Release of core DNA from nucleosomal core particles following (ADP-ribose)n-modification invitro

Mathis, Georg A.; Althaus, Felix R.

doi:10.1016/0006-291x(87)90358-5

Cited by 61 publications

(25 citation statements)

References 15 publications

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“…PAR chains may act as DNA competitors, displacing histones and other proteins in the vicinity of a lesion to facilitate access 11,12 . Specific PAR binding has been demonstrated for the macrodomain 13 , occurring in the histone variant macroH2A 14 and the DNA helicase Alc1 15,16 , and the PBZ domain, found in aprataxin and PNK-like factor (APLF) and CHFR 17 .…”

mentioning

confidence: 99%

The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks

Ali¹,

Timinszky²,

Arribas-Bosacoma³

et al. 2012

Nat Struct Mol Biol

220

196

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Poly(ADP-ribose) polymerase I (PARP1) is a primary DNA damage sensor whose (ADP-ribose) polymerase activity is acutely regulated by interaction with DNA breaks. Upon activation at sites of DNA damage, PARP1 modifies itself and other proteins by covalent addition of long branched polymers of ADP-ribose, which in turn recruit downstream DNA repair and chromatin remodelling factors. PARP1 recognizes DNA damage through its N-terminal DNA-binding domain (DBD), which consists of a tandem repeat of an unusual zinc-finger (ZnF) domain. We have now determined the crystal structure of the human PARP1-DBD bound to a DNA break. Along with functional analysis of PARP1 recruitment to sites of DNA damage in vivo, the structure reveals a dimeric assembly whereby ZnF1 and ZnF2 domains from separate PARP1 molecules form a strand-break recognition module that helps activate PARP1 by facilitating its dimerization and consequent trans-automodification.Short-patch repair of DNA single-strand breaks is initiated by poly(ADP-ribose) polymerase-1 (PARP1) -a multi-domain enzyme activated by binding of its N-terminal DNA-binding domain (DBD) to DNA breaks [1][2][3][4][5] . Activated PARP1 utilises NAD + to Correspondence to: Andreas G. Ladurner; Laurence H. Pearl; Antony W. Oliver. AUTHOR CONTRIBUTIONS A.A.E.A. purified the protein, crystallized the complex and collected the X-ray diffraction data; G.T. designed and constructed the PARP1-EGFP constructs and performed the laser DNA damage experiments; M.K. performed the FRAP experiments; P.O.H. engineered the knockdown PARP1 cell line and the wild-type imaging reporter constructs, and performed the in vitro complementation assays; M.H. and R.A.-B. engineered and purified mutant PARP1 constructs; A.G.L. designed the study and analysed the data; L.H.P designed the study, analysed the data and wrote the paper; A.W.O. made the baculovirus constructs, designed the purification protocol, and solved and refined the crystal structure. All authors discussed the results and commented on the manuscript. We have now determined the crystal structure of the DNA-binding domain of PARP1 (PARP1-DBD) encompassing the first two zinc-finger (ZnF) domains, bound to a DNA break. In contrast with structural analysis of the separated domains 22 , we show that DNA binding by both zinc-finger domains is essential to damage recruitment in vivo, and that ZnF1 and ZnF2 domains from separate PARP1 molecules act as a functional unit to generate a dimeric binding module that specifically recognizes the single-strand / double-strand transition at a recessed DNA break. Mutational analysis in vitro and in cells demonstrates the functional requirement for zinc-finger dimerisation and reveals a mechanism for bringing two PARP1 molecules into close proximity at a DNA break as a prerequisite for transmodification. RESULTS Structure of the PARP1-DBD -DNA ComplexAn N-terminal segment of human PARP1 (residues 5-202) was expressed in insect cells and purified by column chromatography. Screening with a range of DNA molecules...

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mentioning

confidence: 99%

The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks

Ali¹,

Timinszky²,

Arribas-Bosacoma³

et al. 2012

Nat Struct Mol Biol

220

196

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“…Each residue in PAR contains an adenine moiety capable of base stacking and hydrogen bonding, as well as two phosphate groups that carry negative charges (Amé et al 2000). PAR may form definitive structures through intramolecular interactions (Minaga and Kun 1983a,b), and these structures have the potential for noncovalent attractive (or repulsive) interactions with other molecules (Mathis and Althaus 1987;Wesierska-Gadek and Sauermann 1988;Panzeter et al 1992). Thus, PAR may alter protein activity by functioning as a site-specific covalent modification, a protein-binding matrix, or a steric block.…”

Section: The Chemical Biology Of Parmentioning

confidence: 99%

“…Early biochemical studies suggested that PARP-1 could disrupt chromatin structure by PARylating histones and destabilizing nucleosomes (Poirier et al 1982;Mathis and Althaus 1987;Huletsky et al 1989). Histones H1 and H2B are the main histone targets for PARylation in vivo by PARP-1 and PARP-2, respectively (Poirier et al 1982;Huletsky et al 1989), although the other core histones are modified as well (D'Amours et al 1999).…”

Section: Modification Of Chromatin Structurementioning

confidence: 99%

“…Non-histone chromosomal proteins, including high mobility group proteins, are also PARylated in vivo (Tanuma and Johnson 1983). PARylation of histone proteins has been implicated in the decondensation of chromatin through destabilization of nucleosomes (Poirier et al 1982;Mathis and Althaus 1987;Kraus and Lis 2003). Note, however, that although much emphasis has been placed on histone proteins as targets for PARylation, PARP-1 itself is the primary target for PARylation in vivo, with >90% of PAR found on PARP-1 (Ogata et al 1981;Huletsky et al 1989;D'Amours et al 1999).…”

Section: Modification Of Chromatin Structurementioning

confidence: 99%

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Poly(ADP-ribosyl)ation by PARP-1: `PAR-laying' NAD⁺ into a nuclear signal

2005

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Poly(ADP-ribose) (PAR) and the PAR polymerases (PARPs) that catalyze its synthesis from donor nicotinamide adenine dinucleotide (NAD + ) molecules have received considerable attention in the recent literature. Poly(ADP-ribosyl)ation (PARylation) plays diverse roles in many molecular and cellular processes, including DNA damage detection and repair, chromatin modification, transcription, cell death pathways, insulator function, and mitotic apparatus function. These processes are critical for many physiological and pathophysiological outcomes, including genome maintenance, carcinogenesis, aging, inflammation, and neuronal function. This review highlights recent work on the biochemistry, molecular biology, physiology, and pathophysiology of PARylation, focusing on the activity of PARP-1, the most abundantly expressed member of a family of PARP proteins. In addition, connections between nuclear NAD + metabolism and nuclear signaling through PARP-1 are discussed.Structural and functional domains of PARP-1, the founding member of the PARP family PARP-1 is the founding member of the PARP family, which contains as many as 18 distinct proteins in humans (Amé et al. 2004). PARPs catalyze the polymerization of ADP-ribose units from donor NAD + molecules on target proteins, resulting in the attachment of linear or branched polymers (Fig.

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“…Histones are also a physiological target of ADP-ribose modifications in carcinogen-treated mammalian cells in vivo (20,21). Thus, the reversible modification of DNA-protein interactions (14,15,22,23) by protein ADP-ribosylation may be the underlying molecular mechanism for the transient formation of free DNA domains in eukaryotic excision repair.…”

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confidence: 99%

Uncoupling of DNA excision repair and nucleosomal unfolding in poly (ADP-ribose)-depleted mammalian cells

Mathis

Althaus

1990

Carcinogenesis

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The repair of DNA damage in eukaryotic cells is closely coupled with local changes of chromatin structure such that newly synthesized repair patches transiently appear in 'free' DNA domains with increased accessibility to enzymatic and chemical probes. We have isolated these domains from mammalian cells repairing bulky DNA adducts. During the first 3 h of repair, excision of adducts occurred exclusively in free DNA and was closely linked with the appearance of newly synthesized repair patches. Following depletion of chromatin-bound poly(ADP-ribose), the repositioning of repair patches into these domains was completely blocked, although overall repair patch synthesis was unaltered. Concomitantly, DNA adducts were no longer excised and tended to accumulate in free DNA domains. Our results suggest a tight coupling of the excision step with the formation of free DNA domains by a mechanism involving poly ADPrnbosylation of chromatin proteins.In chromatin of mammalian cells, newly synthesized DNA repair patches exhibit a transient micrococcal nuclease hypersensitivity. This hypersensitivity is thought to reflect local disruptions in the tightly packed nucleosomal organization of chromatin, causing exposure of 'free' DNA domains (for review see 1,2). The function of these domains as well as the mechanisms involved in their formation are unknown. We have speculated that the post-translational poly ADP-ribosylation of chromatin proteins might be involved in the formation of free DNA domains in DNA excision repair. Poly ADP-ribosylation is catalyzed by the enzyme poly(ADP-ribose)polymerase (1,3,4; EC 2.4.2.30). Following activation by DNA nicks, this enzyme operates in a strictly processive manner (5). Continuous treatment of living cells with benzamide, a competitive inhibitor of this enzyme (3,4,6), results in the degradation of chromatin-bound ADP-ribose polymers (7) by the enzyme poly(ADP-ribose)glycohydrolase (3,4). Using non-replicating adult rat hepatocytes in primary monolayer culture, we have established conditions for the complete depletion of chromatin-associated poly(ADP-ribose) (7,8). Hepatocytes survive up to 9 days under these conditions and maintain expression of liver-specific functions (8). Thus, poly(ADPribose)-depleted hepatocytes represent a convenient model system to study the role of poly ADP-ribosylation in specific steps of DNA repair.We have previously shown that unfolded free DNA domains can be isolated from the chromatin of intact mammalian cells by taking advantage of their preferential accessibility to 8-methoxypsoralen (9). Upon intercalation into free DNA domains of living cells, 8-methoxypsoralen can be photoactivated to form bifunctional DNA adducts crosslinking the two DNA strands. Crosslinked (free) DNA domains can then be isolated quantitatively following a denaturation/renaturation treatment and subsequent nuclease SI digestion of non-crosslinked DNA strands (for details see 9).Here we have isolated free DNA domains from non-replicating hepatocytes (9

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Release of core DNA from nucleosomal core particles following (ADP-ribose)n-modification invitro

Cited by 61 publications

References 15 publications

The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks

The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks

Poly(ADP-ribosyl)ation by PARP-1: `PAR-laying' NAD⁺ into a nuclear signal

Uncoupling of DNA excision repair and nucleosomal unfolding in poly (ADP-ribose)-depleted mammalian cells

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Release of core DNA from nucleosomal core particles following (ADP-ribose)n-modification invitro

Cited by 61 publications

References 15 publications

The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks

The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks

Poly(ADP-ribosyl)ation by PARP-1: `PAR-laying' NAD+ into a nuclear signal

Uncoupling of DNA excision repair and nucleosomal unfolding in poly (ADP-ribose)-depleted mammalian cells

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Poly(ADP-ribosyl)ation by PARP-1: `PAR-laying' NAD⁺ into a nuclear signal