PARP1 Genomics: Chromatin Immunoprecipitation Approach Using Anti-PARP1 Antibody (ChIP and ChIP-seq)

Methods in Molecular Biology

Volumn 780, Issue , 2011, Pages 191-208

  Lodhi, Niraj ^a   Tulin, Alexei V ^a  

^a FOX CHASE CANCER CENTER   (United States)

Author keywords

ChIP; ChIP seq; Genomics; Human embryonic cells; Mitotic arrest; PARP1

Indexed keywords

ANTIBODY; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE;

ARTICLE; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; GENETICS; GENOMICS; HUMAN; IMMUNOLOGY; METHODOLOGY; WESTERN BLOTTING;

ANTIBODIES; BLOTTING, WESTERN; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; GENOMICS; HUMANS; POLY(ADP-RIBOSE) POLYMERASES;

EID: 80054725731     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-270-0_12     Document Type: Chapter

References (25)

1. D’Amours D, Desnoyers S, D’Silva I, Poirier GG (1999) Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem J 342:249–268
2. Nosseri C, Coppola S, Ghibelli L (1994) Possible involvement of poly(ADP-ribosyl) polymerase in triggering stress-induced apoptosis. Exp Cell Res 212:367–373
3. Dantzer F, Amé JC, Schreiber V, Nakamura J, Ménissier-de MJ, de Murcia G (2006) Poly(ADP-ribose) polymerase-1 activation during DNA damage and repair. Methods Enzymol 409:493–510
4. de Murcia JM, Niedergang C, Trucco C, Ricoul M, Dutrillaux B, Mark M, Oliver FJ, Masson M, Dierich A, LeMeur M, Walztinger C, Chambon P, de Murcia G (1997) Requirement of poly(ADP-ribose) polymerase in recovery from DNA damage in mice and in cells. Proc Natl Acad Sci USA 94:7303–7307
5. Tulin A, Spradling A (2003) Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science 299:560–562
6. Petesch SJ, Lis JT (2008) Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell 134:74–84
7. Dechat T, Pfleghaar K, Sengupta K, Shimi T, Shumaker DK, Solimando L, Goldman RD (2008) Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin. Genes Dev 22:832–853
8. Tulin A, Chinenov Y, Spradling A (2003) Regulation of chromatin structure and gene activity by poly(ADP-ribose) polymerases. Curr Top Dev Biol 56:55–83
9. Frizzell KM, Gamble MJ, Berrocal JG, Zhang T, Krishnakumar R, Cen Y, Sauve AA, Kraus WL (2009) Global analysis of transcriptional regulation by poly(ADP-ribose) polymerase-1 and poly(ADP-ribose) glycohydrolase in MCF-7 human breast cancer cells. J Biol Chem 284:33926–33938
10. Pinnola A, Naumova N, Shah M, Tulin AV (2007) Nucleosomal core histones mediate dynamic regulation of poly(ADP-ribose) polymerase 1 protein binding to chromatin and induction of its enzymatic activity. J Biol Chem 282:32511–32519
11. Krishnakumar R, Gamble MJ, Frizzell KM, Berrocal JG, Kininis M, Kraus WL (2008) Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes. Science 319:819–821
12. Cuddapah S, Jothi R, Schones DE, Roh T-Y, Cui K, Zhao K (2009) Global analysis of the insulator CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19:24–32
13. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502
14. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:1–7
15. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887–898
16. Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG (2009) High-resolution analysis of epigenetic changes associated with X inactivation. Genome Res 19:1361–1373
17. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Nyder M, Gerstein MB (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27:66–75
18. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26:1293–1300
19. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-seq data. Nucleic Acids Res 36:5221–5231
20. Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ (2008) Genome-wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding. Genome Res 18:1906–1917
21. Nix DA, Courdy SJ, Boucher KM (2008) Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinform 9:523
22. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5:829–834
23. Xu H, Wei CL, Lin F, Sung WK (2008) An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 24: 2344–2349
24. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9:R137
25. Collas P and Dahl JA (2008) Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front Biosci 13:929–943