Dynamic De Novo Heterochromatin Assembly and Disassembly at Replication Forks Ensures Fork Stability

Overview

Journal Nat Cell Biol

Specialty Cell Biology

Date 2023 Jul 6

PMID 37414849

Authors

Vincent Gaggioli

Calvin S Y Lo

Nazaret Reveron-Gomez

Zuzana Jasencakova

Heura Domenech

Hong Nguyen

Simone Sidoli

Andrey Tvardovskiy

Sidrit Uruci

Johan A Slotman

Yi Chai

Joao G S C Souto Goncalves

Eleni Maria Manolika

Ole N Jensen

David Wheeler

Sriram Sridharan

Sanjiban Chakrabarty

Jeroen Demmers

Roland Kanaar

Anja Groth

Nitika Taneja

Affiliations

Soon will be listed here.

Abstract

Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces chromatin compaction by accumulating the repressive modifications, H3K9me1/me2/me3, in the vicinity of stressed replication forks. This closed conformation is also favoured by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering single-stranded DNA gap formation and sensitizing cells towards chemotherapeutic drugs. These findings may help in explaining chemotherapy resistance and poor prognosis observed in patients with cancer displaying elevated levels of G9a/H3K9me3.

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References

Luger K, Hansen J . Nucleosome and chromatin fiber dynamics. Curr Opin Struct Biol. 2005; 15(2):188-96. DOI: 10.1016/j.sbi.2005.03.006. View

Alabert C, Groth A . Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol. 2012; 13(3):153-67. DOI: 10.1038/nrm3288. View

Bhaumik S, Smith E, Shilatifard A . Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol. 2007; 14(11):1008-16. DOI: 10.1038/nsmb1337. View

Grewal S, Jia S . Heterochromatin revisited. Nat Rev Genet. 2006; 8(1):35-46. DOI: 10.1038/nrg2008. View

Henikoff S, Shilatifard A . Histone modification: cause or cog?. Trends Genet. 2011; 27(10):389-96. DOI: 10.1016/j.tig.2011.06.006. View

Padeken J, Methot S, Gasser S . Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol. 2022; 23(9):623-640. PMC: 9099300. DOI: 10.1038/s41580-022-00483-w. View

Allshire R, Madhani H . Ten principles of heterochromatin formation and function. Nat Rev Mol Cell Biol. 2017; 19(4):229-244. PMC: 6822695. DOI: 10.1038/nrm.2017.119. View

Hyun K, Jeon J, Park K, Kim J . Writing, erasing and reading histone lysine methylations. Exp Mol Med. 2017; 49(4):e324. PMC: 6130214. DOI: 10.1038/emm.2017.11. View

Cao H, Li L, Yang D, Zeng L, Yewei X, Yu B . Recent progress in histone methyltransferase (G9a) inhibitors as anticancer agents. Eur J Med Chem. 2019; 179:537-546. DOI: 10.1016/j.ejmech.2019.06.072. View

10.

Charles M, Dhayalan A, Hsieh H, Coumar M . Insights for the design of protein lysine methyltransferase G9a inhibitors. Future Med Chem. 2019; 11(9):993-1014. DOI: 10.4155/fmc-2018-0396. View

11.

Haebe J, Bergin C, Sandouka T, Benoit Y . Emerging role of G9a in cancer stemness and promises as a therapeutic target. Oncogenesis. 2021; 10(11):76. PMC: 8590690. DOI: 10.1038/s41389-021-00370-7. View

12.

Ayrapetov M, Gursoy-Yuzugullu O, Xu C, Xu Y, Price B . DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin. Proc Natl Acad Sci U S A. 2014; 111(25):9169-74. PMC: 4078803. DOI: 10.1073/pnas.1403565111. View

13.

Ginjala V, Rodriguez-Colon L, Ganguly B, Gangidi P, Gallina P, Al-Hraishawi H . Protein-lysine methyltransferases G9a and GLP1 promote responses to DNA damage. Sci Rep. 2017; 7(1):16613. PMC: 5709370. DOI: 10.1038/s41598-017-16480-5. View

14.

Stewart-Morgan K, Petryk N, Groth A . Chromatin replication and epigenetic cell memory. Nat Cell Biol. 2020; 22(4):361-371. DOI: 10.1038/s41556-020-0487-y. View

15.

Aguilera A, Garcia-Muse T . Causes of genome instability. Annu Rev Genet. 2013; 47:1-32. DOI: 10.1146/annurev-genet-111212-133232. View

16.

Carr A, Lambert S . Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination. J Mol Biol. 2013; 425(23):4733-44. DOI: 10.1016/j.jmb.2013.04.023. View

17.

Gaillard H, Garcia-Muse T, Aguilera A . Replication stress and cancer. Nat Rev Cancer. 2015; 15(5):276-89. DOI: 10.1038/nrc3916. View

18.

Lecona E, Fernandez-Capetillo O . Replication stress and cancer: it takes two to tango. Exp Cell Res. 2014; 329(1):26-34. PMC: 4878650. DOI: 10.1016/j.yexcr.2014.09.019. View

19.

Bartkova J, Rezaei N, Liontos M, Karakaidos P, Kletsas D, Issaeva N . Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints. Nature. 2006; 444(7119):633-7. DOI: 10.1038/nature05268. View

20.

Di Micco R, Fumagalli M, Cicalese A, Piccinin S, Gasparini P, Luise C . Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication. Nature. 2006; 444(7119):638-42. DOI: 10.1038/nature05327. View