Xu & Chengming Zhu & Jianing Gao & Meili Li & Xiangyang Chen & Cheng Sun & Björn Nashan & Jianye Zang & Ying Zhou & Shouhong Guang & Xuezhu Feng, 2023. "Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    8. Wilfried Engl & Aliz Kunstar-Thomas & Siyi Chen & Woei Shyuan Ng & Hendrik Sielaff & Ziqing Winston Zhao, 2024. "Single-molecule imaging of SWI/SNF chromatin remodelers reveals bromodomain-mediated and cancer-mutants-specific landscape of multi-modal DNA-binding dynamics," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    9. Carlo Yague-Sanz & Valérie Migeot & Marc Larochelle & François Bachand & Maxime Wéry & Antonin Morillon & Damien Hermand, 2023. "Chromatin remodeling by Pol II primes efficient Pol III transcription," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    10. Masaki Kikuchi & Satoshi Morita & Masatoshi Wakamori & Shin Sato & Tomomi Uchikubo-Kamo & Takehiro Suzuki & Naoshi Dohmae & Mikako Shirouzu & Takashi Umehara, 2023. "Epigenetic mechanisms to propagate histone acetylation by p300/CBP," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    11. Fritz Nagae & Yasuto Murayama & Tsuyoshi Terakawa, 2024. "Molecular mechanism of parental H3/H4 recycling at a replication fork," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    12. Zhen Hou & Frank Nightingale & Yanan Zhu & Craig MacGregor-Chatwin & Peijun Zhang, 2023. "Structure of native chromatin fibres revealed by Cryo-ET in situ," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    13. Rina Hirano & Haruhiko Ehara & Tomoya Kujirai & Tamami Uejima & Yoshimasa Takizawa & Shun-ichi Sekine & Hitoshi Kurumizaka, 2022. "Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    14. Shijia Zhu & Guohua Wang & Bo Liu & Yadong Wang, 2013. "Modeling Exon Expression Using Histone Modifications," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-15, June.
    15. Junliang Chen & Mingjie Wu & Yulan Yang & Chunyan Ruan & Yi Luo & Lizhi Song & Ting Wu & Jun Huang & Bing Yang & Ting Liu, 2024. "TFIP11 promotes replication fork reversal to preserve genome stability," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    16. Caojie Liu & Qiuchan Xiong & Qiwen Li & Weimin Lin & Shuang Jiang & Danting Zhang & Yuan Wang & Xiaobo Duan & Ping Gong & Ning Kang, 2022. "CHD7 regulates bone-fat balance by suppressing PPAR-γ signaling," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    17. Joke J F A van Vugt & Martijn de Jager & Magdalena Murawska & Alexander Brehm & John van Noort & Colin Logie, 2009. "Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence," PLOS ONE, Public Library of Science, vol. 4(7), pages 1-14, July.
    18. Takuya Tsujino & Tomoaki Takai & Kunihiko Hinohara & Fu Gui & Takeshi Tsutsumi & Xiao Bai & Chenkui Miao & Chao Feng & Bin Gui & Zsofia Sztupinszki & Antoine Simoneau & Ning Xie & Ladan Fazli & Xuesen, 2023. "CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    19. Marieke R. Wensveen & Aditya A. Dixit & Robin Schendel & Apfrida Kendek & Jan-Paul Lambooij & Marcel Tijsterman & Serafin U. Colmenares & Aniek Janssen, 2024. "Double-strand breaks in facultative heterochromatin require specific movements and chromatin changes for efficient repair," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    20. Sahiti Kuppa & Jaigeeth Deveryshetty & Rahul Chadda & Jenna R. Mattice & Nilisha Pokhrel & Vikas Kaushik & Angela Patterson & Nalini Dhingra & Sushil Pangeni & Marisa K. Sadauskas & Sajad Shiekh & Ham, 2022. "Rtt105 regulates RPA function by configurationally stapling the flexible domains," Nature Communications, Nature, vol. 13(1), pages 1-16, 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:16:y:2025:i:1:d:10.1038_s41467-024-55144-7. 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.