Abstract
Maintaining genome stability is essential to an organism’s health and survival. Breakdown of the mechanisms protecting the genome and the resulting genome instability are an important aspect of the aging process and have been linked to diseases such as cancer. Thus, a large network of interconnected pathways is responsible for ensuring genome integrity in the face of the continuous challenges that induce DNA damage. While these pathways are diverse, epigenetic mechanisms play a central role in many of them. DNA modifications, histone variants and modifications, chromatin structure, and non-coding RNAs all carry out a variety of functions to ensure that genome stability is maintained. Epigenetic mechanisms ensure the functions of centromeres and telomeres that are essential for genome stability. Epigenetic mechanisms also protect the genome from the invasion by transposable elements and contribute to various DNA repair pathways. In this review, we highlight the integral role of epigenetic mechanisms in the maintenance of genome stability and draw attention to issues in need of further study.
Similar content being viewed by others
References
Aguilera A, Garcia-Muse T (2013) Causes of genome instability. Annu Rev Genet 47:1–32. https://doi.org/10.1146/annurev-genet-111212-133232
Akiyoshi B, Gull K (2014) Discovery of unconventional kinetochores in kinetoplastids. Cell 156:1247–1258. https://doi.org/10.1016/j.cell.2014.01.049
Aldrup-MacDonald ME, Kuo ME, Sullivan LL, Chew K, Sullivan BA (2016) Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles. Genome Res 26:1301–1311. https://doi.org/10.1101/gr.206706.116
Amor DJ, Bentley K, Ryan J, Perry J, Wong L, Slater H, Choo KHA (2004) Human centromere repositioning "in progress". Proc Natl Acad Sci USA 101:6542–6547. https://doi.org/10.1073/pnas.0308637101
Aparicio OM, Billington BL, Gottschling DE (1991) Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66:1279–1287. https://doi.org/10.1016/0092-8674(91)90049-5
Bandaria JN, Qin P, Berk V, Chu S, Yildiz A (2016) Shelterin protects chromosome ends by compacting telomeric chromatin. Cell 164:735–746. https://doi.org/10.1016/j.cell.2016.01.036
Barra V, Fachinetti D (2018) The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA. Nat Commun 9:4340. https://doi.org/10.1038/s41467-018-06545-y
Barra V et al (2019) Phosphorylation of CENP-A on serine 7 does not control centromere function. Nature Commun 10:175. https://doi.org/10.1038/s41467-018-08073-1
Baur JA, Zou Y, Shay JW, Wright WE (2001) Telomere position effect in human cells. Science 292:2075–2077. https://doi.org/10.1126/science.1062329
Berg R, Engels WR, Kreber RA (1980) Site-specific X-chromosome rearrangements from hybrid dysgenesis in Drosophila melanogaster. Science 210:427–429. https://doi.org/10.1126/science.6776625
Bergmann JH et al (2012) Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function. J Cell Sci 125:411–421. https://doi.org/10.1242/jcs.090639
Berriman M et al (2005) The genome of the African trypanosome Trypanosoma brucei. Science 309:416–422. https://doi.org/10.1126/science.1112642
Blevins T et al (2014) A two-step process for epigenetic inheritance in Arabidopsis. Mol Cell 54:30–42. https://doi.org/10.1016/j.molcel.2014.02.019
Blower MD, Sullivan BA, Karpen GH (2002) Conserved organization of centromeric chromatin in flies and humans. Dev Cell 2:319–330. https://doi.org/10.1016/s1534-5807(02)00135-1
Booth LN, Brunet A (2016) The aging epigenome. Mol Cell 62:728–744. https://doi.org/10.1016/j.molcel.2016.05.013
Bowman GD, Poirier MG (2015) Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 115:2274–2295. https://doi.org/10.1021/cr500350x
Brandsma I, van Gent DC (2012) Pathway choice in DNA double strand break repair: observations of a balancing act. Genome Integrity 3:9. https://doi.org/10.1186/2041-9414-3-9
Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ (2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322:1387–1392. https://doi.org/10.1126/science.1165171
Brenner M, Hearing VJ (2008) The protective role of melanin against UV damage in human skin. Photochem Photobiol 84:539–549. https://doi.org/10.1111/j.1751-1097.2007.00226.x
Bush KM, Yuen BT, Barrilleaux BL, Riggs JW, O'Geen H, Cotterman RF, Knoepfler PS (2013) Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development. Epigenetics Chromatin 6:7. https://doi.org/10.1186/1756-8935-6-7
Caneus J, Granic A, Rademakers R, Dickson DW, Coughlan CM, Chial HJ, Potter H (2018) Mitotic defects lead to neuronal aneuploidy and apoptosis in frontotemporal lobar degeneration caused by MAPT mutations. Mol Biol Cell 29:575–586. https://doi.org/10.1091/mbc.E17-01-0031
Castro JP, Carareto CM (2004) Drosophila melanogaster P transposable elements: mechanisms of transposition and regulation. Genetica 121:107–118. https://doi.org/10.1023/b:gene.0000040382.48039.a2
Celeste A et al (2002) Genomic instability in mice lacking histone H2AX. Science 296:922–927. https://doi.org/10.1126/science.1069398
Celeste A et al (2003) Histone H2AX phosphorylation is dispensable for the initial recognition of DNA breaks. Nat Cell Biol 5:675–679. https://doi.org/10.1038/ncb1004
Chang HHY, Pannunzio NR, Adachi N, Lieber MR (2017) Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 18:495–506. https://doi.org/10.1038/nrm.2017.48
Chatterjee N, Walker GC (2017) Mechanisms of DNA damage, repair, and mutagenesis. Environ Mol Mutagen 58:235–263. https://doi.org/10.1002/em.22087
Chatzimichail E et al (2014) gamma -H2AX: A novel prognostic marker in a prognosis prediction model of patients with early operable non-small cell lung cancer. Int J Genomics 2014:160236. https://doi.org/10.1155/2014/160236
Choi J-E, Mostoslavsky R (2014) Sirtuins, metabolism, and DNA repair. Curr Opin Genet Dev 26:24–32. https://doi.org/10.1016/j.gde.2014.05.005
Chow TT, Shi X, Wei JH, Guan J, Stadler G, Huang B, Blackburn EH (2018) Local enrichment of HP1alpha at telomeres alters their structure and regulation of telomere protection. Nat Commun 9:3583. https://doi.org/10.1038/s41467-018-05840-y
Choy JS, Mishra PK, Au W-C, Basrai MA (2012) Insights into assembly and regulation of centromeric chromatin in Saccharomyces cerevisiae. Biochim Biophys Acta 1819:776–783. https://doi.org/10.1016/j.bbagrm.2012.02.008
Chunduri NK, Storchova Z (2019) The diverse consequences of aneuploidy. Nat Cell Biol 21:54–62. https://doi.org/10.1038/s41556-018-0243-8
Cohen AK, Huh TY, Helleiner CW (1973) Transcription of satellite DNA in mouse L-cells. Can J Biochem 51:529–532. https://doi.org/10.1139/o73-065
Cordaux R, Batzer MA (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10:691–703. https://doi.org/10.1038/nrg2640
Counter CM, Avilion AA, LeFeuvre CE, Stewart NG, Greider CW, Harley CB, Bacchetti S (1992) Telomere shortening associated with chromosome instability is arrested in immortal cells which express telomerase activity. EMBO J 11:1921–1929
Cuacos M, Franklin FC H, Heckmann S (2015) Atypical centromeres in plants-what they can tell us. Front Plant Sci 6:913–913. https://doi.org/10.3389/fpls.2015.00913
Cuerda-Gil D, Slotkin RK (2016) Non-canonical RNA-directed DNA methylation. Nat Plants 2:16163. https://doi.org/10.1038/nplants.2016.163
Czech B, Munafo M, Ciabrelli F, Eastwood EL, Fabry MH, Kneuss E, Hannon GJ (2018) piRNA-guided genome defense: from biogenesis to silencing. Annu Rev Genet 52:131–157. https://doi.org/10.1146/annurev-genet-120417-031441
Dabin J, Fortuny A, Polo SE (2016) Epigenome maintenance in response to DNA damage. Mol Cell 62:712–727. https://doi.org/10.1016/j.molcel.2016.04.006
de Lange T (2005) Shelterin: the protein complex that shapes and safeguards human telomeres. Genes Dev 19:2100–2110. https://doi.org/10.1101/gad.1346005
de Lange T (2009) How telomeres solve the end-protection problem. Science (New York, NY) 326:948–952. https://doi.org/10.1126/science.1170633
Deniz O, Frost JM, Branco MR (2019) Regulation of transposable elements by DNA modifications. Nat Rev Genet 20:417–431. https://doi.org/10.1038/s41576-019-0106-6
Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ (2007) Dynamics of replication-independent histone turnover in budding yeast. Science 315:1405–1408. https://doi.org/10.1126/science.1134053
Drinnenberg IA, deYoung D, Henikoff S, Malik HS (2014) Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. eLife 3:e03676. https://doi.org/10.7554/eLife.03676
Drinnenberg IA, Henikoff S, Malik HS (2016) Evolutionary turnover of kinetochore proteins: a ship of theseus? Trends Cell Biol 26:498–510. https://doi.org/10.1016/j.tcb.2016.01.005
Dumesic PA, Madhani HD (2014) Recognizing the enemy within: licensing RNA-guided genome defense. Trends Biochem Sci 39:25–34. https://doi.org/10.1016/j.tibs.2013.10.003
Dumesic PA et al (2013) Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell 152:957–968. https://doi.org/10.1016/j.cell.2013.01.046
Ernst C, Odom DT, Kutter C (2017) The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity. Nat Commun 8:1411. https://doi.org/10.1038/s41467-017-01049-7
Fan W, Luo J (2010) SIRT1 regulates UV-induced DNA repair through deacetylating XPA. Mol Cell 39:247–258. https://doi.org/10.1016/j.molcel.2010.07.006
Fell VL, Schild-Poulter C (2012) Ku regulates signaling to DNA damage response pathways through the Ku70 von Willebrand A domain. Mol Cell Biol 32:76–87. https://doi.org/10.1128/MCB.05661-11
Felsenfeld G (2014) A brief history of epigenetics. Cold Spring Harb Perspect Biol 6:a018200. https://doi.org/10.1101/cshperspect.a018200
Fernández MI, Gong Y, Ye Y, Lin J, Chang DW, Kamat AM, Wu X (2013) γ-H2AX level in peripheral blood lymphocytes as a risk predictor for bladder cancer. Carcinogenesis 34:2543–2547. https://doi.org/10.1093/carcin/bgt270
Firsanov DV, Solovjeva LV, Svetlova MP (2011) H2AX phosphorylation at the sites of DNA double-strand breaks in cultivated mammalian cells and tissues. Clin Epigenetics 2:283–297. https://doi.org/10.1007/s13148-011-0044-4
Fischer KE, Riddle NC (2018) Sex differences in aging: genomic instability. J Gerontol A 73:166–174. https://doi.org/10.1093/gerona/glx105
Franklin SG, Zweidler A (1977) Non-allelic variants of histones 2a, 2b and 3 in mammals. Nature 266:273–275. https://doi.org/10.1038/266273a0
Friedli M, Trono D (2015) The developmental control of transposable elements and the evolution of higher species. Annu Rev Cell Dev Biol 31:429–451. https://doi.org/10.1146/annurev-cellbio-100814-125514
Fukagawa T, Earnshaw WC (2014a) The centromere: chromatin foundation for the kinetochore machinery. Dev Cell 30:496–508. https://doi.org/10.1016/j.devcel.2014.08.016
Fukagawa T, Earnshaw WC (2014b) Neocentromeres. Curr Biol 24:R946–947. https://doi.org/10.1016/j.cub.2014.08.032
Furuyama S, Biggins S (2007) Centromere identity is specified by a single centromeric nucleosome in budding yeast. Proc Natl Acad Sci USA 104:14706–14711. https://doi.org/10.1073/pnas.0706985104
Galan A, Garcia-Oliver E, Nuno-Cabanes C, Rubinstein L, Kupiec M, Rodriguez-Navarro S (2018) The evolutionarily conserved factor Sus1/ENY2 plays a role in telomere length maintenance. Curr Genet 64:635–644. https://doi.org/10.1007/s00294-017-0778-4
Gallego-Bartolome J et al (2018) Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain. Proc Natl Acad Sci USA 115:E2125–E2134. https://doi.org/10.1073/pnas.1716945115
Gambogi Craig W, Black Ben E (2019) The nucleosomes that mark centromere location on chromosomes old and new. Essays Biochem 63:15–27. https://doi.org/10.1042/EBC20180060
Gasior SL, Wakeman TP, Xu B, Deininger PL (2006) The human LINE-1 retrotransposon creates DNA double-strand breaks. J Mol Biol 357:1383–1393. https://doi.org/10.1016/j.jmb.2006.01.089
Gent JI, Wang N, Dawe RK (2017) Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives. Genome Biol 18:121. https://doi.org/10.1186/s13059-017-1249-4
Georgoulis A, Vorgias CE, Chrousos GP, Rogakou EP (2017) Genome Instability and gammaH2AX. Int J Mol Sci. https://doi.org/10.3390/ijms18091979
Greider CW, Blackburn EH (1987) The telomere terminal transferase of Tetrahymena is a ribonucleoprotein enzyme with two kinds of primer specificity. Cell 51:887–898. https://doi.org/10.1016/0092-8674(87)90576-9
Greiss S, Gartner A (2009) Sirtuin/Sir2 phylogeny, evolutionary considerations and structural conservation. Mol Cells 28:407–415. https://doi.org/10.1007/s10059-009-0169-x
Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewal SI (2002) Establishment and maintenance of a heterochromatin domain. Science 297:2232–2237. https://doi.org/10.1126/science.1076466
Hancks DC, Kazazian HH Jr (2012) Active human retrotransposons: variation and disease. Curr Opin Genet Dev 22:191–203. https://doi.org/10.1016/j.gde.2012.02.006
He J et al (2019) Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nat Commun 10:34. https://doi.org/10.1038/s41467-018-08006-y
Henikoff S, Furuyama T (2012) The unconventional structure of centromeric nucleosomes. Chromosoma 121:341–352. https://doi.org/10.1007/s00412-012-0372-y
Henikoff S, Smith MM (2015) Histone variants and epigenetics. Cold Spring Harb Perspect Biol 7:a019364–a019364. https://doi.org/10.1101/cshperspect.a019364
Hirakata S, Siomi MC (2019) Assembly and function of gonad-specific non-membranous organelles in Drosophila piRNA biogenesis. Noncoding RNA. https://doi.org/10.3390/ncrna5040052
Howard G, Eiges R, Gaudet F, Jaenisch R, Eden A (2008) Activation and transposition of endogenous retroviral elements in hypomethylation induced tumors in mice. Oncogene 27:404–408. https://doi.org/10.1038/sj.onc.1210631
Huang X, Fejes Toth K, Aravin AA (2017) piRNA biogenesis in Drosophila melanogaster. Trends Genet 33:882–894. https://doi.org/10.1016/j.tig.2017.09.002
Imai S, Armstrong CM, Kaeberlein M, Guarente L (2000) Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:795–800. https://doi.org/10.1038/35001622
Jafri MA, Ansari SA, Alqahtani MH, Shay JW (2016) Roles of telomeres and telomerase in cancer, and advances in telomerase-targeted therapies. Genome Med 8:69. https://doi.org/10.1186/s13073-016-0324-x
Jang CW, Shibata Y, Starmer J, Yee D, Magnuson T (2015) Histone H3.3 maintains genome integrity during mammalian development. Genes Dev 29:1377–1392. https://doi.org/10.1101/gad.264150.115
Janssen A, Colmenares SU, Karpen GH (2018) Heterochromatin: guardian of the genome. Annu Rev Cell Dev Biol 34:265–288. https://doi.org/10.1146/annurev-cellbio-100617-062653
Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22:94–97. https://doi.org/10.1038/8803
Jezek M, Green EM (2019) Histone modifications and the maintenance of telomere integrity. Cells 8:199. https://doi.org/10.3390/cells8020199
Jezek M et al (2017) The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance. Epigenetics 12:93–104. https://doi.org/10.1080/15592294.2016.1265712
Jiao Y et al (2017) Improved maize reference genome with single-molecule technologies. Nature 546:524–527. https://doi.org/10.1038/nature22971
Johnson L, Mollah S, Garcia BA, Muratore TL, Shabanowitz J, Hunt DF, Jacobsen SE (2004) Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res 32:6511–6518. https://doi.org/10.1093/nar/gkh992
Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13:484–492. https://doi.org/10.1038/nrg3230
Karpen GH, Spradling AC (1992) Analysis of subtelomeric heterochromatin in the Drosophila minichromosome Dp1187 by single P element insertional mutagenesis. Genetics 132:737–753
Kelleher ES, Edelman NB, Barbash DA (2012) Drosophila interspecific hybrids phenocopy piRNA-pathway mutants. PLoS Biol 10:e1001428. https://doi.org/10.1371/journal.pbio.1001428
Kidwell MG, Kidwell JF, Sved JA (1977) Hybrid dysgenesis in DROSOPHILA MELANOGASTER: a syndrome of aberrant traits including mutation, sterility and male recombination. Genetics 86:813–833
Kim W, Shay JW (2018) Long-range telomere regulation of gene expression: Telomere looping and telomere position effect over long distances (TPE-OLD). Differentiation 99:1–9. https://doi.org/10.1016/j.diff.2017.11.005
Kim W et al (2016) Regulation of the human telomerase gene TERT by telomere position effect-over long distances (TPE-OLD): implications for aging and cancer. PLoS Biol 14:e2000016. https://doi.org/10.1371/journal.pbio.2000016
Kinner A, Wu W, Staudt C, Iliakis G (2008) Gamma-H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin. Nucleic Acids Res 36:5678–5694. https://doi.org/10.1093/nar/gkn550
Klein SJ, O'Neill RJ (2018) Transposable elements: genome innovation, chromosome diversity, and centromere conflict. Chromosome Res 26:5–23. https://doi.org/10.1007/s10577-017-9569-5
Kohmoto T et al (2017) A 590 kb deletion caused by non-allelic homologous recombination between two LINE-1 elements in a patient with mesomelia-synostosis syndrome. Am J Med Genet A 173:1082–1086. https://doi.org/10.1002/ajmg.a.38122
Lahtz C, Pfeifer GP (2011) Epigenetic changes of DNA repair genes in cancer. J Mol Cell Biol 3:51–58. https://doi.org/10.1093/jmcb/mjq053
Larrivee M, Wellinger RJ (2006) Telomerase- and capping-independent yeast survivors with alternate telomere states. Nat Cell Biol 8:741–747. https://doi.org/10.1038/ncb1429
Lee YCG, Karpen GH (2017) Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution. Elife. https://doi.org/10.7554/eLife.25762
Lens SMA, Medema RH (2019) Cytokinesis defects and cancer. Nat Rev Cancer 19:32–45. https://doi.org/10.1038/s41568-018-0084-6
Levine AJ, Ting DT, Greenbaum BD (2016) P53 and the defenses against genome instability caused by transposons and repetitive elements. BioEssays 38:508–513. https://doi.org/10.1002/bies.201600031
Li K et al (2008) Regulation of WRN protein cellular localization and enzymatic activities by SIRT1-mediated deacetylation. J Biol Chem 283:7590–7598. https://doi.org/10.1074/jbc.M709707200
Li W, Prazak L, Chatterjee N, Grüninger S, Krug L, Theodorou D, Dubnau J (2013) Activation of transposable elements during aging and neuronal decline in Drosophila. Nat Neurosci 16:529–531. https://doi.org/10.1038/nn.3368
Li Q et al (2014) Genetic perturbation of the maize methylome. Plant Cell 26:4602–4616. https://doi.org/10.1105/tpc.114.133140
Lin YH, Yuan J, Pei H, Liu T, Ann DK, Lou Z (2015) KAP1 Deacetylation by SIRT1 promotes non-homologous end-joining repair. PLoS ONE 10:e0123935. https://doi.org/10.1371/journal.pone.0123935
Ling YH, Yuen KWY (2019) Point centromere activity requires an optimal level of centromeric noncoding RNA. Proc Natl Acad Sci USA 116:6270–6279. https://doi.org/10.1073/pnas.1821384116
Liu K, Wessler SR (2017) Transposition of Mutator-like transposable elements (MULEs) resembles hAT and Transib elements and V(D)J recombination. Nucleic Acids Res 45:6644–6655. https://doi.org/10.1093/nar/gkx357
Liu N, Lee CH, Swigut T, Grow E, Gu B, Bassik MC, Wysocka J (2018) Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature 553:228–232. https://doi.org/10.1038/nature25179
Lombard DB, Chua KF, Mostoslavsky R, Franco S, Gostissa M, Alt FW (2005) DNA repair, genome stability, and aging. Cell 120:497–512. https://doi.org/10.1016/j.cell.2005.01.028
Loyola A, Bonaldi T, Roche D, Imhof A, Almouzni G (2006) PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state. Mol Cell 24:309–316. https://doi.org/10.1016/j.molcel.2006.08.019
Maciejowski J, de Lange T (2017) Telomeres in cancer: tumour suppression and genome instability. Nat Rev Mol Cell Biol 18:175–186. https://doi.org/10.1038/nrm.2016.171
Maggert KA, Karpen GH (2001) The activation of a neocentromere in Drosophila requires proximity to an endogenous centromere. Genetics 158:1615–1628
Maison C et al (2002) Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat Genet 30:329–334. https://doi.org/10.1038/ng843
Malik HS, Henikoff S (2003) Phylogenomics of the nucleosome. Nat Struct Biol 10:882–891. https://doi.org/10.1038/nsb996
Malone CD, Lehmann R, Teixeira FK (2015) The cellular basis of hybrid dysgenesis and Stellate regulation in Drosophila. Curr Opin Genet Dev 34:88–94. https://doi.org/10.1016/j.gde.2015.09.003
Maloney KA, Sullivan LL, Matheny JE, Strome ED, Merrett SL, Ferris A, Sullivan BA (2012) Functional epialleles at an endogenous human centromere. Proc Natl Acad Sci USA 109:13704–13709. https://doi.org/10.1073/pnas.1203126109
Matthaios D et al (2012) gamma-H2AX expression detected by immunohistochemistry correlates with prognosis in early operable non-small cell lung cancer. Onco Targets Ther 5:309–314. https://doi.org/10.2147/OTT.S36995
Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15:394–408. https://doi.org/10.1038/nrg3683
Mc CB (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 36:344–355. https://doi.org/10.1073/pnas.36.6.344
McCullers TJ, Steiniger M (2017) Transposable elements in Drosophila. Mob Genet Elements 7:1–18. https://doi.org/10.1080/2159256X.2017.1318201
McKinley KL, Cheeseman IM (2016) The molecular basis for centromere identity and function. Nat Rev Mol Cell Biol 17:16–29. https://doi.org/10.1038/nrm.2015.5
McKittrick E, Gafken PR, Ahmad K, Henikoff S (2004) Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc Natl Acad Sci USA 101:1525–1530. https://doi.org/10.1073/pnas.0308092100
Mehta A, Haber JE (2014) Sources of DNA double-strand breaks and models of recombinational DNA repair. Cold Spring Harb Perspect Biol 6:a016428–a016428. https://doi.org/10.1101/cshperspect.a016428
Melis JPM, van Steeg H, Luijten M (2013) Oxidative DNA damage and nucleotide excision repair. Antioxid Redox Signal 18:2409–2419. https://doi.org/10.1089/ars.2012.5036
Mendez-Bermudez A et al (2018) Genome-wide control of heterochromatin replication by the telomere capping protein TRF2. Mol Cell 70(449–461):e445. https://doi.org/10.1016/j.molcel.2018.03.036
Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411:212–214. https://doi.org/10.1038/35075612
Molaro A, Malik HS (2016) Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline. Curr Opin Genet Dev 37:51–58. https://doi.org/10.1016/j.gde.2015.12.001
Molina O et al (2016) Epigenetic engineering reveals a balance between histone modifications and transcription in kinetochore maintenance. Nat Commun 7:13334–13334. https://doi.org/10.1038/ncomms13334
Muraki K, Nyhan K, Han L, Murnane JP (2012) Mechanisms of telomere loss and their consequences for chromosome instability. Front Oncol 2:135–135. https://doi.org/10.3389/fonc.2012.00135
Nagelkerke A et al (2011) Constitutive expression of γ-H2AX has prognostic relevance in triple negative breast cancer. Radiother Oncol 101:39–45. https://doi.org/10.1016/j.radonc.2011.07.009
Nergadze SG et al (2018) Birth, evolution, and transmission of satellite-free mammalian centromeric domains. Genome Res 28:789–799. https://doi.org/10.1101/gr.231159.117
Ochola DO et al (2019) Persistence of gamma-H2AX foci in bronchial cells correlates with susceptibility to radiation associated lung cancer in mice. Radiat Res 191:67–75. https://doi.org/10.1667/RR14979.1
Ohzeki J-I et al (2016) KAT7/HBO1/MYST2 Regulates CENP-A chromatin assembly by antagonizing Suv39h1-mediated centromere inactivation. Dev Cell 37:413–427. https://doi.org/10.1016/j.devcel.2016.05.006
O'Sullivan RJ, Karlseder J (2010) Telomeres: protecting chromosomes against genome instability. Nat Rev Mol Cell Biol 11:171–181. https://doi.org/10.1038/nrm2848
Ozata DM, Gainetdinov I, Zoch A, O'Carroll D, Zamore PD (2019) PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 20:89–108. https://doi.org/10.1038/s41576-018-0073-3
Padeken J, Zeller P, Gasser SM (2015) Repeat DNA in genome organization and stability. Curr Opin Genet Dev 31:12–19. https://doi.org/10.1016/j.gde.2015.03.009
Pal S, Tyler JK (2016) Epigenetics and aging. Sci Adv 2:e1600584. https://doi.org/10.1126/sciadv.1600584
Palladino F, Laroche T, Gilson E, Axelrod A, Pillus L, Gasser SM (1993) SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell 75:543–555. https://doi.org/10.1016/0092-8674(93)90388-7
Palmer DK, O'Day K, Trong HL, Charbonneau H, Margolis RL (1991) Purification of the centromere-specific protein CENP-A and demonstration that it is a distinctive histone. Proc Natl Acad Sci USA 88:3734–3738. https://doi.org/10.1073/pnas.88.9.3734
Pardue ML, Rashkova S, Casacuberta E, DeBaryshe PG, George JA, Traverse KL (2005) Two retrotransposons maintain telomeres in Drosophila. Chromosome Res 13:443–453. https://doi.org/10.1007/s10577-005-0993-6
Perea-Resa C, Blower MD (2018) Centromere biology: transcription goes on stage. Mol Cell Biol 38:e00263-e00218. https://doi.org/10.1128/MCB.00263-18
Platt RN 2nd, Vandewege MW, Ray DA (2018) Mammalian transposable elements and their impacts on genome evolution. Chromosome Res 26:25–43. https://doi.org/10.1007/s10577-017-9570-z
Plohl M, Meštrović N, Mravinac B (2014) Centromere identity from the DNA point of view. Chromosoma 123:313–325. https://doi.org/10.1007/s00412-014-0462-0
Prendergast JGD, Semple CAM (2011) Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Res 21:1777–1787. https://doi.org/10.1101/gr.122275.111
Riddle NC, Leung W, Haynes KA, Granok H, Wuller J, Elgin SC (2008) An investigation of heterochromatin domains on the fourth chromosome of Drosophila melanogaster. Genetics 178:1177–1191. https://doi.org/10.1534/genetics.107.081828
Riddle NC et al (2011) Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res 21:147–163. https://doi.org/10.1101/gr.110098.110
Rine J, Herskowitz I (1987) Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116:9–22
Robin JD et al (2014) Telomere position effect: regulation of gene expression with progressive telomere shortening over long distances. Genes Dev 28:2464–2476. https://doi.org/10.1101/gad.251041.114
Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM (1998) DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J Biol Chem 273:5858–5868. https://doi.org/10.1074/jbc.273.10.5858
Rošić S, Köhler F, Erhardt S (2014) Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division. J Cell Biol 207:335–349. https://doi.org/10.1083/jcb.201404097
Rosin LF, Mellone BG (2017) Centromeres drive a hard bargain. Trends Genet 33:101–117. https://doi.org/10.1016/j.tig.2016.12.001
Roth M, Wang Z, Chen WY (2016) SIRT1 and LSD1 competitively regulate KU70 functions in DNA repair and mutation acquisition in cancer cells. Oncotarget 7:50195–50214. https://doi.org/10.18632/oncotarget.10328
Sansregret L, Vanhaesebroeck B, Swanton C (2018) Determinants and clinical implications of chromosomal instability in cancer. Nat Rev Clin Oncol 15:139–150. https://doi.org/10.1038/nrclinonc.2017.198
Schnable PS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115. https://doi.org/10.1126/science.1178534
Schneider KL, Xie Z, Wolfgruber TK, Presting GG (2016) Inbreeding drives maize centromere evolution. Proc Natl Acad Sci USA 113:E987–E996. https://doi.org/10.1073/pnas.1522008113
Schoeftner S, Blasco MA (2009) A 'higher order' of telomere regulation: telomere heterochromatin and telomeric RNAs. EMBO J 28:2323–2336. https://doi.org/10.1038/emboj.2009.197
Schwartz BE, Ahmad K (2005) Transcriptional activation triggers deposition and removal of the histone variant H3.3. Genes Dev 19:804–814. https://doi.org/10.1101/gad.1259805
Scott KC, Sullivan BA (2014) Neocentromeres: a place for everything and everything in its place. Trends Genet 30:66–74. https://doi.org/10.1016/j.tig.2013.11.003
Scully R, Panday A, Elango R, Willis NA (2019) DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat Rev Mol Cell Biol 20:698–714. https://doi.org/10.1038/s41580-019-0152-0
Sentmanat M, Wang S, Elgin S (2013) Targeting heterochromatin formation to transposable elements in Drosophila: potential roles of the piRNA system. Biochemistry 78:562–571. https://doi.org/10.1134/S0006297913060023
Shang W-H et al (2013) Chromosome engineering allows the efficient isolation of vertebrate neocentromeres. Dev Cell 24:635–648. https://doi.org/10.1016/j.devcel.2013.02.009
Srivastava S, Foltz DR (2018) Posttranslational modifications of CENP-A: marks of distinction. Chromosoma 127:279–290. https://doi.org/10.1007/s00412-018-0665-x
Stadler G et al (2013) Telomere position effect regulates DUX4 in human facioscapulohumeral muscular dystrophy. Nat Struct Mol Biol 20:671–678. https://doi.org/10.1038/nsmb.2571
Steiner FA, Henikoff S (2015) Diversity in the organization of centromeric chromatin. Curr Opin Genet Dev 31:28–35. https://doi.org/10.1016/j.gde.2015.03.010
Sullivan BA, Karpen GH (2004) Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nat Struct Mol Biol 11:1076–1083. https://doi.org/10.1038/nsmb845
Sun FL et al (2004) cis-Acting determinants of heterochromatin formation on Drosophila melanogaster chromosome four. Mol Cell Biol 24:8210–8220. https://doi.org/10.1128/MCB.24.18.8210-8220.2004
Takada M et al (2017) FBW7 Loss promotes chromosomal instability and tumorigenesis via cyclin E1/CDK2-mediated phosphorylation of CENP-A. Cancer Res 77:4881–4893. https://doi.org/10.1158/0008-5472.CAN-17-1240
Talbert PB, Henikoff S (2017) Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 18:115–126. https://doi.org/10.1038/nrm.2016.148
Talbert PB, Henikoff S (2018) Transcribing centromeres: noncoding RNAs and kinetochore assembly. Trends Genet 34:587–599. https://doi.org/10.1016/j.tig.2018.05.001
Tiwari B, Jones AE, Abrams JM (2018) Transposons, p53 and genome security. Trends Genet 34:846–855. https://doi.org/10.1016/j.tig.2018.08.003
Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ (2011) Impact of chromatin structure on sequence variability in the human genome. Nat Struct Mol Biol 18:510–515. https://doi.org/10.1038/nsmb.2012
Topp CN, Zhong CX, Dawe RK (2004) Centromere-encoded RNAs are integral components of the maize kinetochore. Proc Natl Acad Sci USA 101:15986–15991. https://doi.org/10.1073/pnas.0407154101
Tubbs A, Nussenzweig A (2017) Endogenous DNA damage as a source of genomic instability in cancer. Cell 168:644–656. https://doi.org/10.1016/j.cell.2017.01.002
Varvara PV et al (2019) gamma-H2AX: A potential biomarker in breast cancer. Tumour Biol 41:1010428319878536. https://doi.org/10.1177/1010428319878536
Vijg J, Suh Y (2013) Genome instability and aging. Annu Rev Physiol 75:645–668. https://doi.org/10.1146/annurev-physiol-030212-183715
Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837. https://doi.org/10.1126/science.1074973
Volpe T, Schramke V, Hamilton GL, White SA, Teng G, Martienssen RA, Allshire RC (2003) RNA interference is required for normal centromere function in fission yeast. Chromosome Res 11:137–146
Voullaire LE, Slater HR, Petrovic V, Choo KH (1993) A functional marker centromere with no detectable alpha-satellite, satellite III, or CENP-B protein: activation of a latent centromere? Am J Hum Genet 52:1153–1163
Wallrath LL, Elgin SC (1995) Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev 9:1263–1277. https://doi.org/10.1101/gad.9.10.1263
Wang B, Zhang Z, Xia S, Jiang M, Wang Y (2019) Expression of gamma-H2AX and patient prognosis in breast cancer cohort. J Cell Biochem 120:12958–12965. https://doi.org/10.1002/jcb.28567
Warburton PE et al (1997) Immunolocalization of CENP-A suggests a distinct nucleosome structure at the inner kinetochore plate of active centromeres. Curr Biol 7:901–904. https://doi.org/10.1016/s0960-9822(06)00382-4
Warnecke T, Batada NN, Hurst LD (2008) The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet 4:e1000250–e1000250. https://doi.org/10.1371/journal.pgen.1000250
Washietl S, Machne R, Goldman N (2008) Evolutionary footprints of nucleosome positions in yeast. Trends Genet 24:583–587. https://doi.org/10.1016/j.tig.2008.09.003
Waterborg JH (1990) Sequence analysis of acetylation and methylation in two histone H3 variants of alfalfa. J Biol Chem 265:17157–17161
Weitzman MD, Fradet-Turcotte A (2018) Virus DNA replication and the host DNA damage response. Annu Rev Virol 5:141–164. https://doi.org/10.1146/annurev-virology-092917-043534
Wellinger RJ, Zakian VA (2012) Everything you ever wanted to know about Saccharomyces cerevisiae telomeres: beginning to end. Genetics 191:1073–1105. https://doi.org/10.1534/genetics.111.137851
Wendte JM, Pikaard CS (2017) The RNAs of RNA-directed DNA methylation. Biochim Biophys Acta 1860:140–148. https://doi.org/10.1016/j.bbagrm.2016.08.004
Wierman MB, Smith JS (2014) Yeast sirtuins and the regulation of aging. FEMS Yeast Res 14:73–88. https://doi.org/10.1111/1567-1364.12115
Wright WD, Shah SS, Heyer W-D (2018) Homologous recombination and the repair of DNA double-strand breaks. J Biol Chem 293:10524–10535. https://doi.org/10.1074/jbc.TM118.000372
Wu RA, Upton HE, Vogan JM, Collins K (2017a) Telomerase mechanism of telomere synthesis. Annu Rev Biochem 86:439–460. https://doi.org/10.1146/annurev-biochem-061516-045019
Wu Z, Liu J, Zhang QD, Lv DK, Wu NF, Zhou JQ (2017b) Rad6-Bre1-mediated H2B ubiquitination regulates telomere replication by promoting telomere-end resection. Nucleic Acids Res 45:3308–3322. https://doi.org/10.1093/nar/gkx101
Xin H, Liu D, Songyang Z (2008) The telosome/shelterin complex and its functions. Genome Biol 9:232. https://doi.org/10.1186/gb-2008-9-9-232
Yamamori T et al (2010) SIRT1 deacetylates APE1 and regulates cellular base excision repair. Nucleic Acids Res 38:832–845. https://doi.org/10.1093/nar/gkp1039
Zhang W et al (2016) SIRT1 inhibition impairs non-homologous end joining DNA damage repair by increasing Ku70 acetylation in chronic myeloid leukemia cells. Oncotarget 7:13538–13550. https://doi.org/10.18632/oncotarget.6455
Zhou M, Law JA (2015) RNA Pol IV and V in gene silencing: rebel polymerases evolving away from Pol II's rules. Curr Opin Plant Biol 27:154–164. https://doi.org/10.1016/j.pbi.2015.07.005
Acknowledgements
We would like to thank the members of the Riddle lab for helpful discussions. Work in the Riddle laboratory is supported by the National Science Foundation under Grant No. 1552586.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Feng, J.X., Riddle, N.C. Epigenetics and genome stability. Mamm Genome 31, 181–195 (2020). https://doi.org/10.1007/s00335-020-09836-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00335-020-09836-2