References
- Gaudet F , HodgsonJG , EdenAet al. Induction of tumors in mice by genomic hypomethylation . Science300 ( 5618 ), 489 – 492 ( 2003 ).
- Chen RZ , PetterssonU , BeardC , Jackson-GrusbyL , JaenischR . DNA hypomethylation leads to elevated mutation rates . Nature395 ( 6697 ), 89 ( 1998 ).
- Tubbs A , NussenzweigA . Endogenous DNA damage as a source of genomic instability in cancer . Cell168 ( 4 ), 644 – 656 ( 2017 ).
- Udomsinprasert W , KitkumthornN , MutiranguraA , ChongsrisawatV , PoovorawanY , HonsawekS . Global methylation, oxidative stress, and relative telomere length in biliary atresia patients . Sci. Rep.6 , 26969 ( 2016 ).
- Wang T-C , SongY-S , WangHet al. Oxidative DNA damage and global DNA hypomethylation are related to folate deficiency in chromate manufacturing workers . J. Hazard Mater.213 , 440 – 446 ( 2012 ).
- Patchsung M , BoonlaC , AmnattrakulP , DissayabutraT , MutiranguraA , TosukhowongP . Long interspersed nuclear element-1 hypomethylation and oxidative stress: correlation and bladder cancer diagnostic potential . PLoS ONE7 ( 5 ), e37009 ( 2012 ).
- Deininger P . Alu elements: know the SINEs . Genome Biol.12 ( 12 ), 236 ( 2011 ).
- Chan SW-L , ZilbermanD , XieZ , JohansenLK , CarringtonJC , JacobsenSE . RNA silencing genes control de novo DNA methylation . Science303 ( 5662 ), 1336 – 1336 ( 2004 ).
- Hamilton A , VoinnetO , ChappellL , BaulcombeD . Two classes of short interfering RNA in RNA silencing . EMBO J.21 ( 17 ), 4671 – 4679 ( 2002 ).
- Mette M , AufsatzW , Van Der WindenJ , MatzkeM , MatzkeA . Transcriptional silencing and promoter methylation triggered by double-stranded RNA . EMBO J.19 ( 19 ), 5194 – 5201 ( 2000 ).
- Chen L , DahlstromJE , LeeSH , RangasamyD . Naturally occurring endo-siRNA silences LINE-1 retrotransposons in human cells through DNA methylation . Epigenetics7 ( 7 ), 758 – 771 ( 2012 ).
- Park HK , MinBY , KimNYet al. Short hairpin RNA induces methylation of hepatitis B virus covalently closed circular DNA in human hepatoma cells . Biochem. Biophys. Res. Commun.436 ( 2 ), 152 – 155 ( 2013 ).
- Castanotto D , TommasiS , LiMet al. Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells . Mol. Ther.12 ( 1 ), 179 – 183 ( 2005 ).
- Jintaridth P , MutiranguraA . Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences . Physiol. Genomics41 ( 2 ), 194 – 200 ( 2010 ).
- Lavie L , KitovaM , MaldenerE , MeeseE , MayerJ . CpG methylation directly regulates transcriptional activity of the human endogenous retrovirus family HERV-K (HML-2) . J. Virol.79 ( 2 ), 876 – 883 ( 2005 ).
- Aporntewan C , PhokaewC , PiriyapongsaJet al. Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2 . PLoS ONE6 ( 3 ), e17934 ( 2011 ).
- Tongyoo P , AvihingsanonY , Prom-OnS , MutiranguraA , MhuantongW , HirankarnN . EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes . PLoS ONE12 ( 5 ), e0177119 ( 2017 ).
- López-Otín C , BlascoMA , PartridgeL , SerranoM , KroemerG . The hallmarks of aging . Cell153 ( 6 ), 1194 – 1217 ( 2013 ).
- Hanahan D , WeinbergRA . The hallmarks of cancer . Cell100 ( 1 ), 57 – 70 ( 2000 ).
- Bollati V , SchwartzJ , WrightRet al. Decline in genomic DNA methylation through aging in a cohort of elderly subjects . Mech. Ageing Dev.130 ( 4 ), 234 – 239 ( 2009 ).
- Chalitchagorn K , ShuangshotiS , HourpaiNet al. Distinctive pattern of LINE-1 methylation level in normal tissues and the association with carcinogenesis . Oncogene23 ( 54 ), 8841 ( 2004 ).
- Bollati V , BaccarelliA , HouLet al. Changes in DNA methylation patterns in subjects exposed to low-dose benzene . Cancer Res.67 ( 3 ), 876 – 880 ( 2007 ).
- Puttipanyalears C , SubbalekhaK , MutiranguraA , KitkumthornN . Alu hypomethylation in smoke-exposed epithelia and oral squamous carcinoma . Asian Pac. J. Cancer Prev.14 ( 9 ), 5495 – 5501 ( 2013 ).
- Yegnasubramanian S , HaffnerMC , ZhangYet al. DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity . Cancer Res.68 ( 21 ), 8954 – 8967 ( 2008 ).
- Karpf AR , MatsuiS-I . Genetic disruption of cytosine DNA methyltransferase enzymes induces chromosomal instability in human cancer cells . Cancer Res.65 ( 19 ), 8635 – 8639 ( 2005 ).
- Maraschio P , ZuffardiO , Dalla FiorT , TiepoloL . Immunodeficiency, centromeric heterochromatin instability of chromosomes 1, 9, and 16, and facial anomalies: the ICF syndrome . J. Med. Genetics25 ( 3 ), 173 – 180 ( 1988 ).
- Ji W , HernandezR , ZhangX-Yet al. DNA demethylation and pericentromeric rearrangements of chromosome 1 . Mutat. Res.379 ( 1 ), 33 – 41 ( 1997 ).
- Rerkasem K , RattanatanyongP , RerkasemAet al. Higher alu methylation levels in catch-up growth in twenty-year-old offsprings . PLoS ONE10 ( 3 ), e0120032 ( 2015 ).
- Jintaridth P , TungtrongchitrR , PreutthipanS , MutiranguraA . Hypomethylation of Alu elements in post-menopausal women with osteoporosis . PLoS ONE8 ( 8 ), e70386 ( 2013 ).
- Thongsroy J , PatchsungM , MutiranguraA . The association between Alu hypomethylation and severity of type 2 diabetes mellitus . Clin. Epigenetics9 , 93 ( 2017 ).
- De Bont R , Van LarebekeN . Endogenous DNA damage in humans: a review of quantitative data . Mutagenesis19 ( 3 ), 169 – 185 ( 2004 ).
- Dango S , MosammaparastN , SowaMEet al. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation . Mol. Cell44 ( 3 ), 373 – 384 ( 2011 ).
- Larrosa PF , GreccoMR , GómezDMet al. RAC3 more than a nuclear receptor coactivator: a key inhibitor of senescence that is downregulated in aging . Cell Death Dis.6 ( 10 ), e1902 ( 2015 ).
- Wangsri S , SubbalekhaK , KitkumthornN , MutiranguraA . Patterns and possible roles of LINE-1 methylation changes in smoke-exposed epithelia . PLoS ONE7 ( 9 ), e45292 ( 2012 ).
- Krueger F , AndrewsSR . Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications . Bioinformatics27 ( 11 ), 1571 – 1572 ( 2011 ).
- Phipps SM , BerletchJB , AndrewsLG , TollefsbolTO . Aging cell culture: methods and observations . Biological Aging371 , 9 – 19 ( 2007 ).
- Wendte JM , PikaardCS . The RNAs of RNA-directed DNA methylation . Biochim. Biophys. Acta1860 ( 1 ), 140 – 148 ( 2017 ).
- Hoffmann MJ , SchulzWA . Causes and consequences of DNA hypomethylation in human cancer . Biochem. Cell Biol.83 ( 3 ), 296 – 321 ( 2005 ).
- Ross JP , RandKN , MolloyPL . Hypomethylation of repeated DNA sequences in cancer . Epigenomics2 ( 2 ), 245 – 269 ( 2010 ).
- Baylin SB , EstellerM , RountreeMR , BachmanKE , SchuebelK , HermanJG . Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer . Hum. Mol. Genetics10 ( 7 ), 687 – 692 ( 2001 ).
- Grewal SI , JiaS . Heterochromatin revisited . Nat. Rev. Genetics8 ( 1 ), 35 ( 2007 ).
- Pornthanakasem W , KongruttanachokN , PhuangphairojCet al. LINE-1 methylation status of endogenous DNA double-strand breaks . Nucleic Acids Res.36 ( 11 ), 3667 – 3675 ( 2008 ).
- Kongruttanachok N , PhuangphairojC , ThongnakAet al. Replication independent DNA double-strand break retention may prevent genomic instability . Mol. Cancer9 ( 1 ), 70 ( 2010 ).
- Thongsroy J , MatangkasombutO , ThongnakA , RattanatanyongP , JirawatnotaiS , MutiranguraA . Replication-independent endogenous DNA double-strand breaks in Saccharomyces cerevisiae model . PLoS ONE8 ( 8 ), e72706 ( 2013 ).
- Pongpanich M , PatchsungM , ThongsroyJ , MutiranguraA . Characteristics of replication-independent endogenous double-strand breaks in Saccharomyces cerevisiae . BMC Genomics15 ( 1 ), 750 ( 2014 ).
- Xu Y , XuC , PriceBD . Mechanistic links between ATM and histone methylation codes during DNA repair . Prog. Mol. Biol. Transl. Sci.110 , 263 – 288 ( 2012 ).
- Jakob B , SplinterJ , ConradSet al. DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin . Nucleic Acids Res.39 ( 15 ), 6489 – 6499 ( 2011 ).
- Musich PR , ZouY . DNA-damage accumulation and replicative arrest in Hutchinson–Gilford progeria syndrome . Biochem. Soc. Trans.39 ( 6 ), 1764 – 1769 ( 2011 ).
- Liu Y , RusinolA , SinenskyM , WangY , ZouY . DNA damage responses in progeroid syndromes arise from defective maturation of prelamin A . J. Cell Sci.119 ( 22 ), 4644 – 4649 ( 2006 ).
- Fritsche M , HaesslerC , BrandnerG . Induction of nuclear accumulation of the tumor-suppressor protein p53 by DNA-damaging agents . Oncogene8 ( 2 ), 307 – 318 ( 1993 ).
- Bunz F , DutriauxA , LengauerCet al. Requirement for p53 and p21 to sustain G2 arrest after DNA damage . Science282 ( 5393 ), 1497 – 1501 ( 1998 ).
- Best BP . Nuclear DNA damage as a direct cause of aging . Rejuvenation Res.12 ( 3 ), 199 – 208 ( 2009 ).
- Freitas AA , De MagalhaesJP . A review and appraisal of the DNA damage theory of ageing . Mut. Res.728 ( 1 ), 12 – 22 ( 2011 ).
- Burhans WC , WeinbergerM . DNA replication stress, genome instability and aging . Nucleic Acids Res.35 ( 22 ), 7545 – 7556 ( 2007 ).
- Muller PA , VousdenKH . Mutant p53 in cancer: new functions and therapeutic opportunities . Cancer Cell25 ( 3 ), 304 – 317 ( 2014 ).