XRCC1 protects transcription from toxic PARP1 activity during DNA base excision repair
Jazyk angličtina Země Velká Británie, Anglie Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
MR/P010121/1
Medical Research Council - United Kingdom
PubMed
34811483
PubMed Central
PMC8683375
DOI
10.1038/s41556-021-00792-w
PII: 10.1038/s41556-021-00792-w
Knihovny.cz E-zdroje
- MeSH
- DNA genetika MeSH
- genetická transkripce genetika MeSH
- histony metabolismus MeSH
- jednořetězcové zlomy DNA * MeSH
- lidé MeSH
- myši knockoutované MeSH
- myši MeSH
- nádorové buněčné linie MeSH
- oprava DNA genetika MeSH
- oxidační stres genetika MeSH
- peroxid vodíku toxicita MeSH
- poly(ADP-ribosa)polymerasa 1 genetika metabolismus MeSH
- protein XRCC1 genetika metabolismus MeSH
- specifické proteázy ubikvitinu metabolismus MeSH
- ubikvitinace fyziologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA MeSH
- histony MeSH
- PARP1 protein, human MeSH Prohlížeč
- peroxid vodíku MeSH
- poly(ADP-ribosa)polymerasa 1 MeSH
- protein XRCC1 MeSH
- specifické proteázy ubikvitinu MeSH
- USP3 protein, human MeSH Prohlížeč
- XRCC1 protein, human MeSH Prohlížeč
Genetic defects in the repair of DNA single-strand breaks (SSBs) can result in neurological disease triggered by toxic activity of the single-strand-break sensor protein PARP1. However, the mechanism(s) by which this toxic PARP1 activity triggers cellular dysfunction are unclear. Here we show that human cells lacking XRCC1 fail to rapidly recover transcription following DNA base damage, a phenotype also observed in patient-derived fibroblasts with XRCC1 mutations and Xrcc1-/- mouse neurons. This defect is caused by excessive/aberrant PARP1 activity during DNA base excision repair, resulting from the loss of PARP1 regulation by XRCC1. We show that aberrant PARP1 activity suppresses transcriptional recovery during base excision repair by promoting excessive recruitment and activity of the ubiquitin protease USP3, which as a result reduces the level of monoubiquitinated histones important for normal transcriptional regulation. Importantly, inhibition and/or deletion of PARP1 or USP3 restores transcriptional recovery in XRCC1-/- cells, highlighting PARP1 and USP3 as possible therapeutic targets in neurological disease.
Zobrazit více v PubMed
Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993;362:709–715. PubMed
Yoon G, Caldecott KW. Nonsyndromic cerebellar ataxias associated with disorders of DNA single-strand break repair. Handb. Clin. Neurol. 2018;155:105–115. PubMed
McKinnon PJ. Genome integrity and disease prevention in the nervous system. Genes Dev. 2017;31:1180–1194. PubMed PMC
Caldecott KW. Protein ADP-ribosylation and the cellular response to DNA strand breaks. DNA Repair. 2014;19:108–113. PubMed
Jungmichel S, et al. Proteome-wide identification of poly(ADP-ribosyl)ation targets in different genotoxic stress responses. Mol. Cell. 2013;52:272–285. PubMed
Ray Chaudhuri A, Nussenzweig A. The multifaceted roles of PARP1 in DNA repair and chromatin remodelling. Nat. Rev. Mol. Cell Biol. 2017;18:610–621. PubMed PMC
Satoh MS, Lindahl T. Role of poly(ADP-ribose) formation in DNA repair. Nature. 1992;356:356–358. PubMed
Hanzlikova H, Gittens W, Krejcikova K, Zeng Z, Caldecott KW. Overlapping roles for PARP1 and PARP2 in the recruitment of endogenous XRCC1 and PNKP into oxidized chromatin. Nucleic Acids Res. 2017;45:2546–2557. PubMed PMC
Breslin C, et al. The XRCC1 phosphate-binding pocket binds poly(ADP-ribose) and is required for XRCC1 function. Nucleic Acids Res. 2015;43:6934–6944. PubMed PMC
Masson M, et al. XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage. Mol. Cell Biol. 1998;18:3563–3571. PubMed PMC
Caldecott KW, Aoufouchi S, Johnson P, Shall S. XRCC1 polypeptide interacts with DNA polymerase β and possibly poly(ADP-ribose) polymerase, and DNA ligase III is a novel molecular ‘nick-sensor’ in vitro. Nucleic Acids Res. 1996;24:4387–4394. PubMed PMC
Kubota Y, et al. Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase β and the XRCC1 protein. EMBO J. 1996;15:6662–6670. PubMed PMC
Caldecott KW, McKeown CK, Tucker JD, Ljungquist S, Thompson LH. An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III. Mol. Cell Biol. 1994;14:68–76. PubMed PMC
Loizou JI, et al. The protein kinase CK2 facilitates repair of chromosomal DNA single-strand breaks. Cell. 2004;117:17–28. PubMed
Whitehouse CJ, et al. XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair. Cell. 2001;104:107–117. PubMed
Clements PM, et al. The ataxia-oculomotor apraxia 1 gene product has a role distinct from ATM and interacts with the DNA strand break repair proteins XRCC1 and XRCC4. DNA Repair. 2004;3:1493–1502. PubMed
Luo H, et al. A new XRCC1-containing complex and its role in cellular survival of methyl methanesulfonate treatment. Mol. Cell Biol. 2004;24:8356–8365. PubMed PMC
Hoch NC, et al. XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia. Nature. 2017;541:87–91. PubMed PMC
Komulainen E, et al. Parp1 hyperactivity couples DNA breaks to aberrant neuronal calcium signalling and lethal seizures. EMBO Rep. 2021;22:e51851. PubMed PMC
Zhou W, Doetsch PW. Effects of abasic sites and DNA single-strand breaks on prokaryotic RNA polymerases. Proc. Natl Acad. Sci. USA. 1993;90:6601–6605. PubMed PMC
Kathe SD, Shen GP, Wallace SS. Single-stranded breaks in DNA but not oxidative DNA base damages block transcriptional elongation by RNA polymerase II in HeLa cell nuclear extracts. J. Biol. Chem. 2004;279:18511–18520. PubMed
Neil AJ, Belotserkovskii BP, Hanawalt PC. Transcription blockage by bulky end termini at single-strand breaks in the DNA template: differential effects of 5′ and 3′ adducts. Biochemistry. 2012;51:8964–8970. PubMed PMC
Payne JM, Laybourn PJ, Dahmus ME. The transition of RNA polymerase II from initiation to elongation is associated with phosphorylation of the carboxyl-terminal domain of subunit IIa. J. Biol. Chem. 1989;264:19621–19629. PubMed
O’Brien T, Hardin S, Greenleaf A, Lis JT. Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature. 1994;370:75–77. PubMed
Zaborowska J, Egloff S, Murphy S. The pol II CTD: new twists in the tail. Nat. Struct. Mol. Biol. 2016;23:771–777. PubMed
Lee Y, et al. The genesis of cerebellar interneurons and the prevention of neural DNA damage require XRCC1. Nat. Neurosci. 2009;12:973–980. PubMed PMC
Caldecott KW. XRCC1 protein; Form and function. DNA Repair. 2019;81:102664. PubMed
Rulten SL, Cortes-Ledesma F, Guo L, Iles NJ, Caldecott KW. APLF (C2orf13) is a novel component of poly(ADP-ribose) signaling in mammalian cells. Mol. Cell Biol. 2008;28:4620–4628. PubMed PMC
Ahel I, et al. Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. Nature. 2008;451:81–85. PubMed
Demin AA, et al. XRCC1 prevents toxic PARP1 trapping during DNA base excision repair. Mol. Cell. 2021;81:3018–3030. PubMed PMC
Ikeda S, et al. Purification and characterization of human NTH1, a homolog of Escherichia coli endonuclease III. Direct identification of Lys-212 as the active nucleophilic residue. J. Biol. Chem. 1998;273:21585–21593. PubMed
Aspinwall R, et al. Cloning and characterization of a functional human homolog of Escherichia coli endonuclease III. Proc. Natl Acad. Sci. USA. 1997;94:109–114. PubMed PMC
Xu G, Herzig M, Rotrekl V, Walter CA. Base excision repair, aging and health span. Mech. Ageing Dev. 2008;129:366–382. PubMed PMC
Bartlett E, et al. Interplay of histone marks with serine ADP-ribosylation. Cell Rep. 2018;24:3488–3502. PubMed PMC
Hanzlikova H, et al. Pathogenic ARH3 mutations result in ADP-ribose chromatin scars during DNA strand break repair. Nat. Commun. 2020;11:3391. PubMed PMC
Huang D, et al. Functional interplay between histone H2B ADP-ribosylation and phosphorylation controls adipogenesis. Mol. Cell. 2020;79:934–949. PubMed PMC
Bonfiglio JJ, et al. Serine ADP-ribosylation depends on HPF1. Mol. Cell. 2017;65:932–940. PubMed PMC
Gibbs-Seymour I, Fontana P, Rack JGM, Ahel I. HPF1/C4orf27 Is a PARP-1-interacting protein that regulates PARP-1 ADP-ribosylation activity. Mol. Cell. 2016;62:432–442. PubMed PMC
Rudolph J, Roberts G, Muthurajan UM, Luger K. HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase. eLife. 2021;10:e65773. PubMed PMC
Suskiewicz MJ, et al. HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation. Nature. 2020;579:598–602. PubMed PMC
Polo SE, Kaidi A, Baskcomb L, Galanty Y, Jackson SP. Regulation of DNA-damage responses and cell-cycle progression by the chromatin remodelling factor CHD4. EMBO J. 2010;29:3130–3139. PubMed PMC
Chou DM, et al. 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. USA. 2010;107:18475–18480. PubMed PMC
Fierz B, et al. Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat. Chem. Biol. 2011;7:113–119. PubMed PMC
Pavri R, et al. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell. 2006;125:703–717. PubMed
Tanny JC, Erdjument-Bromage H, Tempst P, Allis CD. Ubiquitylation of histone H2B controls RNA polymerase II transcription elongation independently of histone H3 methylation. Genes Dev. 2007;21:835–847. PubMed PMC
Ting X, et al. USP11 acts as a histone deubiquitinase functioning in chromatin reorganization during DNA repair. Nucleic Acids Res. 2019;47:9721–9740. PubMed PMC
Zhang XY, et al. The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progression. Mol. Cell. 2008;29:102–111. PubMed PMC
DeVine T, Sears RC, Dai MS. The ubiquitin-specific protease USP36 is a conserved histone H2B deubiquitinase. Biochem. Biophys. Res. Commun. 2018;495:2363–2368. PubMed PMC
Gardner RG, Nelson ZW, Gottschling DE. Ubp10/Dot4p regulates the persistence of ubiquitinated histone H2B: distinct roles in telomeric silencing and general chromatin. Mol. Cell Biol. 2005;25:6123–6139. PubMed PMC
Henry KW, et al. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 2003;17:2648–2663. PubMed PMC
Nicassio F, et al. Human USP3 is a chromatin modifier required for S phase progression and genome stability. Curr. Biol. 2007;17:1972–1977. PubMed
Lancini C, et al. Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells. J. Exp. Med. 2014;211:1759–1777. PubMed PMC
Mosbech A, Lukas C, Bekker-Jensen S, Mailand N. The deubiquitylating enzyme USP44 counteracts the DNA double-strand break response mediated by the RNF8 and RNF168 ubiquitin ligases. J. Biol. Chem. 2013;288:16579–16587. PubMed PMC
Posavec Marjanović M, Crawford K, Ahel I. PARP, transcription and chromatin modeling. Semin. Cell Dev. Biol. 2017;63:102–113. PubMed
Kraus WL. Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregulation, and insulation. Curr. Opin. Cell Biol. 2008;20:294–302. PubMed PMC
Caldecott KW. Mammalian DNA base excision repair: dancing in the moonlight. DNA Repair. 2020;93:102921. PubMed
Krishnakumar R, et al. Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes. Science. 2008;319:819–821. PubMed
Wacker DA, et al. The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription. Mol. Cell Biol. 2007;27:7475–7485. PubMed PMC
Kim MY, Mauro S, Gévry N, Lis JT, Kraus WL. NAD+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1. Cell. 2004;119:803–814. PubMed
Tulin A, Spradling A. Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science. 2003;299:560–562. PubMed
Poirier GG, de Murcia G, Jongstra-Bilen J, Niedergang C, Mandel P. Poly(ADP-ribosyl)ation of polynucleosomes causes relaxation of chromatin structure. Proc. Natl Acad. Sci. USA. 1982;79:3423–3427. PubMed PMC
Gibson BA, et al. Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science. 2016;353:45–50. PubMed PMC
Kuraoka I, et al. Effects of endogenous DNA base lesions on transcription elongation by mammalian RNA polymerase II. Implications for transcription-coupled DNA repair and transcriptional mutagenesis. J. Biol. Chem. 2003;278:7294–7299. PubMed
Realini CA, Althaus FR. Histone shuttling by poly(ADP-ribosylation) J. Biol. Chem. 1992;267:18858–18865. PubMed
Muthurajan UM, et al. Automodification switches PARP-1 function from chromatin architectural protein to histone chaperone. Proc. Natl Acad. Sci. USA. 2014;111:12752–12757. PubMed PMC
Luijsterburg MS, et al. PARP1 links CHD2-mediated chromatin expansion and H3.3 deposition to DNA repair by non-homologous end-joining. Mol. Cell. 2016;61:547–562. PubMed PMC
Rother MB, et al. CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks. Nat. Commun. 2020;11:5775. PubMed PMC
Smith R, Sellou H, Chapuis C, Huet S, Timinszky G. CHD3 and CHD4 recruitment and chromatin remodeling activity at DNA breaks is promoted by early poly(ADP-ribose)-dependent chromatin relaxation. Nucleic Acids Res. 2018;46:6087–6098. PubMed PMC
Sharma N, et al. USP3 counteracts RNF168 via deubiquitinating H2A and γH2AX at lysine 13 and 15. Cell Cycle. 2014;13:106–114. PubMed PMC
Schwertman P, Bekker-Jensen S, Mailand N. Regulation of DNA double-strand break repair by ubiquitin and ubiquitin-like modifiers. Nat. Rev. Mol. Cell Biol. 2016;17:379–394. PubMed
Bergink S, et al. DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. Genes Dev. 2006;20:1343–1352. PubMed PMC
Ginjala V, et al. BMI1 is recruited to DNA breaks and contributes to DNA damage-induced H2A ubiquitination and repair. Mol. Cell Biol. 2011;31:1972–1982. PubMed PMC
Marteijn JA, et al. Nucleotide excision repair-induced H2A ubiquitination is dependent on MDC1 and RNF8 and reveals a universal DNA damage response. J. Cell Biol. 2009;186:835–847. PubMed PMC
Wu J, et al. Histone ubiquitination associates with BRCA1-dependent DNA damage response. Mol. Cell Biol. 2009;29:849–860. PubMed PMC
Tamburri S, et al. Histone H2AK119 mono-ubiquitination is essential for polycomb-mediated transcriptional repression. Mol. Cell. 2020;77:840–856. PubMed PMC
Nakagawa T, et al. Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation. Genes Dev. 2008;22:37–49. PubMed PMC
Kim J, Hake SB, Roeder RG. The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions. Mol. Cell. 2005;20:759–770. PubMed
Zhang F, Yu X. WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. Mol. Cell. 2011;41:384–397. PubMed PMC
Sun ZW, Allis CD. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature. 2002;418:104–108. PubMed
Kim J, et al. RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell. 2009;137:459–471. PubMed PMC
Moyal L, et al. Requirement of ATM-dependent monoubiquitylation of histone H2B for timely repair of DNA double-strand breaks. Mol. Cell. 2011;41:529–542. PubMed PMC
Mao P, Meas R, Dorgan KM, Smerdon MJ. UV damage-induced RNA polymerase II stalling stimulates H2B deubiquitylation. Proc. Natl Acad. Sci. USA. 2014;111:12811–12816. PubMed PMC
Wu W, et al. Neuronal enhancers are hotspots for DNA single-strand break repair. Nature. 2021;593:440–444. PubMed PMC
Weber AR, et al. Biochemical reconstitution of TET1-TDG-BER-dependent active DNA demethylation reveals a highly coordinated mechanism. Nat. Commun. 2016;7:10806. PubMed PMC
Hajkova P, et al. Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science. 2010;329:78–82. PubMed PMC
Steinacher R, et al. SUMOylation coordinates BERosome assembly in active DNA demethylation during cell differentiation. EMBO J. 2019;38:e99242. PubMed PMC
Haider L. Inflammation, iron, energy failure, and oxidative stress in the pathogenesis of multiple sclerosis. Oxid. Med. Cell Longev. 2015;2015:725370. PubMed PMC
Polo LM, et al. Efficient single-strand break repair requires binding to both poly(ADP-ribose) and DNA by the central BRCT domain of XRCC1. Cell Rep. 2019;26:573–581. PubMed PMC
Caldecott KW, Tucker JD, Stanker LH, Thompson LH. Characterization of the XRCC1–DNA ligase III complex in vitro and its absence from mutant hamster cells. Nucleic Acids Res. 1995;23:4836–4843. PubMed PMC
Iles N, Rulten S, El-Khamisy SF, Caldecott KW. APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. Mol. Cell Biol. 2007;27:3793–3803. PubMed PMC
Breslin C, et al. Measurement of chromosomal DNA single-strand breaks and replication fork progression rates. Methods Enzymol. 2006;409:410–425. PubMed