[1] | Mariñoramírez L, Kann MG, Shoemaker BA, Landsman D . Histone structure and nucleosome stability. Expert Rev Proteomic, 2005,2(5):719-729. [DOI] | [2] | Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ . Crystal structure of the nucleosome core particle at 2.8Å resolution. Nature, 1997,389(6648):251-260. [DOI] | [3] | Strahl BD, Allis CD . The language of covalent histone modifications. Nature, 2000,403(6765):41-45. [DOI] | [4] | Suganuma T, Workman JL . Crosstalk among histone modifications. Cell, 2008,135(4):604-607. [DOI] | [5] | Lee JS, Smith E, Shilatifard A . The language of histone crosstalk. Cell, 2010,142(5):682-685. [DOI] | [6] | Hershko A, Ciechanover A . The ubiquitin system. Annu Rev Biochem, 1998,67(1):425-479. [DOI] | [7] | Herrmann J, Lerman LO, Lerman A . Ubiquitin and ubiquitin-like proteins in protein regulation. Circ Res, 2007,100(9):1276-1291. [DOI] | [8] | Shaid S, Brandts CH, Serve H, Dikic I . Ubiquitination and selective autophagy. Cell Death Differ, 2013,20(1):21-30. [DOI] | [9] | Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C. A proteome-wide , quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics, 2011, 10(10): M111.013284. [DOI] | [10] | Welchman RL, Gordon C, Mayer RJ . Ubiquitin and ubiquitin-like proteins as multifunctional signals. Nat Rev Mol Cell Bio, 2005,6(8):599-609. [DOI] | [11] | Schnell JD, Hicke L . Non-traditional functions of ubiquitin and ubiquitin-binding proteins. J Biol Chem, 2003,278(38):35857-35860. [DOI] | [12] | Komander D, Rape M . The Ubiquitin Code. Annu Rev Biochem, 2012,81:203-229. [DOI] | [13] | Goldknopf IL, Taylor CW, Baum RM, Yeoman LC, Olson MO, Prestayko AW, Busch H . Isolation and characterization of protein A24, a "histone-like" non-histone chromosomal protein. J Biol Chem, 1975,250(18):7182-7187. [DOI] | [14] | Goldknopf IL, Busch H . Isopeptide linkage between nonhistone and histone 2A polypeptides of chromosomal conjugate-protein A24. Proc Natl Acad Sci USA, 1977,74(3):864-868. [DOI] | [15] | Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, Jones RS, Zhang Y . Role of histone H2A ubiquitination in polycomb silencing. Nature, 2004,431(7010):873-878. [DOI] | [16] | Fang J, Chen TB, Li E, Zhang Y . Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J Biol Chem, 2004,279(51):52812-52815. [DOI] | [17] | Zhou W, Zhu P, Wang J, Pascual G, Ohgi KA, Lozach J, Glass CK, Rosenfeld MG . Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerrase II transcriptional elongation. Mol Cell, 2008,29(1):69-80. [DOI] | [18] | Ginjala V, Nacerddine K, Kulkarni A, Oza J, Hill SJ, Yao M, Citterio E, Lohuizen MV, Ganesan S . BMI1 is recruited to DNA breaks and contributes to DNA damage-induced H2A ubiquitination and repair. Mol Cell Biol, 2011,31(10):1972-1982. [DOI] | [19] | Blackledge NP, Farcas AM, Kondo T, King HW, McGouran JF, Hanssen LL, Ito S, Cooper S, Kondo K, Koseki Y, Ishikura T, Long HK, Sheahan TW, Brockdorff N, Kessler BM, Koseki H, Klose RJ . Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell, 2014,157(6):1445-1459. [DOI] | [20] | Ismail IH, Andrin C, Mcdonald D, Hendzel MJ . BMI1- mediated histone ubiquitylation promotes DNA double- strand break repair. J Biol Chem, 2010,191(1):45-60. [DOI] | [21] | Chitale S, Richly H . Nuclear organization of nucleotide excision repair is mediated by RING1B dependent H2A- ubiquitylation. Oncotarget, 2017,8(19):30870-30887. [DOI] | [22] | Shanbhag NM, Rafalska-Metcalf IU, Balane-Bolivar C, Janicki SM, Greenberg RA . ATM-dependent chromatin changes silence transcription in cis to DNA double-strand breaks. Cell, 2010,141(6):970-981. [DOI] | [23] | Kakarougkas A, Ismail A, Chambers AL, Riballo E, Herbert AD, Künzel J, Löbrich M, Jeggo PA, Downs JA . Requirement for PBAF in transcriptional repression and repair at DNA breaks in actively transcribed regions of chromatin. Mol Cell, 2014,55(5):723-732. [DOI] | [24] | Chandler H, Patel H, Palermo R, Brookes S, Matthews N, Peters G . Role of polycomb group proteins in the DNA damage response - a reassessment. PLoS One, 2014,9(7):e102968. [DOI] | [25] | Bergink S, Salomons FA, Hoogstraten D, Groothuis TA, De WH, Wu J, Yuan L, Citterio E, Houtsmuller AB, Neefjes J, Hoeijmakers JH, Vermeulen W, Dantuma NP . DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. Gene Dev, 2006,20(10):1343-1352. [DOI] | [26] | Zhu Q, Wani G, Arab HH, El-Mahdy MA, Ray A, Wani AA . Chromatin restoration following nucleotide excision repair involves the incorporation of ubiquitinated H2A at damaged genomic sites. DNA Repair, 2009,8(2):262-273. [DOI] | [27] | Uckelmann M, Sixma TK . Histone ubiquitination in the DNA damage response. DNA Repair, 2017,56:92-101. [DOI] | [28] | Stucki M, Clapperton JA, Mohammad D, Yaffe MB, Smerdon SJ, Jackson SP . MDC1 directly binds phosphorrylated histone H2AX to regulate cellular responses to DNA double-strand breaks. Cell, 2005,123(7):1213-1226. [DOI] | [29] | Huen MS, Grant R, Manke I, Minn K, Yu X, Yaffe MB, Chen J . RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly. Cell, 2007,131(5):901-914. [DOI] | [30] | Mailand N, Bekker-Jensen S, Faustrup H, Melander F, Bartek J, Lukas C, Lukas J . RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell, 2007,131(5):887-900. [DOI] | [31] | Doil C, Mailand N, Bekker-Jensen S, Menard P, Larsen DH, Pepperkok R, Ellenberg J, Panier S, Durocher D, Bartek J . RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell, 2009,136(3):435-446. [DOI] | [32] | Mattiroli F, Vissers JH, van Dijk WJ, Ikpa P, Citterio E, Vermeulen W, Marteijn JA, Sixma TK . RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling. Cell, 2012,150(6):1182-1195. [DOI] | [33] | Thorslund T, Ripplinger A, Hoffmann S, Wild T, Uckelmann M, Villumsen B, Narita T, Sixma TK, Choudhary C, Bekkerjensen S, Mailand N . Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage. Nature, 2015,527(7578):389-393. [DOI] | [34] | Savage KI, Harkin DP . BRCA1, a 'complex' protein involved in the maintenance of genomic stability. FEBS J, 2015,282(4):630-646. [DOI] | [35] | Sobhian B, Shao G, Lilli DR, Culhane AC, Moreau LA, Xia B, Livingston DM, Greenberg RA . RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science, 2007,316(5828):1198-1202. [DOI] | [36] | Ng HM, Wei LZ, Lan L, Huen MSY . The Lys 63- deubiquitylating enzyme BRCC36 limits DNA break processing and repair . J Biol Chem, 2016,291(31):16197-16207. [DOI] | [37] | Fradetturcotte A, Canny MD, Escribanodíaz C, Orthwein A, Leung CC, Huang H, Landry MC, Kitevskileblanc J, Noordermeer SM, Sicheri F, Durocher D . 53BP1 is a reader of the DNA-damage-induced H2A lys 15 ubiquitin mark. Nature, 2013,499(7456):50-54. [DOI] | [38] | Wilson MD, Benlekbir S, Fradet-Turcotte A, Sherker A, Julien JP, Mcewan A, Noordermeer SM, Sicheri F, Rubinstein JL, Durocher D . The structural basis of modified nucleosome recognition by 53BP1. Nature, 2016,536(7614):100-103. [DOI] | [39] | Ochs F, Somyajit K, Altmeyer M, Rask MB, Lukas J, Lukas C . 53BP1 fosters fidelity of homology-directed DNA repair. Nat Struct Mol Biol, 2016,23(8):714-721. [DOI] | [40] | Kalb R, Mallery D, Larkin C, Huang JJ, Hiom K . BRCA1 is a histone-H2A-specific ubiquitin ligase. Cell Rep, 2014,8(4):999-1005. [DOI] | [41] | Densham RM, Morris JR . The BRCA1 ubiquitin ligase function sets a new trend for remodelling in DNA repair. Nucleus, 2017,8(2):116-125. [DOI] | [42] | Densham RM, Garvin AJ, Stone HR, Strachan J, Baldock RA, Daza-Martin M, Fletcher A, Blair-Reid S, Beesley J, Johal B, Pearl LH, Neely R, Keep NH, Watts FZ, Morris JR . Human BRCA1-BARD1 ubiquitin ligase activity counteracts chromatin barriers to DNA resection. Nat Struct Mol Biol, 2016,23(7):647-655. [DOI] | [43] | Gieni RS, Ismail IH, Campbell S, Hendzel MJ . Polycomb group proteins in the DNA damage response: a link between radiation resistance and "stemness". Cell Cycle, 2011,10(6):883-894. [DOI] | [44] | Cruz-García A, López-Saavedra A, Huertas P . BRCA1 accelerates CtIP-mediated DNA-end resection. Cell Rep, 2014,9(2):451-459. [DOI] | [45] | Polato F, Callen E, Wong N, Faryabi R, Bunting S, Chen HT, Kozak M, Kruhlak MJ, Reczek CR, Lee WH, Ludwig T, Baer R, Feigenbaum L, Jackson S, Nussenzweig A . CtIP-mediated resection is essential for viability and can operate independently of BRCA1. J Eep Med, 2014,211(6):1027-1036. [DOI] | [46] | Hannah J, Zhou P . Distinct and overlapping functions of the cullin E3 ligase scaffolding proteins CUL4A and CUL4B. Genes, 2015,573(1):33-45. [DOI] | [47] | Hess MT, Schwitter U, Petretta M, Giese B, Naegeli H . Bipartite substrate discrimination by human nucleotide excision repair. Proc Natl Acad Sci USA, 1997,94(13):6664-6669. [DOI] | [48] | Lan L, Nakajima S, Kapetanaki MG, Hsieh CL, Fagerburg M, Thickman K, Rodriguez-Collazo P, Leuba SH, Levine AS, Rapić-Otrin V . Monoubiquitinated histone H2A destabilizes photolesion-containing nucleosomes with concomitant release of UV-damaged DNA-binding protein E3 ligase. J Biol Chem, 2012,287(15):12036-12049. [DOI] | [49] | Hannah J, Zhou P . Regulation of DNA damage response pathways by the cullin-RING ubiquitin ligases. DNA Repair, 2009,8(4):536-543. [DOI] | [50] | Kapetanaki MG, Guerrero-Santoro J, Bisi DC, Hsieh CL, Rapić-Otrin V, Levine AS . The DDB1-CUL4A DDB2 ubiquitin ligase is deficient in xeroderma pigmentosum group E and targets histone H2A at UV-damaged DNA sites . Proc Natl Acad Sci USA, 2006,103(8):2588-2593. [DOI] | [51] | Puumalainen MR, Lessel D, Rüthemann P, Kaczmarek N, Bachmann K, Ramadan K, Naegeli H . Chromatin retention of DNA damage sensors DDB2 and XPC through loss of p97 segregase causes genotoxicity. Nat Commun, 2014,5:3695. [DOI] | [52] | El-Mahdy MA, Zhu Q, Wang QE, Wani G, Praetorius-Ibba M, Wani AA . Cullin 4A-mediated proteolysis of DDB2 protein at DNA damage sites regulates in vivo lesion recognition by XPC. J Biol Chem, 2006,281(19):13404-13411. [DOI] | [53] | Sugasawa K, Okuda Y, Saijo M, Nishi R, Matsuda N, Chu G, Mori T, Iwai S, Tanaka K, Tanaka K, Hanaoka F . UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex. Cell, 2005,121(3):387-400. [DOI] | [54] | Meas R, Mao P . Histone ubiquitylation and its roles in transcription and DNA damage response. DNA Repair, 2015,36:36-42. [DOI] | [55] | Shiloh Y, Shema E, Moyal L, Oren M . RNF20-RNF40: A ubiquitin-driven link between gene expression and the DNA damage response. FEBS Lett, 2011,585(18):2795-2802. [DOI] | [56] | Hérissant L, Moehle EA, Bertaccini D, Dorsselaer AV, Schaefferreiss C, Guthrie C, Dargemont C . H2B ubiquitylation modulates spliceosome assembly and function in budding yeast. Biol Cell, 2014,106(4):126-138. [DOI] | [57] | Weake VM, Workman JL . Histone ubiquitination: triggering gene activity. Mol Cell, 2008,29(6):653-663. [DOI] | [58] | Moyal L, Lerenthal Y, Gana-Weisz M, Mass G, So S, Wang SY, Eppink B, Chung YM, Shalev G, Shema E, Shkedy D, Smorodinsky NI, van Vliet N, Kuster B, Mann M, Ciechanover A, Dahm-Daphi J, Kanaar R, Hu MC, Chen DJ, Oren M, Shiloh Y . Requirement of ATM- dependent monoubiquitylation of histone H2B for timely repair of DNA double-strand breaks. Mol Cell, 2011,41(5):529-542. [DOI] | [59] | Huyen Y, Zgheib O, Ditullio RA, Gorgoulis VG, Zacharatos P, Petty TJ, Sheston EA, Mellert HS, Stavridi ES, Halazonetis TD . Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature, 2004,432(7015):406-411. [DOI] | [60] | Wakeman TP, Wang Q, Feng J, Wang XF . Bat3 facilitates H3K79 dimethylation by DOT1L and promotes DNA damage-induced 53BP1 foci at G1/G2 cell-cycle phases. EMBO J, 2012,31(9):2169-2181. [DOI] | [61] | Zhou LJ, Holt MT, Ohashi N, Zhao AS, Muller MM, Wang BY, Muir TW . Evidence that ubiquitylated H2B corrals hDot1L on the nucleosomal surface to induce H3K79 methylation. Nat Commun, 2016,7:10589. [DOI] | [62] | Kato A, Komatsu K . RNF20-SNF2H pathway of chromatin relaxation in DNA double-strand break repair. Genes (Basel), 2015,6(3):592-606. [DOI] | [63] | Kim J, Guermah M, McGinty RK, Lee J-S, Tang Z, Milne TA, Shilatifard A, Muir TW, Roeder RG . RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell, 2009,137(3):459-471. [DOI] | [64] | Fierz B, Chatterjee C, McGinty RK, Bar-Dagan M, Raleigh DP, Muir TW . Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat Chem Biol, 2011,7(2):113-119. [DOI] | [65] | Robinson PJJ, An W, Routh A, Martino F, Chapman L, Roeder RG, Rhodes D . 30 nm chromatin fibre decompaction requires both H4-K16 acetylation and linker histone eviction. J Mol Biol, 2008,381(4):816-825. [DOI] | [66] | Kari V, Shchebet A, Neumann H, Johnsen SA . The H2B ubiquitin ligase RNF40 cooperates with SUPT16H to induce dynamic changes in chromatin structure during DNA double-strand break repair. Cell Cycle, 2011,10(20):3495-3504. [DOI] | [67] | Nair DM, Ge Z, Mersfelder EL, Parthun MR . Genetic interactions between POB3 and the acetylation of newly synthesized histones. Curr Genet, 2011,57(4):271-286. [DOI] | [68] | Vlaming H, van Welsem T, de Graaf EL, Ontoso D, Altelaar AF, San-Segundo PA, Heck AJ, van Leeuwen F . Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo. EMBO Rep, 2014,15(10):1077-1084. [DOI] | [69] | Nakanishi S, Lee JS, Gardner KE, Gardner JM, Takahashi Y, Chandrasekharan MB, Sun ZW, Osley MA, Strahl BD, Jaspersen SL, Shilatifard A . Histone H2BK123 monoubiquitination is the critical determinant for H3K4 and H3K79 trimethylation by COMPASS and Dot1. J Biol Chem, 2009,186(3):371-377. [DOI] | [70] | Tatum D, Li S . Evidence that the histone methyltransferase Dot1 mediates global genomic repair by methylating histone H3 on lysine 79. J Biol Chem, 2011,286(20):17530-17535. [DOI] | [71] | Hung SH, Wong RP, Ulrich HD, Kao CF . Monoubiquitylation of histone H2B contributes to the bypass of DNA damage during and after DNA replication. Proc Natl Acad Sci USA, 2017,114(11):E2205-E2214. [DOI] | [72] | Northam MR, Trujillo KM . Histone H2B mono- ubiquitylation maintains genomic integrity at stalled replication forks. Nucleic Acids Res, 2016,44(19):9245-9255. [DOI] | [73] | Wang H, Zhai L, Xu J, Joo HY, Jackson S, Erdjument- Bromage H, Tempst P, Xiong Y, Zhang Y . Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage. Mol Cell, 2006,22(3):383-394. [DOI] | [74] | Zhu QZ, Wei SC, Sharma N, Wani G, He JS, Wani AA . Human CRL4 DDB2 ubiquitin ligase preferentially regulates post-repair chromatin restoration of H3K56Ac through recruitment of histone chaperon CAF-1 . Oncotarget, 2017,8(61):104525-104542. [DOI] | [75] | Adam S, Polo SE, Almouzni G . Transcription recovery after DNA damage requires chromatin priming by the H3.3 histone chaperone HIRA. Cell, 2013,155(1):94-106. [DOI] | [76] | Tropberger P, Schneider R . Scratching the (lateral) surface of chromatin regulation by histone modifications. Nat Struct Mol Biol, 2013,20(6):657-661. [DOI] | [77] | Yan Q, Dutt S, Xu R, Graves K, Juszczynski P, Manis JP, Shipp MA . BBAP monoubiquitylates histone H4 at lysine 91 and selectively modulates the DNA damage response. Mol Cell, 2009,36(1):110-120. [DOI] | [78] | Yan Q, Xu R, Zhu L, Cheng X, Wang Z, Manis J, Shipp MA . BAL1 and its partner E3 ligase, BBAP, link poly (ADP-ribose) activation, ubiquitylation, and double-strand DNA repair independent of ATM, MDC1, and RNF8. Mol Cell Biol, 2013,33(4):845-857. [DOI] | [79] | Lancini C, van den Berk PC, Vissers JH, Gargiulo G, Song JY, Hulsman D, Serresi M, Tanger E, Blom M, Vens C, van Lohuizen M, Jacobs H, Citterio E . Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells. J Exp Med, 2014,211(9):1759-1777. [DOI] | [80] | Hu M, Li P, Li M, Li W, Yao T, Wu JW, Gu W, Cohen RE, Shi Y . Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell, 2002,111(7):1041-1054. [DOI] | [81] | Joo HY, Zhai L, Yang C, Nie S, Erdjument-Bromage H, Tempst P, Chang C, Wang H . Regulation of cell cycle progression and gene expression by H2A deubiquitination. Nature, 2007,449(7165):1068-1072. [DOI] | [82] | Sahtoe DD, van Dijk WJ, Ekkebus R, Ovaa H, Sixma TK . BAP1/ASXL1 recruitment and activation for H2A deubiquitination. Nat Commun, 2016,7:10292. [DOI] | [83] | Jullien J, Vodnala M, Pasque V, Oikawa M, Miyamoto K, Allen G, David SA, Brochard V, Wang S, Bradshaw C, Koseki H, Sartorelli V, Beaujean N, Gurdon J . Gene resistance to transcriptional reprogramming following nuclear transfer is directly mediated by multiple chromatin- repressive pathways. Mol Cell, 2017,65(5): 873- 884. e8. [DOI] | [84] | Sharma N, Zhu Q, Wani G, He J, Wang QE, Wani AA . USP3 counteracts RNF168 via deubiquitinating H2A and γH2AX at lysine 13 and 15. Cell Cycle, 2014,13(1):106-114. [DOI] | [85] | Wang ZQ, Zhang HL, Liu J, Cheruiyot A, Lee JH, Ordog T, Lou ZK, You ZS, Zhang ZG . USP51 deubiquitylates H2AK13,15ub and regulates DNA damage response. Genes Dev, 2016,30(8):946-959. [DOI] | [86] | Uckelmann M, Densham RM, Baas R, Winterwerp HHK, Fish A, Sixma TK, Morris JR . USP48 restrains resection by site-specific cleavage of the BRCA1 ubiquitin mark from H2A. Nat Commun, 2018,9:229. [DOI] | [87] | Morgan MT, Haj-Yahya M, Ringel AE, Bandi P, Brik A, Wolberger C . Structural basis for histone H2B deubiquitination by the SAGA DUB module. Science, 2016,351(6274):725-728. [DOI] | [88] | Ramachandran S, Haddad D, Li C, Le MX, Ling AK, So CC, Nepal RM, Gommerman JL, Yu K, Ketela T, Moffat J, Martin A . The SAGA deubiquitination module promotes DNA repair and class switch recombination through ATM and DNAPK-mediated γH2AX ormation. Cell Rep, 2016,15(7):1554-1565. [DOI] |
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