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Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions
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D'Amours D., Desnoyers S., D'Silva I., and Poirier G. Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem J 342 (1999) 249-268
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D'Amours, D.1
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Poly(ADP-ribosyl)ation by PARP-1: 'PAR-laying' NAD+ into a nuclear signal
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Kim M.Y., Zhang T., and Kraus W.L. Poly(ADP-ribosyl)ation by PARP-1: 'PAR-laying' NAD+ into a nuclear signal. Genes Dev 19 (2005) 1951-1967
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Kim, M.Y.1
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PARP goes transcription
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Kraus W.L., and Lis J. PARP goes transcription. Cell 113 (2003) 677-683
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Cell
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Kraus, W.L.1
Lis, J.2
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+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1
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+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1. Cell 119 (2004) 803-814
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Cell
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Kim, M.Y.1
Mauro, S.2
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Lis, J.4
Kraus, W.L.5
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6
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35648955118
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The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription
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This paper provides direct visual evidence for PARP-1-dependent compaction of chromatin by using atomic force microscopy of individual molecules of chromatin assembled in vitro. In addition, this paper demonstrates that first, the DBD of PARP-1 is necessary and sufficient for binding to nucleosomes, but alone is unable to promote chromatin compaction and second, the catalytic domain of PARP-1, which does not bind nucleosomes on its own, cooperates with the DBD to promote chromatin compaction in a manner independent of its enzymatic activity. Thus, the catalytic domain of PARP-1 plays a previously uncharacterized role in chromatin compaction.
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Wacker D.A., Ruhl D.D., Balagamwala E.H., Hope K.M., Zhang T., and Kraus W.L. The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription. Mol Cell Biol 27 (2007) 7475-7485. This paper provides direct visual evidence for PARP-1-dependent compaction of chromatin by using atomic force microscopy of individual molecules of chromatin assembled in vitro. In addition, this paper demonstrates that first, the DBD of PARP-1 is necessary and sufficient for binding to nucleosomes, but alone is unable to promote chromatin compaction and second, the catalytic domain of PARP-1, which does not bind nucleosomes on its own, cooperates with the DBD to promote chromatin compaction in a manner independent of its enzymatic activity. Thus, the catalytic domain of PARP-1 plays a previously uncharacterized role in chromatin compaction.
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(2007)
Mol Cell Biol
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, pp. 7475-7485
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Wacker, D.A.1
Ruhl, D.D.2
Balagamwala, E.H.3
Hope, K.M.4
Zhang, T.5
Kraus, W.L.6
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7
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17144404217
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Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding
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Lonskaya I., Potaman V.N., Shlyakhtenko L.S., Oussatcheva E.A., Lyubchenko Y.L., and Soldatenkov V.A. Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding. J Biol Chem 280 (2005) 17076-17083
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J Biol Chem
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Lonskaya, I.1
Potaman, V.N.2
Shlyakhtenko, L.S.3
Oussatcheva, E.A.4
Lyubchenko, Y.L.5
Soldatenkov, V.A.6
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8
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Specific binding of poly(ADP-ribose) polymerase-1 to cruciform hairpins
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Potaman V.N., Shlyakhtenko L.S., Oussatcheva E.A., Lyubchenko Y.L., and Soldatenkov V.A. Specific binding of poly(ADP-ribose) polymerase-1 to cruciform hairpins. J Mol Biol 348 (2005) 609-615
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J Mol Biol
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Potaman, V.N.1
Shlyakhtenko, L.S.2
Oussatcheva, E.A.3
Lyubchenko, Y.L.4
Soldatenkov, V.A.5
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9
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2+, histones H1 and H3, and ATP
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2+, histones H1 and H3, and ATP. Biochemistry 43 (2004) 210-216
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Biochemistry
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Kun, E.1
Kirsten, E.2
Mendeleyev, J.3
Ordahl, C.P.4
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10
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41549108573
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A third zinc-binding domain of human poly(ADP-ribose) polymerase-1 coordinates DNA-dependent enzyme activation
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Using spectroscopic and crystallographic analyses, this paper identifies and characterizes a previously unidentified third zinc-binding domain in PARP-1. This new zinc-binding domain, which is located between the amino-terminal zinc fingers in the DBD and the BRCT motif in the AMD, mediates interdomain contacts important for DNA-dependent enzyme activation. The crystal structure reveals a zinc ribbon fold and points to conserved residues that could form interdomain contacts that may help to couple the DNA binding and catalytic functions of PARP-1. Together, the results described in this paper provide a structural and mechanistic basis for the DBD-dependent allosteric activation of PARP-1 enzymatic activity.
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Langelier M.F., Servent K.M., Rogers E.E., and Pascal J.M. A third zinc-binding domain of human poly(ADP-ribose) polymerase-1 coordinates DNA-dependent enzyme activation. J Biol Chem 283 (2008) 4105-4114. Using spectroscopic and crystallographic analyses, this paper identifies and characterizes a previously unidentified third zinc-binding domain in PARP-1. This new zinc-binding domain, which is located between the amino-terminal zinc fingers in the DBD and the BRCT motif in the AMD, mediates interdomain contacts important for DNA-dependent enzyme activation. The crystal structure reveals a zinc ribbon fold and points to conserved residues that could form interdomain contacts that may help to couple the DNA binding and catalytic functions of PARP-1. Together, the results described in this paper provide a structural and mechanistic basis for the DBD-dependent allosteric activation of PARP-1 enzymatic activity.
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(2008)
J Biol Chem
, vol.283
, pp. 4105-4114
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Langelier, M.F.1
Servent, K.M.2
Rogers, E.E.3
Pascal, J.M.4
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11
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40649125860
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PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system
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Droit A., Hunter J.M., Rouleau M., Ethier C., Picard-Cloutier A., Bourgais D., and Poirier G.G. PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system. BMC Bioinformatics 8 (2007) 483
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BMC Bioinformatics
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Droit, A.1
Hunter, J.M.2
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Ethier, C.4
Picard-Cloutier, A.5
Bourgais, D.6
Poirier, G.G.7
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12
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10944253639
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Activating the PARP-1 sensor component of the groucho/TLE1 corepressor complex mediates a CaMKinase IIdelta-dependent neurogenic gene activation pathway
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Ju B.G., Solum D., Song E.J., Lee K.J., Rose D.W., Glass C.K., and Rosenfeld M.G. Activating the PARP-1 sensor component of the groucho/TLE1 corepressor complex mediates a CaMKinase IIdelta-dependent neurogenic gene activation pathway. Cell 119 (2004) 815-829
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Cell
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Ju, B.G.1
Solum, D.2
Song, E.J.3
Lee, K.J.4
Rose, D.W.5
Glass, C.K.6
Rosenfeld, M.G.7
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13
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20144389926
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PARP-1 determines specificity in a retinoid signaling pathway via direct modulation of Mediator
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Pavri R., Lewis B., Kim T.K., Dilworth F.J., Erdjument-Bromage H., Tempst P., de Murcia G., Evans R., Chambon P., and Reinberg D. PARP-1 determines specificity in a retinoid signaling pathway via direct modulation of Mediator. Mol Cell 18 (2005) 83-96
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(2005)
Mol Cell
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Pavri, R.1
Lewis, B.2
Kim, T.K.3
Dilworth, F.J.4
Erdjument-Bromage, H.5
Tempst, P.6
de Murcia, G.7
Evans, R.8
Chambon, P.9
Reinberg, D.10
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14
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33644858558
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Condensin I interacts with the PARP-1-XRCC1 complex and functions in DNA single-strand break repair
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Heale J.T., Ball Jr. A.R., Schmiesing J.A., Kim J.S., Kong X., Zhou S., Hudson D.F., Earnshaw W.C., and Yokomori K. Condensin I interacts with the PARP-1-XRCC1 complex and functions in DNA single-strand break repair. Mol Cell 21 (2006) 837-848
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Mol Cell
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Heale, J.T.1
Ball Jr., A.R.2
Schmiesing, J.A.3
Kim, J.S.4
Kong, X.5
Zhou, S.6
Hudson, D.F.7
Earnshaw, W.C.8
Yokomori, K.9
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15
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33845445006
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The histone variant mH2A1.1 interferes with transcription by down-regulating PARP-1 enzymatic activity
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•], this paper describes interactions between PARP-1 and the 'nonhistone' domain of the histone variant macroH2A1 (specifically the 1.1 splice variant in this case), which may help to bring PARP-1 to chromatin and inhibit its enzymatic activity. These interactions between PARP-1 and macroH2A1 play a role in regulating gene expression. Specifically, this paper shows that RNAi-mediated depletion of macroH2A1 or PARP-1 blocks heat-shock-induced expression of the HSP70.1 gene. Together, these studies suggest an interesting functional link between PARP-1 and macroH2A.
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•], this paper describes interactions between PARP-1 and the 'nonhistone' domain of the histone variant macroH2A1 (specifically the 1.1 splice variant in this case), which may help to bring PARP-1 to chromatin and inhibit its enzymatic activity. These interactions between PARP-1 and macroH2A1 play a role in regulating gene expression. Specifically, this paper shows that RNAi-mediated depletion of macroH2A1 or PARP-1 blocks heat-shock-induced expression of the HSP70.1 gene. Together, these studies suggest an interesting functional link between PARP-1 and macroH2A.
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(2006)
Genes Dev
, vol.20
, pp. 3324-3336
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Ouararhni, K.1
Hadj-Slimane, R.2
Ait-Si-Ali, S.3
Robin, P.4
Mietton, F.5
Harel-Bellan, A.6
Dimitrov, S.7
Hamiche, A.8
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16
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6944231017
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Poly(ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation
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Yu W., Ginjala V., Pant V., Chernukhin I., Whitehead J., Docquier F., Farrar D., Tavoosidana G., Mukhopadhyay R., Kanduri C., et al. Poly(ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation. Nat Genet 36 (2004) 1105-1110
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(2004)
Nat Genet
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Yu, W.1
Ginjala, V.2
Pant, V.3
Chernukhin, I.4
Whitehead, J.5
Docquier, F.6
Farrar, D.7
Tavoosidana, G.8
Mukhopadhyay, R.9
Kanduri, C.10
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17
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0842310349
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CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species
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Yusufzai T.M., Tagami H., Nakatani Y., and Felsenfeld G. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol Cell 13 (2004) 291-298
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Mol Cell
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Yusufzai, T.M.1
Tagami, H.2
Nakatani, Y.3
Felsenfeld, G.4
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18
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38949198773
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Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes
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Using ChIP-chip, this paper provides the first high-resolution map of PARP-1 and histone H1 localization across a mammalian genome. The data show that PARP-1 and H1 exhibit a reciprocal localization pattern at many Pol II-transcribed promoters, with enriched PARP-1 and depleted H1. This high PARP-1/H1 ratio is associated with actively transcribed genes. Gene-specific studies showed that PARP-1 acts to exclude H1 from a subset of PARP-1-stimulated promoters, suggesting a functional interplay between PARP-1 and H1 at the level of nucleosome binding reminiscent of the results from the biochemical studies presented in [5]. Together, these data indicate that PARP-1 and H1 have opposing actions at many Pol II-transcribed promoters.
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Krishnakumar R., Gamble M.J., Frizzell K.M., Berrocal J.G., Kininis M., and Kraus W.L. Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes. Science 319 (2008) 819-821. Using ChIP-chip, this paper provides the first high-resolution map of PARP-1 and histone H1 localization across a mammalian genome. The data show that PARP-1 and H1 exhibit a reciprocal localization pattern at many Pol II-transcribed promoters, with enriched PARP-1 and depleted H1. This high PARP-1/H1 ratio is associated with actively transcribed genes. Gene-specific studies showed that PARP-1 acts to exclude H1 from a subset of PARP-1-stimulated promoters, suggesting a functional interplay between PARP-1 and H1 at the level of nucleosome binding reminiscent of the results from the biochemical studies presented in [5]. Together, these data indicate that PARP-1 and H1 have opposing actions at many Pol II-transcribed promoters.
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(2008)
Science
, vol.319
, pp. 819-821
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Krishnakumar, R.1
Gamble, M.J.2
Frizzell, K.M.3
Berrocal, J.G.4
Kininis, M.5
Kraus, W.L.6
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19
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33847784252
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Loss of Parp-1 affects gene expression profile in a genome-wide manner in ES cells and liver cells
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[see Erratum in BMC Genomics 2007, 8:227]
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Ogino H., Nozaki T., Gunji A., Maeda M., Suzuki H., Ohta T., Murakami Y., Nakagama H., Sugimura T., and Masutani M. Loss of Parp-1 affects gene expression profile in a genome-wide manner in ES cells and liver cells. BMC Genomics 8 (2007) 41 [see Erratum in BMC Genomics 2007, 8:227]
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Ogino, H.1
Nozaki, T.2
Gunji, A.3
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Suzuki, H.5
Ohta, T.6
Murakami, Y.7
Nakagama, H.8
Sugimura, T.9
Masutani, M.10
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0034633783
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Misregulation of gene expression in primary fibroblasts lacking poly(ADP-ribose) polymerase
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Simbulan-Rosenthal C.M., Ly D.H., Rosenthal D.S., Konopka G., Luo R., Wang Z.Q., Schultz P.G., and Smulson M.E. Misregulation of gene expression in primary fibroblasts lacking poly(ADP-ribose) polymerase. Proc Natl Acad Sci U S A 97 (2000) 11274-11279
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Proc Natl Acad Sci U S A
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Simbulan-Rosenthal, C.M.1
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Rosenthal, D.S.3
Konopka, G.4
Luo, R.5
Wang, Z.Q.6
Schultz, P.G.7
Smulson, M.E.8
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21
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Absence of poly(ADP-ribose)polymerase-1 alters nuclear factor-kappa B activation and gene expression of apoptosis regulators after reperfusion injury
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Zingarelli B., Hake P.W., O'Connor M., Denenberg A., Kong S., and Aronow B.J. Absence of poly(ADP-ribose)polymerase-1 alters nuclear factor-kappa B activation and gene expression of apoptosis regulators after reperfusion injury. Mol Med 9 (2003) 143-153
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Mol Med
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Zingarelli, B.1
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Kong, S.5
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Mice lacking ADPRT and poly(ADP-ribosyl)ation develop normally but are susceptible to skin disease
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Wang Z.Q., Auer B., Stingl L., Berghammer H., Haidacher D., Schweiger M., and Wagner E.F. Mice lacking ADPRT and poly(ADP-ribosyl)ation develop normally but are susceptible to skin disease. Genes Dev 9 (1995) 509-520
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Wang, Z.Q.1
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Schweiger, M.6
Wagner, E.F.7
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33745255099
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A topoisomerase IIβ-mediated dsDNA break required for regulated transcription
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This paper describes intriguing actions of PARP-1 at target gene promoters, adding a new twist to the exchange factor model. Specifically, this paper uses the estrogen-regulated TFF1 gene to study hormone-induced gene activation in the context of chromatin. Before activation, the TFF1 promoter is bound by a PARP-1 corepressor complex containing NCoR and the histone deacetylase HDAC3. Estrogen exposure rapidly promotes an exchange of the corepressor complex for a PARP-1 coactivator complex containing TopoIIβ, which transiently cleaves the promoter DNA. Recruitment of the PARP-1 coactivator complex also promotes the release of histone H1, the recruitment of HMGB1/2, changes in chromatin architecture, and ultimately increased transcription of the gene. This novel mechanism links the actions of two DNA-associated enzymes, namely PARP-1 and TopoIIβ, in the regulation of gene expression.
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Ju B.G., Lunyak V.V., Perissi V., Garcia-Bassets I., Rose D.W., Glass C.K., and Rosenfeld M.G. A topoisomerase IIβ-mediated dsDNA break required for regulated transcription. Science 312 (2006) 1798-1802. This paper describes intriguing actions of PARP-1 at target gene promoters, adding a new twist to the exchange factor model. Specifically, this paper uses the estrogen-regulated TFF1 gene to study hormone-induced gene activation in the context of chromatin. Before activation, the TFF1 promoter is bound by a PARP-1 corepressor complex containing NCoR and the histone deacetylase HDAC3. Estrogen exposure rapidly promotes an exchange of the corepressor complex for a PARP-1 coactivator complex containing TopoIIβ, which transiently cleaves the promoter DNA. Recruitment of the PARP-1 coactivator complex also promotes the release of histone H1, the recruitment of HMGB1/2, changes in chromatin architecture, and ultimately increased transcription of the gene. This novel mechanism links the actions of two DNA-associated enzymes, namely PARP-1 and TopoIIβ, in the regulation of gene expression.
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(2006)
Science
, vol.312
, pp. 1798-1802
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Ju, B.G.1
Lunyak, V.V.2
Perissi, V.3
Garcia-Bassets, I.4
Rose, D.W.5
Glass, C.K.6
Rosenfeld, M.G.7
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24
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DNA oxidation as triggered by H3K9me2 demethylation drives estrogen-induced gene expression
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Perillo B., Ombra M.N., Bertoni A., Cuozzo C., Sacchetti S., Sasso A., Chiariotti L., Malorni A., Abbondanza C., and Avvedimento E.V. DNA oxidation as triggered by H3K9me2 demethylation drives estrogen-induced gene expression. Science 319 (2008) 202-206
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Perillo, B.1
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Chiariotti, L.7
Malorni, A.8
Abbondanza, C.9
Avvedimento, E.V.10
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The role of poly(ADP-ribose) in the DNA damage signaling network
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Malanga M., and Althaus F.R. The role of poly(ADP-ribose) in the DNA damage signaling network. Biochem Cell Biol 83 (2005) 354-364
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The effect of poly(ADP-ribosyl)ation on native and H1-depleted chromatin. A role of poly(ADP-ribosyl)ation on core nucleosome structure
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Huletsky A., de Murcia G., Muller S., Hengartner M., Menard L., Lamarre D., and Poirier G.G. The effect of poly(ADP-ribosyl)ation on native and H1-depleted chromatin. A role of poly(ADP-ribosyl)ation on core nucleosome structure. J Biol Chem 264 (1989) 8878-8886
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Poirier, G.G.7
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The Drosophila heterochromatic gene encoding poly(ADP-ribose) polymerase (PARP) is required to modulate chromatin structure during development
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Tulin A., Stewart D., and Spradling A.C. The Drosophila heterochromatic gene encoding poly(ADP-ribose) polymerase (PARP) is required to modulate chromatin structure during development. Genes Dev 16 (2002) 2108-2119
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Tulin A., and Spradling A. Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science 299 (2003) 560-562
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SET and PARP1 remove DEK from chromatin to permit access by the transcription machinery
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+, PARP-1 PARylates and evicts DEK and itself from chromatin to permit the loading of the transcriptional machinery in a SET-independent manner. Thus, these studies point to a role for PARP-1 in regulating the composition of chromatin.
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+, PARP-1 PARylates and evicts DEK and itself from chromatin to permit the loading of the transcriptional machinery in a SET-independent manner. Thus, these studies point to a role for PARP-1 in regulating the composition of chromatin.
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Nat Struct Mol Biol
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, pp. 548-555
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Gamble, M.J.1
Fisher, R.P.2
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34250359929
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Poly(ADP-ribose) polymerase 1 is inhibited by a histone H2A variant, macroH2A, and contributes to silencing of the inactive X chromosome
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••], this paper describes interactions between PARP-1 and the 'nonhistone' domain of the histone variant macroH2A1 (specifically the 1.2 splice variant in this case), which may help to bring PARP-1 to chromatin and inhibit its enzymatic activity. RNAi-mediated depletion of macroH2A1 or PARP-1 reactivates expression of an inactive X-linked GFP transgene in mouse embryo fibroblast cells, suggesting that PARP-1 participates in the maintenance of silencing. Together, these studies suggest an interesting functional link between PARP-1 and macroH2A.
-
••], this paper describes interactions between PARP-1 and the 'nonhistone' domain of the histone variant macroH2A1 (specifically the 1.2 splice variant in this case), which may help to bring PARP-1 to chromatin and inhibit its enzymatic activity. RNAi-mediated depletion of macroH2A1 or PARP-1 reactivates expression of an inactive X-linked GFP transgene in mouse embryo fibroblast cells, suggesting that PARP-1 participates in the maintenance of silencing. Together, these studies suggest an interesting functional link between PARP-1 and macroH2A.
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(2007)
J Biol Chem
, vol.282
, pp. 12851-12859
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Nusinow, D.A.1
Hernandez-Munoz, I.2
Fazzio, T.G.3
Shah, G.M.4
Kraus, W.L.5
Panning, B.6
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32
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Analysis of nucleotide sequence-dependent DNA binding of poly(ADP-ribose) polymerase in a purified system
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Huang K., Tidyman W.E., Le K.U., Kirsten E., Kun E., and Ordahl C.P. Analysis of nucleotide sequence-dependent DNA binding of poly(ADP-ribose) polymerase in a purified system. Biochemistry 43 (2004) 217-223
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Biochemistry
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33
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•] provide new examples of gene regulation through sequence-specific binding of PARP-1 to DNA regulatory elements. This paper identifies a conserved regulatory element in the first intron of the BCL6 gene to which PARP-1 binds. PARP inhibitors and PARP-1 depletion by RNAi induce BCL6 expression, suggesting that PARP-1 activation plays a role in inhibiting BCL6 expression.
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••]. This paper first, demonstrates that direct phosphorylation of PARP-1 by ERK1/2 can enhance PARP-1 activity and second, identifies ERK1/2 phosphorylation sites on PARP-1 by mass spectrometry and site-directed mutagenesis. Although ERK1/2 pathway inhibitors blocked PARP-1 activation and PARP-1-mediated neuronal death, the effects on PARP-1-dependent gene expression were not determined.
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+ synthase NMNAT-1 in the regulation of PARP-1 enzymatic activity. Specifically, the results show that NMNAT-1 stimulates PARP-1 automodification, as well as binds to PAR. Phosphorylation of NMNAT-1 by protein kinase C reduces its binding to PAR, suggesting that NMNAT-1 may be an endpoint of cell signaling pathways. Together, these results demonstrate that NMNAT-1 can enhance the activity of PARP-1 and, thus, amplify PARylation.
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