Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability.
Journal
Nature cell biology
ISSN: 1476-4679
Titre abrégé: Nat Cell Biol
Pays: England
ID NLM: 100890575
Informations de publication
Date de publication:
Jul 2023
Jul 2023
Historique:
received:
11
11
2022
accepted:
16
05
2023
medline:
17
7
2023
pubmed:
7
7
2023
entrez:
6
7
2023
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 37414849
doi: 10.1038/s41556-023-01167-z
pii: 10.1038/s41556-023-01167-z
pmc: PMC10344782
doi:
Substances chimiques
Histones
0
Heterochromatin
0
Chromatin
0
EHMT2 protein, human
EC 2.1.1.43
Histocompatibility Antigens
0
Histone-Lysine N-Methyltransferase
EC 2.1.1.43
KDM3A protein, human
EC 1.14.11.-
Jumonji Domain-Containing Histone Demethylases
EC 1.14.11.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1017-1032Subventions
Organisme : European Research Council
ID : 101078750
Pays : International
Informations de copyright
© 2023. The Author(s).
Références
Luger, K. & Hansen, J. C. Nucleosome and chromatin fiber dynamics. Curr. Opin. Struct. Biol. 15, 188–196 (2005).
pubmed: 15837178
doi: 10.1016/j.sbi.2005.03.006
Alabert, C. & Groth, A. Chromatin replication and epigenome maintenance. Nat. Rev. Mol. Cell Biol. 13, 153–167 (2012).
pubmed: 22358331
doi: 10.1038/nrm3288
Bhaumik, S. R., Smith, E. & Shilatifard, A. Covalent modifications of histones during development and disease pathogenesis. Nat. Struct. Mol. Biol. 14, 1008–1016 (2007).
pubmed: 17984963
doi: 10.1038/nsmb1337
Grewal, S. I. & Jia, S. Heterochromatin revisited. Nat. Rev. Genet. 8, 35–46 (2007).
pubmed: 17173056
doi: 10.1038/nrg2008
Henikoff, S. & Shilatifard, A. Histone modification: cause or cog? Trends Genet. 27, 389–396 (2011).
pubmed: 21764166
doi: 10.1016/j.tig.2011.06.006
Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022).
pubmed: 35562425
pmcid: 9099300
doi: 10.1038/s41580-022-00483-w
Allshire, R. C. & Madhani, H. D. Ten principles of heterochromatin formation and function. Nat. Rev. Mol. Cell Biol. 19, 229–244 (2018).
pubmed: 29235574
doi: 10.1038/nrm.2017.119
Hyun, K., Jeon, J., Park, K. & Kim, J. Writing, erasing and reading histone lysine methylations. Exp. Mol. Med 49, e324 (2017).
pubmed: 28450737
pmcid: 6130214
doi: 10.1038/emm.2017.11
Cao, H. et al. Recent progress in histone methyltransferase (G9a) inhibitors as anticancer agents. Eur. J. Med. Chem. 179, 537–546 (2019).
pubmed: 31276898
doi: 10.1016/j.ejmech.2019.06.072
Charles, M. R. C., Dhayalan, A., Hsieh, H. P. & Coumar, M. S. Insights for the design of protein lysine methyltransferase G9a inhibitors. Future Med. Chem. 11, 993–1014 (2019).
pubmed: 31141392
doi: 10.4155/fmc-2018-0396
Haebe, J. R., Bergin, C. J., Sandouka, T. & Benoit, Y. D. Emerging role of G9a in cancer stemness and promises as a therapeutic target. Oncogenesis 10, 76 (2021).
pubmed: 34775469
pmcid: 8590690
doi: 10.1038/s41389-021-00370-7
Ayrapetov, M. K., Gursoy-Yuzugullu, O., Xu, C., Xu, Y. & Price, B. D. DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin. Proc. Natl Acad. Sci. USA 111, 9169–9174 (2014).
pubmed: 24927542
pmcid: 4078803
doi: 10.1073/pnas.1403565111
Ginjala, V. et al. Protein-lysine methyltransferases G9a and GLP1 promote responses to DNA damage. Sci. Rep. 7, 16613 (2017).
pubmed: 29192276
pmcid: 5709370
doi: 10.1038/s41598-017-16480-5
Stewart-Morgan, K. R., Petryk, N. & Groth, A. Chromatin replication and epigenetic cell memory. Nat. Cell Biol. 22, 361–371 (2020).
pubmed: 32231312
doi: 10.1038/s41556-020-0487-y
Aguilera, A. & Garcia-Muse, T. Causes of genome instability. Annu. Rev. Genet 47, 1–32 (2013).
pubmed: 23909437
doi: 10.1146/annurev-genet-111212-133232
Carr, A. M. & Lambert, S. Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination. J. Mol. Biol. 425, 4733–4744 (2013).
pubmed: 23643490
doi: 10.1016/j.jmb.2013.04.023
Gaillard, H., Garcia-Muse, T. & Aguilera, A. Replication stress and cancer. Nat. Rev. Cancer 15, 276–289 (2015).
pubmed: 25907220
doi: 10.1038/nrc3916
Lecona, E. & Fernandez-Capetillo, O. Replication stress and cancer: it takes two to tango. Exp. Cell. Res. 329, 26–34 (2014).
pubmed: 25257608
pmcid: 4878650
doi: 10.1016/j.yexcr.2014.09.019
Macheret, M. & Halazonetis, T. D. DNA replication stress as a hallmark of cancer. Annu Rev. Pathol. Mech. 10, 425–448 (2015).
doi: 10.1146/annurev-pathol-012414-040424
Bartkova, J. et al. Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints. Nature 444, 633–637 (2006).
pubmed: 17136093
doi: 10.1038/nature05268
Di Micco, R. et al. Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication. Nature 444, 638–642 (2006).
pubmed: 17136094
doi: 10.1038/nature05327
Gorgoulis, V. G. et al. Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature 434, 907–913 (2005).
pubmed: 15829965
doi: 10.1038/nature03485
Nikolaev, S. I. et al. A single-nucleotide substitution mutator phenotype revealed by exome sequencing of human colon adenomas. Cancer Res. 72, 6279–6289 (2012).
pubmed: 23204322
doi: 10.1158/0008-5472.CAN-12-3869
Ghandi, M. et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019).
pubmed: 31068700
pmcid: 6697103
doi: 10.1038/s41586-019-1186-3
Bywater, M. J., Pearson, R. B., McArthur, G. A. & Hannan, R. D. Dysregulation of the basal RNA polymerase transcription apparatus in cancer. Nat. Rev. Cancer 13, 299–314 (2013).
pubmed: 23612459
doi: 10.1038/nrc3496
Villicana, C., Cruz, G. & Zurita, M. The basal transcription machinery as a target for cancer therapy. Cancer Cell Int. 14, 18 (2014).
pubmed: 24576043
pmcid: 3942515
doi: 10.1186/1475-2867-14-18
Lin, Y. L. & Pasero, P. Replication stress: from chromatin to immunity and beyond. Curr. Opin. Genet Dev. 71, 136–142 (2021).
pubmed: 34455237
doi: 10.1016/j.gde.2021.08.004
Lossaint, G. et al. Reciprocal regulation of p21 and Chk1 controls the cyclin D1-RB pathway to mediate senescence onset after G2 arrest. J. Cell Sci. 135, jcs259114 (2022).
pubmed: 35343565
doi: 10.1242/jcs.259114
Di Micco, R. et al. Interplay between oncogene-induced DNA damage response and heterochromatin in senescence and cancer. Nat. Cell Biol. 13, 292–302 (2011).
pubmed: 21336312
pmcid: 3918344
doi: 10.1038/ncb2170
Kosar, M. et al. Senescence-associated heterochromatin foci are dispensable for cellular senescence, occur in a cell type- and insult-dependent manner and follow expression of p16(ink4a). Cell Cycle 10, 457–468 (2011).
pubmed: 21248468
doi: 10.4161/cc.10.3.14707
Alabert, C. et al. Two distinct modes for propagation of histone PTMs across the cell cycle. Genes Dev. 29, 585–590 (2015).
pubmed: 25792596
pmcid: 4378191
doi: 10.1101/gad.256354.114
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
pubmed: 17512414
doi: 10.1016/j.cell.2007.05.009
Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).
pubmed: 17603471
pmcid: 2921165
doi: 10.1038/nature06008
Anders, S. Visualization of genomic data with the Hilbert curve. Bioinformatics 25, 1231–1235 (2009).
pubmed: 19297348
pmcid: 2677744
doi: 10.1093/bioinformatics/btp152
Maya-Mendoza, A. et al. Immortalised breast epithelia survive prolonged DNA replication stress and return to cycle from a senescent-like state. Cell Death Dis. 5, e1351 (2014).
pubmed: 25058425
pmcid: 4123104
doi: 10.1038/cddis.2014.315
Hozak, P. & Cook, P. R. Replication factories. Trends Cell Biol. 4, 48–52 (1994).
pubmed: 14731866
doi: 10.1016/0962-8924(94)90009-4
Meister, P., Taddei, A., Ponti, A., Baldacci, G. & Gasser, S. M. Replication foci dynamics: replication patterns are modulated by S-phase checkpoint kinases in fission yeast. EMBO J. 26, 1315–1326 (2007).
pubmed: 17304223
pmcid: 1817620
doi: 10.1038/sj.emboj.7601538
Dunleavy, E. M., Almouzni, G. & Karpen, G. H. H3.3 is deposited at centromeres in S phase as a placeholder for newly assembled CENP-A in G(1) phase. Nucleus 2, 146–157 (2011).
pubmed: 21738837
pmcid: 3127096
doi: 10.4161/nucl.2.2.15211
Wooten, M. et al. Superresolution imaging of chromatin fibers to visualize epigenetic information on replicative DNA. Nat. Protoc. 15, 1188–1208 (2020).
pubmed: 32051613
pmcid: 7255620
doi: 10.1038/s41596-019-0283-y
Nakamura, K. et al. Proteome dynamics at broken replication forks reveal a distinct ATM-directed repair response suppressing DNA double-strand break ubiquitination. Mol. Cell 81, 1084–1099 e1086 (2021).
pubmed: 33450211
pmcid: 7939521
doi: 10.1016/j.molcel.2020.12.025
Jasencakova, Z. et al. Replication stress interferes with histone recycling and predeposition marking of new histones. Mol. Cell 37, 736–743 (2010).
pubmed: 20227376
doi: 10.1016/j.molcel.2010.01.033
Roy, S., Luzwick, J. W. & Schlacher, K. Correction: SIRF: quantitative in situ analysis of protein interactions at DNA replication forks. J. Cell Biol. 217, 1553 (2018).
pubmed: 29572381
pmcid: 5881508
doi: 10.1083/JCB.20170912103212018c
Peters, A. H. et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12, 1577–1589 (2003).
pubmed: 14690609
doi: 10.1016/S1097-2765(03)00477-5
Rice, J. C. et al. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 12, 1591–1598 (2003).
pubmed: 14690610
doi: 10.1016/S1097-2765(03)00479-9
Shinkai, Y. & Tachibana, M. H3K9 methyltransferase G9a and the related molecule GLP. Genes Dev. 25, 781–788 (2011).
pubmed: 21498567
pmcid: 3078703
doi: 10.1101/gad.2027411
Esteve, P. O. et al. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev. 20, 3089–3103 (2006).
pubmed: 17085482
pmcid: 1635145
doi: 10.1101/gad.1463706
Sirbu, B. M. et al. Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry. J. Biol. Chem. 288, 31458–31467 (2013).
pubmed: 24047897
pmcid: 3814742
doi: 10.1074/jbc.M113.511337
Cao, Y. P. et al. Inhibition of G9a by a small molecule inhibitor, UNC0642, induces apoptosis of human bladder cancer cells. Acta Pharmacol. Sin. 40, 1076–1084 (2019).
pubmed: 30765842
pmcid: 6786297
doi: 10.1038/s41401-018-0205-5
Matsuoka, S. et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316, 1160–1166 (2007).
pubmed: 17525332
doi: 10.1126/science.1140321
Collins, R. E. et al. In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J. Biol. Chem. 280, 5563–5570 (2005).
pubmed: 15590646
doi: 10.1074/jbc.M410483200
Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000).
pubmed: 10949293
doi: 10.1038/35020506
Shogren-Knaak, M. et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847 (2006).
pubmed: 16469925
doi: 10.1126/science.1124000
Aygun, O., Mehta, S. & Grewal, S. I. HDAC-mediated suppression of histone turnover promotes epigenetic stability of heterochromatin. Nat. Struct. Mol. Biol. 20, 547–554 (2013).
pubmed: 23604080
pmcid: 3661211
doi: 10.1038/nsmb.2565
Taneja, N. et al. SNF2 family protein Fft3 suppresses nucleosome turnover to promote epigenetic inheritance and proper replication. Mol. Cell 66, 50–62 e56 (2017).
pubmed: 28318821
pmcid: 5407362
doi: 10.1016/j.molcel.2017.02.006
Kruhlak, M. J. et al. Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J. Cell Biol. 172, 823–834 (2006).
pubmed: 16520385
pmcid: 2063727
doi: 10.1083/jcb.200510015
Luijsterburg, M. S. et al. PARP1 links CHD2-mediated chromatin expansion and H3.3 deposition to DNA repair by non-homologous end-joining. Mol. Cell 61, 547–562 (2016).
pubmed: 26895424
pmcid: 4769320
doi: 10.1016/j.molcel.2016.01.019
Rother, M. B. et al. CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks. Nat. Commun. 11, 5775 (2020).
pubmed: 33188175
pmcid: 7666215
doi: 10.1038/s41467-020-19502-5
Smeenk, G. et al. Poly(ADP-ribosyl)ation links the chromatin remodeler SMARCA5/SNF2H to RNF168-dependent DNA damage signaling. J. Cell Sci. 126, 889–903 (2013).
pubmed: 23264744
Lo, C. S. Y. et al. SMARCAD1-mediated active replication fork stability maintains genome integrity. Sci. Adv. 7, eabe7804 (2021).
pubmed: 33952518
pmcid: 8099181
doi: 10.1126/sciadv.abe7804
Nakamura, K. et al. H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nat. Cell Biol. 21, 311–318 (2019).
pubmed: 30804502
pmcid: 6420097
doi: 10.1038/s41556-019-0282-9
Schlacher, K., Wu, H. & Jasin, M. A distinct replication fork protection pathway connects Fanconi anemia tumor suppressors to RAD51-BRCA1/2. Cancer Cell 22, 106–116 (2012).
pubmed: 22789542
pmcid: 3954744
doi: 10.1016/j.ccr.2012.05.015
Petermann, E., Woodcock, M. & Helleday, T. Chk1 promotes replication fork progression by controlling replication initiation. Proc. Natl Acad. Sci. USA 107, 16090–16095 (2010).
pubmed: 20805465
pmcid: 2941317
doi: 10.1073/pnas.1005031107
Zhong, Y. et al. The level of origin firing inversely affects the rate of replication fork progression. J. Cell Biol. 201, 373–383 (2013).
pubmed: 23629964
pmcid: 3639389
doi: 10.1083/jcb.201208060
Tirman, S. et al. Temporally distinct post-replicative repair mechanisms fill PRIMPOL-dependent ssDNA gaps in human cells. Mol. Cell 81, 4026–4040 e4028 (2021).
pubmed: 34624216
pmcid: 8555837
doi: 10.1016/j.molcel.2021.09.013
Berti, M., Cortez, D. & Lopes, M. The plasticity of DNA replication forks in response to clinically relevant genotoxic stress. Nat. Rev. Mol. Cell Biol. 21, 633–651 (2020).
pubmed: 32612242
doi: 10.1038/s41580-020-0257-5
Cong, K. & Cantor, S. B. Exploiting replication gaps for cancer therapy. Mol. Cell 82, 2363–2369 (2022).
pubmed: 35568026
pmcid: 9271608
doi: 10.1016/j.molcel.2022.04.023
Quinet, A. et al. PRIMPOL-mediated adaptive response suppresses replication fork reversal in BRCA-deficient cells. Mol. Cell 77, 461–474 e469 (2020).
pubmed: 31676232
pmcid: 7007862
doi: 10.1016/j.molcel.2019.10.008
Casciello, F., Windloch, K., Gannon, F. & Lee, J. S. Functional role of G9a histone methyltransferase in cancer. Front. Immunol. 6, 487 (2015).
pubmed: 26441991
pmcid: 4585248
doi: 10.3389/fimmu.2015.00487
Hua, K. T. et al. The H3K9 methyltransferase G9a is a marker of aggressive ovarian cancer that promotes peritoneal metastasis. Mol. Cancer 13, 189 (2014).
pubmed: 25115793
pmcid: 4260797
doi: 10.1186/1476-4598-13-189
Rahman, Z., Bazaz, M. R., Devabattula, G., Khan, M. A. & Godugu, C. Targeting H3K9 methyltransferase G9a and its related molecule GLP as a potential therapeutic strategy for cancer. J. Biochem. Mol. Toxicol. 35, e22674 (2021).
pubmed: 33283949
doi: 10.1002/jbt.22674
Watson, Z. L. et al. Histone methyltransferases EHMT1 and EHMT2 (GLP/G9A) maintain PARP inhibitor resistance in high-grade serous ovarian carcinoma. Clin. Epigenetics 11, 165 (2019).
pubmed: 31775874
pmcid: 6882350
doi: 10.1186/s13148-019-0758-2
Schwab, R. A., Nieminuszczy, J., Shin-ya, K. & Niedzwiedz, W. FANCJ couples replication past natural fork barriers with maintenance of chromatin structure. J. Cell Biol. 201, 33–48 (2013).
pubmed: 23530069
pmcid: 3613694
doi: 10.1083/jcb.201208009
Teng, Y. C. et al. ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress. Nat. Commun. 12, 3887 (2021).
pubmed: 34162889
pmcid: 8222256
doi: 10.1038/s41467-021-24206-5
Carraro, M. et al. DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network. Mol. Cell 83, 1075–1092.e9 (2023).
pubmed: 36868228
pmcid: 10114496
doi: 10.1016/j.molcel.2023.02.009
Feng, G. et al. Replication fork stalling elicits chromatin compaction for the stability of stalling replication forks. Proc. Natl Acad. Sci. USA 116, 14563–14572 (2019).
pubmed: 31262821
pmcid: 6642376
doi: 10.1073/pnas.1821475116
Ramachandran, S. & Henikoff, S. Transcriptional regulators compete with nucleosomes post-replication. Cell 165, 580–592 (2016).
pubmed: 27062929
pmcid: 4855302
doi: 10.1016/j.cell.2016.02.062
Reveron-Gomez, N. et al. Accurate recycling of parental histones reproduces the histone modification landscape during DNA replication. Mol. Cell 72, 239–249 e235 (2018).
pubmed: 30146316
pmcid: 6202308
doi: 10.1016/j.molcel.2018.08.010
Stewart-Morgan, K. R., Reveron-Gomez, N. & Groth, A. Transcription restart establishes chromatin accessibility after DNA replication. Mol. Cell 75, 408–414 (2019).
pubmed: 31348880
doi: 10.1016/j.molcel.2019.06.035
Fnu, S. et al. Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining. Proc. Natl Acad. Sci. USA 108, 540–545 (2011).
pubmed: 21187428
doi: 10.1073/pnas.1013571108
Jiang, Y. et al. Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation. Nat. Cell Biol. 17, 1158–1168 (2015).
pubmed: 26237645
pmcid: 4800990
doi: 10.1038/ncb3209
Kim, H. S., Rhee, D. K. & Jang, Y. K. Methylations of histone H3 lysine 9 and lysine 36 are functionally linked to DNA replication checkpoint control in fission yeast. Biochem. Biophys. Res. Commun. 368, 419–425 (2008).
pubmed: 18252195
doi: 10.1016/j.bbrc.2008.01.104
Yuan, S. et al. Global regulation of the histone mark H3K36me2 underlies epithelial plasticity and metastatic progression. Cancer Discov. 10, 854–871 (2020).
pubmed: 32188706
pmcid: 7269857
doi: 10.1158/2159-8290.CD-19-1299
Kuo, A. J. et al. NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. Mol. Cell 44, 609–620 (2011).
pubmed: 22099308
pmcid: 3222870
doi: 10.1016/j.molcel.2011.08.042
Sui, Y., Gu, R. & Janknecht, R. Crucial functions of the JMJD1/KDM3 epigenetic regulators in cancer. Mol. Cancer Res 19, 3–13 (2021).
pubmed: 32605929
doi: 10.1158/1541-7786.MCR-20-0404
Whetstine, J. R. et al. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125, 467–481 (2006).
pubmed: 16603238
doi: 10.1016/j.cell.2006.03.028
Becker, J. R. et al. BARD1 reads H2A lysine 15 ubiquitination to direct homologous recombination. Nature 596, 433–437 (2021).
pubmed: 34321663
doi: 10.1038/s41586-021-03776-w
Hu, Q. et al. Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation. Nature 597, E5 (2021).
pubmed: 34404953
doi: 10.1038/s41586-021-03881-w
Wu, W. et al. Interaction of BARD1 and HP1 is required for BRCA1 retention at sites of DNA damage. Cancer Res. 75, 1311–1321 (2015).
pubmed: 25634209
pmcid: 5003120
doi: 10.1158/0008-5472.CAN-14-2796
Padeken, J. et al. Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression. Genes Dev. 33, 436–451 (2019).
pubmed: 30804228
pmcid: 6446544
doi: 10.1101/gad.322495.118
Cai, L., Ma, X., Huang, Y., Zou, Y. & Chen, X. Aberrant histone methylation and the effect of Suv39H1 siRNA on gastric carcinoma. Oncol. Rep. 31, 2593–2600 (2014).
pubmed: 24737085
doi: 10.3892/or.2014.3135
Chiba, T. et al. Histone lysine methyltransferase SUV39H1 is a potent target for epigenetic therapy of hepatocellular carcinoma. Int. J. Cancer 136, 289–298 (2015).
pubmed: 24844570
doi: 10.1002/ijc.28985
Park, Y. S. et al. The global histone modification pattern correlates with cancer recurrence and overall survival in gastric adenocarcinoma. Ann. Surg. Oncol. 15, 1968–1976 (2008).
pubmed: 18470569
doi: 10.1245/s10434-008-9927-9
Xia, R. et al. High expression of H3K9me3 is a strong predictor of poor survival in patients with salivary adenoid cystic carcinoma. Arch. Pathol. Lab Med 137, 1761–1769 (2013).
pubmed: 24283856
doi: 10.5858/arpa.2012-0704-OA
Yokoyama, Y. et al. Cancer-associated upregulation of histone H3 lysine 9 trimethylation promotes cell motility in vitro and drives tumor formation in vivo. Cancer Sci. 104, 889–895 (2013).
pubmed: 23557258
pmcid: 7657232
doi: 10.1111/cas.12166
Gyorffy, B. Discovery and ranking of the most robust prognostic biomarkers in serous ovarian cancer. Geroscience https://doi.org/10.1007/s11357-023-00742-4 (2023).
Gyorffy, B., Lanczky, A. & Szallasi, Z. Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients. Endocr. Relat. Cancer 19, 197–208 (2012).
pubmed: 22277193
doi: 10.1530/ERC-11-0329
Labit, H. et al. A simple and optimized method of producing silanized surfaces for FISH and replication mapping on combed DNA fibers. Biotechniques 45, 649–652 (2008).
pubmed: 19238795
doi: 10.2144/000113002
Sørensen, C. S. et al. Chk1 regulates the S phase checkpoint by coupling the physiological turnover and ionizing radiation-induced accelerated proteolysis of Cdc25A. Cancer Cell 3, 247–258 (2003).
pubmed: 12676583
doi: 10.1016/S1535-6108(03)00048-5
Jakobsen, J. S. et al. Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Res. 23, 592–603 (2013).
pubmed: 23403033
pmcid: 3613577
doi: 10.1101/gr.146399.112
Kharchenko, P. V., Tolstorukov, M. Y. & Park, P. J. Design and analysis of ChIP–seq experiments for DNA-binding proteins. Nat. Biotechnol. 26, 1351–1359 (2008).
pubmed: 19029915
pmcid: 2597701
doi: 10.1038/nbt.1508
Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S. & Karolchik, D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26, 2204–2207 (2010).
pubmed: 20639541
pmcid: 2922891
doi: 10.1093/bioinformatics/btq351
Kent, W. J. et al. The human genome browser at UCSC. Genome Res 12, 996–1006 (2002).
pubmed: 12045153
pmcid: 186604
doi: 10.1101/gr.229102
Raney, B. J. et al. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30, 1003–1005 (2014).
pubmed: 24227676
doi: 10.1093/bioinformatics/btt637
Liu, T. et al. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 12, R83 (2011).
pubmed: 21859476
pmcid: 3245621
doi: 10.1186/gb-2011-12-8-r83
Shin, H., Liu, T., Manrai, A. K. & Liu, X. S. CEAS: cis-regulatory element annotation system. Bioinformatics 25, 2605–2606 (2009).
pubmed: 19689956
doi: 10.1093/bioinformatics/btp479