The emerging role of lysine demethylases in DNA damage response: dissecting the recruitment mode of KDM4D/JMJD2D to DNA damage sites

References

• Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993; 362:709-15; PMID:8469282; http://dx.doi.org/10.1038/362709a0
   PubMed Web of Science ®Google Scholar
• Lindahl T, Barnes DE. Repair of endogenous DNA damage. Cold Spring Harbor Symp Quant Biol 2000; 65:127-33; PMID:12760027; http://dx.doi.org/10.1101/sqb.2000.65.127
   PubMedGoogle Scholar
• Jackson SP, Bartek J. The DNA-damage response in human biology and disease. Nature 2009; 461:1071-8; PMID:19847258; http://dx.doi.org/10.1038/nature08467
   PubMed Web of Science ®Google Scholar
• Lord CJ, Ashworth A. The DNA damage response and cancer therapy. Nature 2012; 481:287-94; PMID:22258607; http://dx.doi.org/10.1038/nature10760
   PubMed Web of Science ®Google Scholar
• Cassidy LD, Liau SS, Venkitaraman AR. Chromosome instability and carcinogenesis: insights from murine models of human pancreatic cancer associated with BRCA2 inactivation. Mol Oncol 2014; 8:161-8; PMID:24268522; http://dx.doi.org/10.1016/j.molonc.2013.10.005
   PubMed Web of Science ®Google Scholar
• Huang LC, Clarkin KC, Wahl GM. Sensitivity and selectivity of the DNA damage sensor responsible for activating p53-dependent G1 arrest. Proc Natl Acad Sci U S A 1996; 93:4827-32; PMID:8643488; http://dx.doi.org/10.1073/pnas.93.10.4827
   PubMed Web of Science ®Google Scholar
• Bennett CB, Lewis AL, Baldwin KK, Resnick MA. Lethality induced by a single site-specific double-strand break in a dispensable yeast plasmid. Proc Natl Acad Sci U S A 1993; 90:5613-7; PMID:8516308; http://dx.doi.org/10.1073/pnas.90.12.5613
   PubMed Web of Science ®Google Scholar
• Rich T, Allen RL, Wyllie AH. Defying death after DNA damage. Nature 2000; 407:777-83; PMID:11048728; http://dx.doi.org/10.1038/35037717
   PubMed Web of Science ®Google Scholar
• Daley JM, Sung P. 53BP1, BRCA1, and the choice between recombination and end joining at DNA double-strand breaks. Mol Cell Biol 2014; 34:1380-8; PMID:24469398; http://dx.doi.org/10.1128/MCB.01639-13
   PubMed Web of Science ®Google Scholar
• Kakarougkas A, Jeggo PA. DNA DSB repair pathway choice: an orchestrated handover mechanism. Br J Radiol 2014; 87:20130685; PMID:24363387; http://dx.doi.org/10.1259/bjr.20130685
   PubMed Web of Science ®Google Scholar
• Rothkamm K, Kruger I, Thompson LH, Lobrich M. Pathways of DNA double-strand break repair during the mammalian cell cycle. Mol Cell Biol 2003; 23:5706-15; PMID:12897142; http://dx.doi.org/10.1128/MCB.23.16.5706-5715.2003
   PubMed Web of Science ®Google Scholar
• Hinz JM, Yamada NA, Salazar EP, Tebbs RS, Thompson LH. Influence of double-strand-break repair pathways on radiosensitivity throughout the cell cycle in CHO cells. DNA Repair (Amst) 2005; 4:782-92; PMID:15951249; http://dx.doi.org/10.1016/j.dnarep.2005.03.005
   PubMed Web of Science ®Google Scholar
• Mao Z, Bozzella M, Seluanov A, Gorbunova V. DNA repair by nonhomologous end joining and homologous recombination during cell cycle in human cells. Cell Cycle 2008; 7:2902-6; PMID:18769152; http://dx.doi.org/10.4161/cc.7.18.6679
   PubMed Web of Science ®Google Scholar
• Hartlerode AJ, Scully R. Mechanisms of double-strand break repair in somatic mammalian cells. Biochem J 2009; 423:157-68; PMID:19772495; http://dx.doi.org/10.1042/BJ20090942
   PubMed Web of Science ®Google Scholar
• Chapman JR, Taylor MR, Boulton SJ. Playing the end game: DNA double-strand break repair pathway choice. Mol Cell 2012; 47:497-510; PMID:22920291; http://dx.doi.org/10.1016/j.molcel.2012.07.029
   PubMed Web of Science ®Google Scholar
• Polo SE, Jackson SP. Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev 2011; 25:409-33; PMID:21363960; http://dx.doi.org/10.1101/gad.2021311
   PubMed Web of Science ®Google Scholar
• Venkitaraman AR. Modifying chromatin architecture during the response to DNA breakage. Crit Rev Biochem Mol Biol 2010; 45:2-13; PMID:19874211; http://dx.doi.org/10.3109/10409230903325446
   PubMed Web of Science ®Google Scholar
• Shiloh Y, Ziv Y. The ATM protein kinase: regulating the cellular response to genotoxic stress, and more. Nat Rev Mol Cell Biol 2013; 14:197-210; ; http://dx.doi.org/10.1038/nrm3546
   Web of Science ®Google Scholar
• Polo SE. Reshaping chromatin after DNA damage: the choreography of histone proteins. J Mol Biol 2014; PMID:24887097; http://dx.doi.org/10.1016/j.jmb.2014.05.025
   PubMed Web of Science ®Google Scholar
• Rashi-Elkeles S, Warnatz HJ, Elkon R, Kupershtein A, Chobod Y, Paz A, Amstislavskiy V, Sultan M, Safer H, Nietfeld W, et al. Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation. Sci Signaling 2014; 7:rs3; PMID:24825921; http://dx.doi.org/10.1126/scisignal.2005032
   PubMed Web of Science ®Google Scholar
• Storici F, Bebenek K, Kunkel TA, Gordenin DA, Resnick MA. RNA-templated DNA repair. Nature 2007; 447:338-41; PMID:17429354; http://dx.doi.org/10.1038/nature05720
   PubMed Web of Science ®Google Scholar
• Shen Y, Nandi P, Taylor MB, Stuckey S, Bhadsavle HP, Weiss B, Storici F. RNA-driven genetic changes in bacteria and in human cells. Mutat Res 2011; 717:91-8; PMID:21515292; http://dx.doi.org/10.1016/j.mrfmmm.2011.03.016
   PubMed Web of Science ®Google Scholar
• Keskin H, Shen Y, Huang F, Patel M, Yang T, Ashley K, Mazin AV, Storici F. Transcript-RNA-templated DNA recombination and repair. Nature 2014; 515:436-9; PMID:25186730; http://dx.doi.org/10.1038/nature13682
   PubMed Web of Science ®Google Scholar
• Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Leveille N, Kalluri R, et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 2013; 49:524-35; PMID:23273978; http://dx.doi.org/10.1016/j.molcel.2012.11.021
   PubMed Web of Science ®Google Scholar
• Wang Y, Huang JW, Calses P, Kemp CJ, Taniguchi T. MiR-96 downregulates REV1 and RAD51 to promote cellular sensitivity to cisplatin and PARP inhibition. Cancer Res 2012; 72:4037-46; PMID:22761336; http://dx.doi.org/10.1158/0008-5472.CAN-12-0103
   PubMed Web of Science ®Google Scholar
• Hu H, Du L, Nagabayashi G, Seeger RC, Gatti RA. ATM is down-regulated by N-Myc-regulated microRNA-421. Proc Natl Acad Sci U S A 2010; 107:1506-11; PMID:20080624; http://dx.doi.org/10.1073/pnas.0907763107
   PubMed Web of Science ®Google Scholar
• Lal A, Pan Y, Navarro F, Dykxhoorn DM, Moreau L, Meire E, Bentwich Z, Lieberman J, Chowdhury D. miR-24-mediated downregulation of H2AX suppresses DNA repair in terminally differentiated blood cells. Nat Struct Mol Biol 2009; 16:492-8; PMID:19377482; http://dx.doi.org/10.1038/nsmb.1589
   PubMed Web of Science ®Google Scholar
• Moskwa P, Buffa FM, Pan Y, Panchakshari R, Gottipati P, Muschel RJ, Beech J, Kulshrestha R, Abdelmohsen K, Weinstock DM, et al. miR-182-mediated downregulation of BRCA1 impacts DNA repair and sensitivity to PARP inhibitors. Mol Cell 2011; 41:210-20; PMID:21195000; http://dx.doi.org/10.1016/j.molcel.2010.12.005
   PubMed Web of Science ®Google Scholar
• Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell 2013; 152:1298-307; PMID:23498938; http://dx.doi.org/10.1016/j.cell.2013.02.012
   PubMed Web of Science ®Google Scholar
• d'Adda di Fagagna F. A direct role for small non-coding RNAs in DNA damage response. Trends Cell Biol 2014; 24:171-8; PMID:24156824; http://dx.doi.org/10.1016/j.tcb.2013.09.008
   PubMed Web of Science ®Google Scholar
• Wei W, Ba Z, Gao M, Wu Y, Ma Y, Amiard S, White CI, Rendtlew Danielsen JM, Yang YG, Qi Y. A role for small RNAs in DNA double-strand break repair. Cell 2012; 149:101-12; PMID:22445173; http://dx.doi.org/10.1016/j.cell.2012.03.002
   PubMed Web of Science ®Google Scholar
• Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P, d'Adda di Fagagna F. Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 2012; 488:231-5; PMID:22722852; http://dx.doi.org/10.1038/nature11179
   PubMed Web of Science ®Google Scholar
• Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K, Dalla-Favera R. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci U S A 2013; 110:1404-9; PMID:23297232; http://dx.doi.org/10.1073/pnas.1206761110
   PubMed Web of Science ®Google Scholar
• Ruby JG, Jan CH, Bartel DP. Intronic microRNA precursors that bypass Drosha processing. Nature 2007; 448:83-6; PMID:17589500; http://dx.doi.org/10.1038/nature05983
   PubMed Web of Science ®Google Scholar
• Bogerd HP, Karnowski HW, Cai X, Shin J, Pohlers M, Cullen BR. A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. Mol Cell 2010; 37:135-42; PMID:20129062; http://dx.doi.org/10.1016/j.molcel.2009.12.016
   PubMed Web of Science ®Google Scholar
• Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 2010; 465:584-9; PMID:20424607; http://dx.doi.org/10.1038/nature09092
   PubMed Web of Science ®Google Scholar
• Deem AK, Li X, Tyler JK. Epigenetic regulation of genomic integrity. Chromosoma 2012; 121:131-51; PMID:22249206; http://dx.doi.org/10.1007/s00412-011-0358-1
   PubMed Web of Science ®Google Scholar
• Shi L, Oberdoerffer P. Chromatin dynamics in DNA double-strand break repair. Biochim Biophys Acta 2012; 1819:811-9; PMID:22285574; http://dx.doi.org/10.1016/j.bbagrm.2012.01.002
   PubMed Web of Science ®Google Scholar
• Greenberg RA. Histone tails: directing the chromatin response to DNA damage. FEBS letters 2011; 585:2883-90; PMID:21621538; http://dx.doi.org/10.1016/j.febslet.2011.05.037
   PubMed Web of Science ®Google Scholar
• Luijsterburg MS, van Attikum H. Chromatin and the DNA damage response: the cancer connection. Mol Oncol 2011; 5:349-67; PMID:21782533; http://dx.doi.org/10.1016/j.molonc.2011.06.001
   PubMed Web of Science ®Google Scholar
• Black JC, Van Rechem C, Whetstine JR. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol Cell 2012; 48:491-507; PMID:23200123; http://dx.doi.org/10.1016/j.molcel.2012.11.006
   PubMed Web of Science ®Google Scholar
• Liu H, Galka M, Mori E, Liu X, Lin YF, Wei R, Pittock P, Voss C, Dhami G, Li X, et al. A method for systematic mapping of protein lysine methylation identifies functions for HP1beta in DNA damage response. Mol Cell 2013; 50:723-35; PMID:23707759; http://dx.doi.org/10.1016/j.molcel.2013.04.025
   PubMed Web of Science ®Google Scholar
• Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004; 119:941-53; PMID:15620353; http://dx.doi.org/10.1016/j.cell.2004.12.012
   PubMed Web of Science ®Google Scholar
• Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2006; 439:811-6; PMID:16362057; http://dx.doi.org/10.1038/nature04433
   PubMed Web of Science ®Google Scholar
• Shi Y, Whetstine JR. Dynamic regulation of histone lysine methylation by demethylases. Mol Cell 2007; 25:1-14; PMID:17218267; http://dx.doi.org/10.1016/j.molcel.2006.12.010
   PubMed Web of Science ®Google Scholar
• Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, Kutateladze TG, Simpson M, Mao Q, Pan CH, Dai S, et al. Structural insights into histone demethylation by JMJD2 family members. Cell 2006; 125:691-702; PMID:16677698; http://dx.doi.org/10.1016/j.cell.2006.04.024
   PubMed Web of Science ®Google Scholar
• Shi YG, Tsukada Y. The discovery of histone demethylases. Cold Spring Harbor Perspect Biol 2013; 5; PMID:24003214; http://dx.doi.org/10.1101/cshperspect.a017947
   PubMed Web of Science ®Google Scholar
• Wissmann M, Yin N, Muller JM, Greschik H, Fodor BD, Jenuwein T, Vogler C, Schneider R, Gunther T, Buettner R, et al. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat Cell Biol 2007; 9:347-53; PMID:17277772; http://dx.doi.org/10.1038/ncb1546
   PubMed Web of Science ®Google Scholar
• Shin S, Janknecht R. Activation of androgen receptor by histone demethylases JMJD2A and JMJD2D. Biochem Biophys Res Commun 2007; 359:742-6; PMID:17555712; http://dx.doi.org/10.1016/j.bbrc.2007.05.179
   PubMed Web of Science ®Google Scholar
• Zhang D, Yoon HG, Wong J. JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol 2005; 25:6404-14; PMID:16024779; http://dx.doi.org/10.1128/MCB.25.15.6404-6414.2005
   PubMed Web of Science ®Google Scholar
• Mallette FA, Richard S. JMJD2A promotes cellular transformation by blocking cellular senescence through transcriptional repression of the tumor suppressor CHD5. Cell Rep 2012; 2:1233-43; PMID:23168260; http://dx.doi.org/10.1016/j.celrep.2012.09.033
   PubMed Web of Science ®Google Scholar
• Kim TD, Oh S, Shin S, Janknecht R. Regulation of tumor suppressor p53 and HCT116 cell physiology by histone demethylase JMJD2D/KDM4D. PLoS One 2012; 7:e34618; PMID:22514644; http://dx.doi.org/10.1371/journal.pone.0034618
   PubMed Web of Science ®Google Scholar
• Cloos PA, Christensen J, Agger K, Helin K. Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev 2008; 22:1115-40; PMID:18451103; http://dx.doi.org/10.1101/gad.1652908
   PubMed Web of Science ®Google Scholar
• Black JC, Allen A, Van Rechem C, Forbes E, Longworth M, Tschop K, Rinehart C, Quiton J, Walsh R, Smallwood A, et al. Conserved antagonism between JMJD2A/KDM4A and HP1gamma during cell cycle progression. Mol Cell 2010; 40:736-48; PMID:21145482; http://dx.doi.org/10.1016/j.molcel.2010.11.008
   PubMed Web of Science ®Google Scholar
• Mallette FA, Mattiroli F, Cui G, Young LC, Hendzel MJ, Mer G, Sixma TK, Richard S. RNF8- and RNF168-dependent degradation of KDM4A/JMJD2A triggers 53BP1 recruitment to DNA damage sites. Embo J 2012; 31:1865-78; PMID:22373579; http://dx.doi.org/10.1038/emboj.2012.47
   PubMed Web of Science ®Google Scholar
• Palomera-Sanchez Z, Bucio-Mendez A, Valadez-Graham V, Reynaud E, Zurita M. Drosophila p53 is required to increase the levels of the dKDM4B demethylase after UV induced DNA damage to demethylate histone H3-lysine 9. J Biol Chem 2010; PMID:20675387
   PubMed Web of Science ®Google Scholar
• Young LC, McDonald DW, Hendzel MJ. Kdm4b histone demethylase is a DNA damage response protein and confers a survival advantage following gamma-irradiation. J Biol Chem 2013; 288:21376-88; PMID:23744078; http://dx.doi.org/10.1074/jbc.M113.491514
   PubMed Web of Science ®Google Scholar
• Khoury-Haddad H, Guttmann-Raviv N, Ipenberg I, Huggins D, Jeyasekharan AD, Ayoub N. PARP1-dependent recruitment of KDM4D histone demethylase to DNA damage sites promotes double-strand break repair. Proc Natl Acad Sci U S A 2014; 111:E728-37; PMID:24550317; http://dx.doi.org/10.1073/pnas.1317585111
   PubMed Web of Science ®Google Scholar
• Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, et al. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 2006; 125:467-81; PMID:16603238; http://dx.doi.org/10.1016/j.cell.2006.03.028
   PubMed Web of Science ®Google Scholar
• Loh YH, Zhang W, Chen X, George J, Ng HH. Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev 2007; 21:2545-57; PMID:17938240; http://dx.doi.org/10.1101/gad.1588207
   PubMed Web of Science ®Google Scholar
• Pedersen MT, Helin K. Histone demethylases in development and disease. Trends Cell Biol 2010; 20:662-71; PMID:20863703; http://dx.doi.org/10.1016/j.tcb.2010.08.011
   PubMed Web of Science ®Google Scholar
• Zoabi M, Nadar-Ponniah PT, Khoury-Haddad H, Usaj M, Budowski-Tal I, Haran T, Henn A, Mandel-Gutfreund Y, Ayoub N. RNA-dependent chromatin localization of KDM4D lysine demethylase promotes H3K9me3 demethylation. Nucleic Acids Res 2014; 42:13026-38; PMID:25378304; http://dx.doi.org/10.1093/nar/gku1021
   PubMed Web of Science ®Google Scholar
• Gibson BA, Kraus WL. New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs. Nat Rev Mol Cell Biol 2012; 13:411-24; PMID:22713970; http://dx.doi.org/10.1038/nrm3376
   PubMed Web of Science ®Google Scholar
• Sajish M, Zhou Q, Kishi S, Valdez DM Jr, Kapoor M, Guo M, Lee S, Kim S, Yang XL, Schimmel P. Trp-tRNA synthetase bridges DNA-PKcs to PARP-1 to link IFN-gamma and p53 signaling. Nat Chem Biol 2012; 8:547-54; PMID:22504299; http://dx.doi.org/10.1038/nchembio.937
   PubMed Web of Science ®Google Scholar
• Ahel I, Ahel D, Matsusaka T, Clark AJ, Pines J, Boulton SJ, West SC. Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. Nature 2008; 451:81-5; PMID:18172500; http://dx.doi.org/10.1038/nature06420
   PubMed Web of Science ®Google Scholar
• Pleschke JM, Kleczkowska HE, Strohm M, Althaus FR. Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins. J Biol Chem 2000; 275:40974-80; PMID:11016934; http://dx.doi.org/10.1074/jbc.M006520200
   PubMed Web of Science ®Google Scholar
• Gagne JP, Isabelle M, Lo KS, Bourassa S, Hendzel MJ, Dawson VL, Dawson TM, Poirier GG. Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes. Nucleic Acids Res 2008; 36:6959-76; PMID:18981049; http://dx.doi.org/10.1093/nar/gkn771
   PubMed Web of Science ®Google Scholar
• Zaja R, Mikoc A, Barkauskaite E, Ahel I. Molecular insights into poly(ADP-ribose) recognition and processing. Biomolecules 2012; 3:1-17; PMID:24970154; http://dx.doi.org/10.3390/biom3010001
   PubMedGoogle Scholar
• Ahel D, Horejsi Z, Wiechens N, Polo SE, Garcia-Wilson E, Ahel I, Flynn H, Skehel M, West SC, Jackson SP, et al. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 2009; 325:1240-3; PMID:19661379; http://dx.doi.org/10.1126/science.1177321
   PubMed Web of Science ®Google Scholar
• Chou DM, Adamson B, Dephoure NE, Tan X, Nottke AC, Hurov KE, Gygi SP, Colaiacovo MP, Elledge SJ. A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage. Proc Natl Acad Sci U S A 2010; 107:18475-80; PMID:20937877; http://dx.doi.org/10.1073/pnas.1012946107
   PubMed Web of Science ®Google Scholar
• Li GY, McCulloch RD, Fenton AL, Cheung M, Meng L, Ikura M, Koch CA. Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response. Proc Natl Acad Sci U S A 2010; 107:9129-34; PMID:20439749; http://dx.doi.org/10.1073/pnas.1000556107
   PubMed Web of Science ®Google Scholar
• Okano S, Lan L, Caldecott KW, Mori T, Yasui A. Spatial and temporal cellular responses to single-strand breaks in human cells. Mol Cell Biol 2003; 23:3974-81; PMID:12748298; http://dx.doi.org/10.1128/MCB.23.11.3974-3981.2003
   PubMed Web of Science ®Google Scholar
• Haince JF, McDonald D, Rodrigue A, Dery U, Masson JY, Hendzel MJ, Poirier GG. PARP1-dependent kinetics of recruitment of MRE11 and NBS1 proteins to multiple DNA damage sites. J Biol Chem 2008; 283:1197-208; PMID:18025084; http://dx.doi.org/10.1074/jbc.M706734200
   PubMed Web of Science ®Google Scholar
• Zhang F, Chen Y, Li M, Yu X. The oligonucleotide/oligosaccharide-binding fold motif is a poly(ADP-ribose)-binding domain that mediates DNA damage response. Proc Natl Acad Sci U S A 2014; 111:7278-83; PMID:24799691; http://dx.doi.org/10.1073/pnas.1318367111
   PubMed Web of Science ®Google Scholar
• Li M, Yu X. Function of BRCA1 in the DNA damage response is mediated by ADP-ribosylation. Cancer Cell 2013; 23:693-704; PMID:23680151; http://dx.doi.org/10.1016/j.ccr.2013.03.025
   PubMed Web of Science ®Google Scholar
• Jha DK, Strahl BD. An RNA polymerase II-coupled function for histone H3K36 methylation in checkpoint activation and DSB repair. Nat Commun 2014; 5:3965; PMID:24910128; http://dx.doi.org/10.1038/ncomms4965
   PubMed Web of Science ®Google Scholar
• Seward DJ, Cubberley G, Kim S, Schonewald M, Zhang L, Tripet B, Bentley DL. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat Struct Mol Biol 2007; 14:240-2; PMID:17310255; http://dx.doi.org/10.1038/nsmb1200
   PubMed Web of Science ®Google Scholar
• Christensen J, Agger K, Cloos PA, Pasini D, Rose S, Sennels L, Rappsilber J, Hansen KH, Salcini AE, Helin K. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 2007; 128:1063-76; PMID:17320161; http://dx.doi.org/10.1016/j.cell.2007.02.003
   PubMed Web of Science ®Google Scholar
• Yamane K, Tateishi K, Klose RJ, Fang J, Fabrizio LA, Erdjument-Bromage H, Taylor-Papadimitriou J, Tempst P, Zhang Y. PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell 2007; 25:801-12; PMID:17363312; http://dx.doi.org/10.1016/j.molcel.2007.03.001
   PubMed Web of Science ®Google Scholar
• Li X, Liu L, Yang S, Song N, Zhou X, Gao J, Yu N, Shan L, Wang Q, Liang J, et al. Histone demethylase KDM5B is a key regulator of genome stability. Proc Natl Acad Sci U S A 2014; 111:7096-101; PMID:24778210; http://dx.doi.org/10.1073/pnas.1324036111
   PubMed Web of Science ®Google Scholar
• Watanabe S, Watanabe K, Akimov V, Bartkova J, Blagoev B, Lukas J, Bartek J. JMJD1C demethylates MDC1 to regulate the RNF8 and BRCA1-mediated chromatin response to DNA breaks. Nat Struct Mol Biol 2013; 20:1425-33; PMID:24240613; http://dx.doi.org/10.1038/nsmb.2702
   PubMed Web of Science ®Google Scholar
• Mosammaparast N, Kim H, Laurent B, Zhao Y, Lim HJ, Majid MC, Dango S, Luo Y, Hempel K, Sowa ME, et al. The histone demethylase LSD1/KDM1A promotes the DNA damage response. J Cell Biol 2013; 203:457-70; PMID:24217620; http://dx.doi.org/10.1083/jcb.201302092
   PubMed Web of Science ®Google Scholar
• Ayoub N, Jeyasekharan AD, Bernal JA, Venkitaraman AR. HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response. Nature 2008; 453:682-6; PMID:18438399; http://dx.doi.org/10.1038/nature06875
   PubMed Web of Science ®Google Scholar
• Sun Y, Jiang X, Xu Y, Ayrapetov MK, Moreau LA, Whetstine JR, Price BD. Histone H3 methylation links DNA damage detection to activation of the tumour suppressor Tip60. Nat Cell Biol 2009; 11:1376-82; PMID:19783983; http://dx.doi.org/10.1038/ncb1982
   PubMed Web of Science ®Google Scholar
• Trojer P, Zhang J, Yonezawa M, Schmidt A, Zheng H, Jenuwein T, Reinberg D. Dynamic histone H1 isotype 4 methylation and demethylation by histone lysine methyltransferase G9a/KMT1C and the Jumonji domain-containing JMJD2/KDM4 proteins. J Biol Chem 2009; 284:8395-405; PMID:19144645; http://dx.doi.org/10.1074/jbc.M807818200
   PubMed Web of Science ®Google Scholar
• Jack AP, Bussemer S, Hahn M, Punzeler S, Snyder M, Wells M, Csankovszki G, Solovei I, Schotta G, Hake SB. H3K56me3 is a novel, conserved heterochromatic mark that largely but not completely overlaps with H3K9me3 in both regulation and localization. PLoS One 2013; 8:e51765; PMID:23451023; http://dx.doi.org/10.1371/journal.pone.0051765
   PubMed Web of Science ®Google Scholar
• Falk M, Lukasova E, Gabrielova B, Ondrej V, Kozubek S. Chromatin dynamics during DSB repair. Biochim Biophys Acta 2007; 1773:1534-45; PMID:17850903; http://dx.doi.org/10.1016/j.bbamcr.2007.07.002
   PubMed Web of Science ®Google Scholar
• Ayrapetov MK, Gursoy-Yuzugullu O, Xu C, Xu Y, Price BD. DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin. Proc Natl Acad Sci U S A 2014; 111:9169-74; PMID:24927542; http://dx.doi.org/10.1073/pnas.1403565111
   PubMed Web of Science ®Google Scholar
• Ayoub N, Jeyasekharan AD, Venkitaraman AR. Mobilization and recruitment of HP1: a bimodal response to DNA breakage. Cell Cycle 2009; 8:2945-50; PMID:19657222
   PubMed Web of Science ®Google Scholar
• Ayoub N, Jeyasekharan AD, Bernal JA, Venkitaraman AR. Paving the way for H2AX phosphorylation: chromatin changes in the DNA damage response. Cell Cycle 2009; 8:1494-500; PMID:19377276; http://dx.doi.org/10.4161/cc.8.10.8501
   PubMed Web of Science ®Google Scholar
• Li ML, Yuan G, Greenberg RA. Chromatin yo-yo: expansion and condensation during DNA repair. Trends Cell Biol 2014; 24:616-8; PMID:25305135; http://dx.doi.org/10.1016/j.tcb.2014.09.004
   PubMed Web of Science ®Google Scholar
• Chiolo I, Minoda A, Colmenares SU, Polyzos A, Costes SV, Karpen GH. Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell 2011; 144:732-44; PMID:21353298; http://dx.doi.org/10.1016/j.cell.2011.02.012
   PubMed Web of Science ®Google Scholar
• Adam S, Polo SE. Blurring the line between the DNA damage response and transcription: the importance of chromatin dynamics. Exp Cell Res 2014; 329:148-53; PMID:25062983; http://dx.doi.org/10.1016/j.yexcr.2014.07.017
   PubMed Web of Science ®Google Scholar
• Huang J, Sengupta R, Espejo AB, Lee MG, Dorsey JA, Richter M, Opravil S, Shiekhattar R, Bedford MT, Jenuwein T, et al. p53 is regulated by the lysine demethylase LSD1. Nature 2007; 449:105-8; PMID:17805299; http://dx.doi.org/10.1038/nature06092
   PubMed Web of Science ®Google Scholar
• Huang J, Perez-Burgos L, Placek BJ, Sengupta R, Richter M, Dorsey JA, Kubicek S, Opravil S, Jenuwein T, Berger SL. Repression of p53 activity by Smyd2-mediated methylation. Nature 2006; 444:629-32; PMID:17108971; http://dx.doi.org/10.1038/nature05287
   PubMed Web of Science ®Google Scholar
• Shi X, Kachirskaia I, Yamaguchi H, West LE, Wen H, Wang EW, Dutta S, Appella E, Gozani O. Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol Cell 2007; 27:636-46; PMID:17707234; http://dx.doi.org/10.1016/j.molcel.2007.07.012
   PubMed Web of Science ®Google Scholar
• Black JC, Manning AL, Van Rechem C, Kim J, Ladd B, Cho J, Pineda CM, Murphy N, Daniels DL, Montagna C, et al. KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors. Cell 2013; 154:541-55; PMID:23871696; http://dx.doi.org/10.1016/j.cell.2013.06.051
   PubMed Web of Science ®Google Scholar
• Berry WL, Janknecht R. KDM4/JMJD2 histone demethylases: epigenetic regulators in cancer cells. Cancer Res 2013; 73:2936-42; PMID:23644528; http://dx.doi.org/10.1158/0008-5472.CAN-12-4300
   PubMed Web of Science ®Google Scholar
• Kupershmit I, Khoury-Haddad H, Awwad SW, Guttmann-Raviv N, Ayoub N. KDM4C (GASC1) lysine demethylase is associated with mitotic chromatin and regulates chromosome segregation during mitosis. Nucleic Acids Res 2014; 42:6168-82; PMID:24728997; http://dx.doi.org/10.1093/nar/gku253
   PubMed Web of Science ®Google Scholar
• Frescas D, Guardavaccaro D, Kuchay SM, Kato H, Poleshko A, Basrur V, Elenitoba-Johnson KS, Katz RA, Pagano M. KDM2A represses transcription of centromeric satellite repeats and maintains the heterochromatic state. Cell Cycle 2008; 7:3539-47; PMID:19001877; http://dx.doi.org/10.4161/cc.7.22.7062
   PubMed Web of Science ®Google Scholar
• Cheng Z, Cheung P, Kuo AJ, Yukl ET, Wilmot CM, Gozani O, Patel DJ. A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36. Genes Dev 2014; 28:1758-71; PMID:25128496; http://dx.doi.org/10.1101/gad.246561.114
   PubMed Web of Science ®Google Scholar