Making it or breaking it: DNA methylation and genome integrity (2024)

1. Chatterjee N and Walker GC (2017) Mechanisms of DNA damage, repair, and mutagenesis. Environ. Mol. Mutagen58, 235–263, 10.1002/em.22087 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

2. Jackson SP and Bartek J (2009) The DNA-damage response in human biology and disease. Nature461, 1071–1078, 10.1038/nature08467 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

3. Tubbs A and Nussenzweig A (2017) Endogenous DNA damage as a source of genomic instability in cancer. Cell168, 644–656, 10.1016/j.cell.2017.01.002 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

4. Puget N, Miller KM and Legube G (2019) Non-canonical DNA/RNA structures during transcription-coupled double-strand break repair: roadblocks or bona fide repair intermediates?DNA Repair (Amst.)81, 102661, 10.1016/j.dnarep.2019.102661 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

5. Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal Aet al. (2019) Systematic bromodomain protein screens identify hom*ologous recombination and R-loop suppression pathways involved in genome integrity. Genes Dev. 33, 1751–1774 [PMC free article] [PubMed] [Google Scholar]

6. Jeggo PA, Pearl LH and Carr AM (2016) DNA repair, genome stability and cancer: a historical perspective. Nat. Rev. Cancer16, 35–42, 10.1038/nrc.2015.4 [PubMed] [CrossRef] [Google Scholar]

7. Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet13, 484–492, 10.1038/nrg3230 [PubMed] [CrossRef] [Google Scholar]

8. Goto T and Monk M (1998) Regulation of X-chromosome inactivation in development in mice and humans. Microbiol. Mol. Biol. Rev62, 362–378, 10.1128/MMBR.62.2.362-378.1998 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

9. Hermann A, Goyal R and Jeltsch A (2004) The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J. Biol. Chem279, 48350–48359, 10.1074/jbc.M403427200 [PubMed] [CrossRef] [Google Scholar]

10. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S and Jacobsen SE (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science317, 1760–1764, 10.1126/science.1147939 [PubMed] [CrossRef] [Google Scholar]

11. Okano M, Bell DW, Haber DA and Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell99, 247–257, 10.1016/S0092-8674(00)81656-6 [PubMed] [CrossRef] [Google Scholar]

12. Hata K, Okano M, Lei H and Li E (2002) Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development129, 1983–1993 [PubMed] [Google Scholar]

13. Bourc’his D, Xu G-L, Lin C-S, Bollman B and Bestor TH (2001) Dnmt3L and the establishment of maternal genomic imprints. Science294, 2536, 10.1126/science.1065848 [PubMed] [CrossRef] [Google Scholar]

14. Goll MG, Kirpekar F, Maggert KA, Yoder JA, Hsieh CL, Zhang Xet al. (2006) Methylation of tRNAAsp by the DNA methyltransferase hom*olog Dnmt2. Science311, 395–398, 10.1126/science.1120976 [PubMed] [CrossRef] [Google Scholar]

15. Xhemalce B (2013) From histones to RNA: role of methylation in cancer. Brief. Funct. Genomics12, 244–253, 10.1093/bfgp/els064 [PubMed] [CrossRef] [Google Scholar]

16. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Yet al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science324, 930–935, 10.1126/science.1170116 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

17. Iyer LM, Tahiliani M, Rao A and Aravind L (2009) Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle8, 1698–1710, 10.4161/cc.8.11.8580 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

18. He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Qet al. (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science333, 1303–1307, 10.1126/science.1210944 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

19. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JAet al. (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science333, 1300–1303, 10.1126/science.1210597 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

20. Maiti A and Drohat AC (2011) Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. J. Biol. Chem286, 35334–35338, 10.1074/jbc.C111.284620 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

21. Li Z, Gu TP, Weber AR, Shen JZ, Li BZ, Xie ZGet al. (2015) Gadd45a promotes DNA demethylation through TDG. Nucleic Acids Res. 43, 3986–3997, 10.1093/nar/gkv283 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

22. Rai K, Huggins IJ, James SR, Karpf AR, Jones DA and Cairns BR (2008) DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell135, 1201–1212, 10.1016/j.cell.2008.11.042 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

23. Wu SC and Zhang Y (2010) Active DNA demethylation: many roads lead to Rome. Nat. Rev. Mol. Cell Biol11, 607–620, 10.1038/nrm2950 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

24. Kagiwada S, Kurimoto K, Hirota T, Yamaji M and Saitou M (2013) Replication-coupled passive DNA demethylation for the erasure of genome imprints in mice. EMBO J. 32, 340–353, 10.1038/emboj.2012.331 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

25. Hudson NO and Buck-Koehntop BA (2018) Zinc finger readers of methylated DNA. Molecules23, 10.3390/molecules23102555 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

26. Vilas CK, Emery LE, Denchi EL and Miller KM (2018) Caught with one’s zinc fingers in the genome integrity cookie jar. Trends Genet. 34, 313–325, 10.1016/j.tig.2017.12.011 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

27. Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RMet al. (2017) Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucleic Acids Res. 45, 2503–2515, 10.1093/nar/gkx057 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

28. Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed Set al. (2017) Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science356, eaaj2239, 10.1126/science.aaj2239 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

29. Ginder GD and Williams DC Jr (2018) Readers of DNA methylation, the MBD family as potential therapeutic targets. Pharmacol. Ther184, 98–111, 10.1016/j.pharmthera.2017.11.002 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

30. Mahmood N and Rabbani SA (2019) DNA methylation readers and cancer: mechanistic and therapeutic applications. Front. Oncol9, 489, 10.3389/fonc.2019.00489 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

31. Zhang Y, Ng HH, Erdjument-Bromage H, Tempst P, Bird A and Reinberg D (1999) Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev. 13, 1924–1935, 10.1101/gad.13.15.1924 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

32. Stirzaker C, Song JZ, Ng W, Du Q, Armstrong NJ, Locke WJet al. (2017) Methyl-CpG-binding protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer. Oncogene36, 1328–1338, 10.1038/onc.2016.297 [PubMed] [CrossRef] [Google Scholar]

33. Hendrich B and Bird A (1998) Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol18, 6538–6547, 10.1128/MCB.18.11.6538 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

34. Leighton G and Williams DC Jr (2019) The Methyl-CpG-binding domain 2 and 3 proteins and formation of the nucleosome remodeling and deacetylase complex. J. Mol. Biol432, 1624–1639, 10.1016/j.jmb.2019.10.007 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

35. Hendrich B, Hardeland U, Ng HH, Jiricny J and Bird A (1999) The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature401, 301–304, 10.1038/45843 [PubMed] [CrossRef] [Google Scholar]

36. Kimura H and Shiota K (2003) Methyl-CpG-binding protein, MeCP2, is a target molecule for maintenance DNA methyltransferase, Dnmt1. J. Biol. Chem278, 4806–4812, 10.1074/jbc.M209923200 [PubMed] [CrossRef] [Google Scholar]

37. Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo TAet al. (2007) The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature450, 908–912, 10.1038/nature06397 [PubMed] [CrossRef] [Google Scholar]

38. Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu Bet al. (2014) Structural basis for hydroxymethylcytosine recognition by the SRA domain of UHRF2. Mol. Cell54, 879–886, 10.1016/j.molcel.2014.04.003 [PubMed] [CrossRef] [Google Scholar]

39. Prokhortchouk A, Hendrich B, Jorgensen H, Ruzov A, Wilm M, Georgiev Get al. (2001) The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor. Genes Dev. 15, 1613–1618 [PMC free article] [PubMed] [Google Scholar]

40. Filion GJ, Zhenilo S, Salozhin S, Yamada D, Prokhortchouk E and Defossez PA (2006) A family of human zinc finger proteins that bind methylated DNA and repress transcription. Mol. Cell. Biol26, 169–181, 10.1128/MCB.26.1.169-181.2006 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

41. Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IAet al. (2012) Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso. Proc. Natl. Acad. Sci. U.S.A109, 15229–15234, 10.1073/pnas.1213726109 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

42. Hodges AJ, Hudson NO and Buck-Koehntop BA (2019) Cys2His2 zinc finger methyl-CpG binding proteins: getting a handle on methylated DNA. J. Mol. Biol432, 1640–1660, 10.1016/j.jmb.2019.09.012 [PubMed] [CrossRef] [Google Scholar]

43. Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli Fet al. (2012) Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res. 22, 1680–1688, 10.1101/gr.136101.111 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

44. Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG and Cheng X (2017) Structural basis for the versatile and methylation-dependent binding of CTCF to DNA. Mol. Cell66, 711.e3–720.e3, 10.1016/j.molcel.2017.05.004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

45. Lang F, Li X, Zheng W, Li Z, Lu D, Chen Get al. (2017) CTCF prevents genomic instability by promoting hom*ologous recombination-directed DNA double-strand break repair. Proc. Natl. Acad. Sci. U.S.A114, 10912–10917, 10.1073/pnas.1704076114 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

46. Hilmi K, Jangal M, Marques M, Zhao T, Saad A, Zhang Cet al. (2017) CTCF facilitates DNA double-strand break repair by enhancing hom*ologous recombination repair. Sci. Adv3, e1601898, 10.1126/sciadv.1601898 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

47. Xiao CL, Zhu S, He M, Chen D, Zhang Q, Chen Yet al. (2018) N(6)-Methyladenine DNA modification in the human genome. Mol. Cell71, 306.e7–318.e7, 10.1016/j.molcel.2018.06.015 [PubMed] [CrossRef] [Google Scholar]

48. Woodco*ck CB, Yu D, Hajian T, Li J, Huang Y, Dai Net al. (2019) Human MettL3-MettL14 complex is a sequence-specific DNA adenine methyltransferase active on single-strand and unpaired DNA in vitro. Cell Discov. 5, 63, 10.1038/s41421-019-0136-4 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

49. Hao Z, Wu T, Cui X, Zhu P, Tan C, Dou Xet al. (2020) N(6)-Deoxyadenosine methylation in mammalian mitochondrial DNA. Mol. Cell78, 382–395.e8, 10.1016/j.molcel.2020.02.018 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

50. Xiong J, Ye TT, Ma CJ, Cheng QY, Yuan BF and Feng YQ (2019) N(6)-Hydroxymethyladenine: a hydroxylation derivative of N6-methyladenine in genomic DNA of mammals. Nucleic Acids Res. 47, 1268–1277, 10.1093/nar/gky1218 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

51. Greenblatt MS, Bennett WP, Hollstein M and Harris CC (1994) Mutations in the p53 tumor suppressor gene: clues to cancer etiology and molecular pathogenesis. Cancer Res. 54, 4855–4878 [PubMed] [Google Scholar]

52. Sassa A, Kanemaru Y, Kamosh*ta N, Honma M and Yasui M (2016) Mutagenic consequences of cytosine alterations site-specifically embedded in the human genome. Genes Environ. 38, 17, 10.1186/s41021-016-0045-9 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

53. Tommasi S, Denissenko MF and Pfeifer GP (1997) Sunlight induces pyrimidine dimers preferentially at 5-methylcytosine bases. Cancer Res. 57, 4727–4730 [PubMed] [Google Scholar]

54. Deniz Ö, Frost JM and Branco MR (2019) Regulation of transposable elements by DNA modifications. Nat. Rev. Genet20, 417–431, 10.1038/s41576-019-0117-3 [PubMed] [CrossRef] [Google Scholar]

55. Rodic N, Sharma R, Sharma R, Zampella J, Dai L, Taylor MSet al. (2014) Long interspersed element-1 protein expression is a hallmark of many human cancers. Am. J. Pathol184, 1280–1286, 10.1016/j.ajpath.2014.01.007 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

56. Moldovan GL, Pfander B and Jentsch S (2007) PCNA, the maestro of the replication fork. Cell129, 665–679, 10.1016/j.cell.2007.05.003 [PubMed] [CrossRef] [Google Scholar]

57. Zeman MK and Cimprich KA (2014) Causes and consequences of replication stress. Nat. Cell Biol16, 2–9, 10.1038/ncb2897 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

58. Mirkin EV and Mirkin SM (2007) Replication fork stalling at natural impediments. Microbiol. Mol. Biol. Rev71, 13–35, 10.1128/MMBR.00030-06 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

59. Chuang LS, Ian HI, Koh TW, Ng HH, Xu G and Li BF (1997) Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science277, 1996–2000, 10.1126/science.277.5334.1996 [PubMed] [CrossRef] [Google Scholar]

60. Pradhan S and Kim GD (2002) The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity. EMBO J. 21, 779–788, 10.1093/emboj/21.4.779 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

61. Xia J, Chiu LY, Nehring RB, Bravo Nunez MA, Mei Q, Perez Met al. (2019) Bacteria-to-human protein networks reveal origins of endogenous DNA damage. Cell176, 127.e24–143.e24, 10.1016/j.cell.2018.12.008 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

62. Ren W, Fan H, Grimm SA, Guo Y, Kim JJ, Yin Jet al. (2020) Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation. Proc. Natl. Acad. Sci. U.S.A117, 18439–18447, 10.1073/pnas.2009316117 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

63. Jones PA and Gonzalgo ML (1997) Altered DNA methylation and genome instability: a new pathway to cancer?Proc. Natl. Acad. Sci. U.S.A94, 2103–2105, 10.1073/pnas.94.6.2103 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

64. Chen T, Hevi S, Gay F, Tsujimoto N, He T, Zhang Bet al. (2007) Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nat. Genet39, 391–396, 10.1038/ng1982 [PubMed] [CrossRef] [Google Scholar]

65. Okano M and Li E (2002) Genetic analyses of DNA methyltransferase genes in mouse model system. J. Nutr132, 2462S–2465S, 10.1093/jn/132.8.2462S [PubMed] [CrossRef] [Google Scholar]

66. Ha K, Lee GE, Palii SS, Brown KD, Takeda Y, Liu Ket al. (2011) Rapid and transient recruitment of DNMT1 to DNA double-strand breaks is mediated by its interaction with multiple components of the DNA damage response machinery. Hum. Mol. Genet20, 126–140, 10.1093/hmg/ddq451 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

67. Mortusewicz O, Schermelleh L, Walter J, Cardoso MC and Leonhardt H (2005) Recruitment of DNA methyltransferase I to DNA repair sites. Proc. Natl. Acad. Sci. U.S.A102, 8905–8909, 10.1073/pnas.0501034102 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

68. O’Hagan HM, Mohammad HP and Baylin SB (2008) Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island. PLoS Genet. 4, e1000155, 10.1371/journal.pgen.1000155 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

69. Lee GE, Kim JH, Taylor M and Muller MT (2010) DNA methyltransferase 1-associated protein (DMAP1) is a co-repressor that stimulates DNA methylation globally and locally at sites of double strand break repair. J. Biol. Chem285, 37630–37640, 10.1074/jbc.M110.148536 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

70. Morano A, Angrisano T, Russo G, Landi R, Pezone A, Bartollino Set al. (2014) Targeted DNA methylation by hom*ology-directed repair in mammalian cells. Transcription reshapes methylation on the repaired gene. Nucleic Acids Res. 42, 804–821, 10.1093/nar/gkt920 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

71. Jackson-Grusby L, Beard C, Possemato R, Tudor M, Fambrough D, Csankovszki Get al. (2001) Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat. Genet27, 31–39, 10.1038/83730 [PubMed] [CrossRef] [Google Scholar]

72. Georgia S, Kanji M and Bhushan A (2013) DNMT1 represses p53 to maintain progenitor cell survival during pancreatic organogenesis. Genes Dev. 27, 372–377 [PMC free article] [PubMed] [Google Scholar]

73. Loughery JEP, Dunne PD, O’Neill KM, Meehan RR, McDaid JR and Walsh CP (2011) DNMT1 deficiency triggers mismatch repair defects in human cells through depletion of repair protein levels in a process involving the DNA damage response. Hum. Mol. Genet20, 3241–3255, 10.1093/hmg/ddr236 [PubMed] [CrossRef] [Google Scholar]

74. Xia L, Huang W, Bellani M, Seidman MM, Wu K, Fan Det al. (2017) CHD4 has oncogenic functions in initiating and maintaining epigenetic suppression of multiple tumor suppressor genes. Cancer Cell31, 653.e7–668.e7, 10.1016/j.ccell.2017.04.005 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

75. Cuozzo C, Porcellini A, Angrisano T, Morano A, Lee B, Di Pardo Aet al. (2007) DNA damage, hom*ology-directed repair, and DNA methylation. PLoS Genet. 3, e110, 10.1371/journal.pgen.0030110 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

76. Kafer GR, Li X, Horii T, Suetake I, Tajima S, Hatada Iet al. (2016) 5-Hydroxymethylcytosine marks sites of DNA damage and promotes genome stability. Cell Rep. 14, 1283–1292, 10.1016/j.celrep.2016.01.035 [PubMed] [CrossRef] [Google Scholar]

77. Jiang D, Wei S, Chen F, Zhang Y and Li J (2017) TET3-mediated DNA oxidation promotes ATR-dependent DNA damage response. EMBO Rep. 18, 781–796, 10.15252/embr.201643179 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

78. Jiang D, Zhang Y, Hart RP, Chen J, Herrup K and Li J (2015) Alteration in 5-hydroxymethylcytosine-mediated epigenetic regulation leads to Purkinje cell vulnerability in ATM deficiency. Brain138, 3520–3536, 10.1093/brain/awv284 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

79. Lahtz C and Pfeifer GP (2011) Epigenetic changes of DNA repair genes in cancer. J. Mol. Cell Biol3, 51–58, 10.1093/jmcb/mjq053 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

80. Turcan S, Rohle D, Goenka A, Walsh LA, Fang F, Yilmaz Eet al. (2012) IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature483, 479–483, 10.1038/nature10866 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

81. Kang JH, Kim SJ, Noh DY, Park IA, Choe KJ, Yoo OJet al. (2001) Methylation in the p53 promoter is a supplementary route to breast carcinogenesis: correlation between CpG methylation in the p53 promoter and the mutation of the p53 gene in the progression from ductal carcinoma in situ to invasive ductal carcinoma. Lab. Invest81, 573–579, 10.1038/labinvest.3780266 [PubMed] [CrossRef] [Google Scholar]

82. Chmelarova M, Krepinska E, Spacek J, Laco J, Beranek M and Palicka V (2013) Methylation in the p53 promoter in epithelial ovarian cancer. Clin. Transl. Oncol15, 160–163, 10.1007/s12094-012-0894-z [PubMed] [CrossRef] [Google Scholar]

83. Esteller M, Silva JM, Dominguez G, Bonilla F, Matias-Guiu X, Lerma Eet al. (2000) Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors. J. Natl. Cancer Inst92, 564–569, 10.1093/jnci/92.7.564 [PubMed] [CrossRef] [Google Scholar]

84. Polak P, Kim J, Braunstein LZ, Karlic R, Haradhavala NJ, Tiao Get al. (2017) A mutational signature reveals alterations underlying deficient hom*ologous recombination repair in breast cancer. Nat. Genet49, 1476–1486, 10.1038/ng.3934 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

85. Jin B and Robertson KD (2013) DNA methyltransferases, DNA damage repair, and cancer. Adv. Exp. Med. Biol754, 3–29, 10.1007/978-1-4419-9967-21 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

86. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DEet al. (2010) DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med363, 2424–2433, 10.1056/NEJMoa1005143 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

87. Yan X-J, Xu J, Gu Z-H, Pan C-M, Lu G, Shen Yet al. (2011) Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat. Genet43, 309–315, 10.1038/ng.788 [PubMed] [CrossRef] [Google Scholar]

88. Roller A, Grossmann V, Bacher U, Poetzinger F, Weissmann S, Nadarajah Net al. (2013) Landmark analysis of DNMT3A mutations in hematological malignancies. Leukemia27, 1573–1578, 10.1038/leu.2013.65 [PubMed] [CrossRef] [Google Scholar]

89. Shah MY and Licht JD (2011) DNMT3A mutations in acute myeloid leukemia. Nat. Genet43, 289–290, 10.1038/ng0411-289 [PubMed] [CrossRef] [Google Scholar]

90. Park DJ, Kwon A, Cho BS, Kim HJ, Hwang KA, Kim Met al. (2020) Characteristics of DNMT3A mutations in acute myeloid leukemia. Blood Res. 55, 17–26, 10.5045/br.2020.55.1.17 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

91. Ferreira HJ, Heyn H, Vizoso M, Moutinho C, Vidal E, Gomez Aet al. (2016) DNMT3A mutations mediate the epigenetic reactivation of the leukemogenic factor MEIS1 in acute myeloid leukemia. Oncogene35, 3079–3082, 10.1038/onc.2015.359 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

92. Kohlmann A, Schoch C, Dugas M, Schnittger S, Hiddemann W, Kern Wet al. (2005) New insights into MLL gene rearranged acute leukemias using gene expression profiling: shared pathways, lineage commitment, and partner genes. Leukemia19, 953–964, 10.1038/sj.leu.2403746 [PubMed] [CrossRef] [Google Scholar]

93. Langemeijer SM, Kuiper RP, Berends M, Knops R, Aslanyan MG, Massop Met al. (2009) Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat. Genet41, 838–842, 10.1038/ng.391 [PubMed] [CrossRef] [Google Scholar]

94. Ko M, Huang Y, Jankowska AM, Pape UJ, Tahiliani M, Bandukwala HSet al. (2010) Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature468, 839–843, 10.1038/nature09586 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

95. Cimmino L, Dawlaty MM, Ndiaye-Lobry D, Yap YS, Bakogianni S, Yu Yet al. (2015) TET1 is a tumor suppressor of hematopoietic malignancy. Nat. Immunol16, 653–662, 10.1038/ni.3148 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

96. Huang H, Jiang X, Li Z, Li Y, Song CX, He Cet al. (2013) TET1 plays an essential oncogenic role in MLL-rearranged leukemia. Proc. Natl. Acad. Sci. U.S.A110, 11994–11999, 10.1073/pnas.1310656110 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

97. Subramaniam D, Thombre R, Dhar A and Anant S (2014) DNA methyltransferases: a novel target for prevention and therapy. Front. Oncol4, 80, 10.3389/fonc.2014.00080 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

98. Ganesan A, Arimondo PB, Rots MG, Jeronimo C and Berdasco M (2019) The timeline of epigenetic drug discovery: from reality to dreams. Clin. Epigenet11, 174, 10.1186/s13148-019-0776-0 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

99. Christman JK (2002) 5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy. Oncogene21, 5483–5495, 10.1038/sj.onc.1205699 [PubMed] [CrossRef] [Google Scholar]

100. Santi DV, Norment A and Garrett CE (1984) Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine. Proc. Natl. Acad. Sci. U.S.A81, 6993–6997, 10.1073/pnas.81.22.6993 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

101. Palii SS, Van Emburgh BO, Sankpal UT, Brown KD and Robertson KD (2008) DNA methylation inhibitor 5-Aza-2′-deoxycytidine induces reversible genome-wide DNA damage that is distinctly influenced by DNA methyltransferases 1 and 3B. Mol. Cell. Biol28, 752–771, 10.1128/MCB.01799-07 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

102. Orta ML, Calderon-Montano JM, Dominguez I, Pastor N, Burgos-Moron E, Lopez-Lazaro Met al. (2013) 5-Aza-2′-deoxycytidine causes replication lesions that require Fanconi anemia-dependent hom*ologous recombination for repair. Nucleic Acids Res. 41, 5827–5836, 10.1093/nar/gkt270 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

103. Zambrano P, Segura-Pacheco B, Perez-Cardenas E, Cetina L, Revilla-Vazquez A, Taja-Chayeb Let al. (2005) A phase I study of hydralazine to demethylate and reactivate the expression of tumor suppressor genes. BMC Cancer5, 44, 10.1186/1471-2407-5-44 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

104. Cheng JC, Matsen CB, Gonzales FA, Ye W, Greer S, Marquez VEet al. (2003) Inhibition of DNA methylation and reactivation of silenced genes by zebularine. J. Natl. Cancer Inst95, 399–409, 10.1093/jnci/95.5.399 [PubMed] [CrossRef] [Google Scholar]

105. Cheng JC, Weisenberger DJ, Gonzales FA, Liang G, Xu GL, Hu YGet al. (2004) Continuous zebularine treatment effectively sustains demethylation in human bladder cancer cells. Mol. Cell. Biol24, 1270–1278, 10.1128/MCB.24.3.1270-1278.2004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

106. Johnson WD, Harder JB, Naylor J, McCormick DL, Detrisac CJ, Glaze ERet al. (2006) A pharmaco*kinetic/pharmacodynamic approach to evaluating the safety of zebularine in non-human primates. Cancer Res. 66, 309–310 [Google Scholar]

107. Zacharioudakis E, Agarwal P, Bartoli A, Abell N, Kunalingam L, Bergoglio Vet al. (2017) Chromatin regulates genome targeting with cisplatin. Angew. Chem. Int. Ed. Engl56, 6483–6487, 10.1002/anie.201701144 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

108. Pohlmann P, DiLeone LP, Cancella AI, Caldas AP, Dal Lago L, Campos O Jret al. (2002) Phase II trial of cisplatin plus decitabine, a new DNA hypomethylating agent, in patients with advanced squamous cell carcinoma of the cervix. Am. J. Clin. Oncol25, 496–501, 10.1097/00000421-200210000-00015 [PubMed] [CrossRef] [Google Scholar]

109. Viet CT, Dang D, Achdjian S, Ye Y, Katz SG and Schmidt BL (2014) Decitabine rescues cisplatin resistance in head and neck squamous cell carcinoma. PLoS ONE9, e112880, 10.1371/journal.pone.0112880 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

110. Khandelwal M, Anand V, Appunni S, Seth A, Singh P, Mathur Set al. (2018) Decitabine augments cytotoxicity of cisplatin and doxorubicin to bladder cancer cells by activating hippo pathway through RASSF1A. Mol. Cell. Biochem446, 105–114, 10.1007/s11010-018-3278-z [PubMed] [CrossRef] [Google Scholar]

111. Benson EA, Skaar TC, Liu Y, Nephew KP and Matei D (2015) Carboplatin with decitabine therapy, in recurrent platinum resistant ovarian cancer, alters circulating miRNAs concentrations: a pilot study. PLoS ONE10, e0141279, 10.1371/journal.pone.0141279 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

112. Muvarak NE, Chowdhury K, Xia L, Robert C, Choi EY, Cai Yet al. (2016) Enhancing the cytotoxic effects of PARP inhibitors with DNA demethylating agents - a potential therapy for cancer. Cancer Cell30, 637–650, 10.1016/j.ccell.2016.09.002 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

113. Caron MC, Sharma AK, O’Sullivan J, Myler LR, Ferreira MT, Rodrigue Aet al. (2019) Poly(ADP-ribose) polymerase-1 antagonizes DNA resection at double-strand breaks. Nat. Commun10, 2954, 10.1038/s41467-019-10741-9 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

114. Luijsterburg MS, de Krijger I, Wiegant WW, Shah RG, Smeenk G, de Groot AJLet al. (2016) PARP1 links CHD2-mediated chromatin expansion and H3.3 deposition to DNA repair by non-hom*ologous end-joining. Mol. Cell61, 547–562, 10.1016/j.molcel.2016.01.019 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

115. Giri AK and Aittokallio T (2019) DNMT inhibitors increase methylation in the cancer genome. Front. Pharmacol10, 10.3389/fphar.2019.00385 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

116. Ding N, Bonham EM, Hannon BE, Amick TR, Baylin SB and O’Hagan HM (2016) Mismatch repair proteins recruit DNA methyltransferase 1 to sites of oxidative DNA damage. J. Mol. Cell Biol8, 244–254, 10.1093/jmcb/mjv050 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

117. Gong F, Clouaire T, Aguirrebengoa M, Legube G and Miller KM (2017) Histone demethylase KDM5A regulates the ZMYND8-NuRD chromatin remodeler to promote DNA repair. J. Cell Biol216, 1959–1974, 10.1083/jcb.201611135 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

118. Gong F, Chiu LY, Cox B, Aymard F, Clouaire T, Leung JWet al. (2015) Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes hom*ologous recombination. Genes Dev. 29, 197–211, 10.1101/gad.252189.114 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

119. Bernstein C and Bernstein H (2015) Epigenetic reduction of DNA repair in progression to gastrointestinal cancer. World. J. Gastrointest. Oncol7, 30–46, 10.4251/wjgo.v7.i5.30 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

120. Tessitore A, Cicciarelli G, Del Vecchio F, Gaggiano A, Verzella D, Fischietti Met al. (2014) MicroRNAs in the DNA damage/repair network and cancer. Int. J. Genomics2014, 820248, 10.1155/2014/820248 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

121. Juhasz S, Elbakry A, Mathes A and Lobrich M (2018) ATRX promotes DNA repair synthesis and sister chromatid exchange during hom*ologous recombination. Mol. Cell71, 11.e7–24.e7, 10.1016/j.molcel.2018.05.014 [PubMed] [CrossRef] [Google Scholar]

122. Hsieh P and Zhang Y (2017) The Devil is in the details for DNA mismatch repair. Proc. Natl. Acad. Sci. U.S.A114, 3552–3554, 10.1073/pnas.1702747114 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

123. Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile Get al. (2017) Intragenic DNA methylation prevents spurious transcription initiation. Nature543, 72–77, 10.1038/nature21373 [PubMed] [CrossRef] [Google Scholar]

124. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJet al. (2010) Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 6, e1001134, 10.1371/journal.pgen.1001134 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

125. Yang X, Han H, De Carvalho DD, Lay FD, Jones PA and Liang G (2014) Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell26, 577–590, 10.1016/j.ccr.2014.07.028 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

126. Arab K, Karaulanov E, Musheev M, Trnka P, Schäfer A, Grummt Iet al. (2019) GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat. Genet51, 217–223, 10.1038/s41588-018-0306-6 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

127. Hansel-Hertsch R, Di Antonio M and Balasubramanian S (2017) DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential. Nat. Rev. Mol. Cell Biol18, 279–284, 10.1038/nrm.2017.3 [PubMed] [CrossRef] [Google Scholar]

128. Mao S-Q, Ghanbarian AT, Spiegel J, Martínez Cuesta S, Beraldi D, Di Antonio Met al. (2018) DNA G-quadruplex structures mold the DNA methylome. Nat. Struct. Mol. Biol25, 951–957, 10.1038/s41594-018-0131-8 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

129. Joyce BT, Zheng Y, Nannini D, Zhang Z, Liu L, Gao Tet al. (2018) DNA methylation of telomere-related genes and cancer risk. Cancer Prev. Res11, 511–522, 10.1158/1940-6207.CAPR-17-0413 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

130. Carroll PE, Okuda M, Horn HF, Biddinger P, Stambrook PJ, Gleich LLet al. (1999) Centrosome hyperamplification in human cancer: chromosome instability induced by p53 mutation and/or Mdm2 overexpression. Oncogene18, 1935–1944, 10.1038/sj.onc.1202515 [PubMed] [CrossRef] [Google Scholar]

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