Advertisement

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

  • Niraj Lodhi
  • Alexei V. Tulin
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 780)

Abstract

Poly(ADP-ribose) polymerase1 (PARP1) is a global regulator of different cellular mechanisms, ranging from DNA damage repair to control of gene expression. Since PARP1 protein and pADPr have been shown to persist in chromatin through cell cycle, they may both act as epigenetic markers. However, it is not known how many loci are occupied by PARP1 protein during mitosis genome-wide. To reveal the genome-wide PARP1 binding sites, we used the ChIP-seq approach, an emerging technique to study genome-wide PARP1 protein interaction with chromatin. Here, we describe how to perform ChIP-seq in the context of PARP1 binding sites identification in chromatin, using human embryonic kidney cell lines.

Key words

PARP1 Genomics Human embryonic cells Mitotic arrest ChIP ChIP-seq 

Notes

Acknowledgments

We thank D. Martin and K. Pechenkina for comments on the manuscript. We also thank Greg Donahue (University of Pennsylvania Medical School) and Yan Zhou (Fox Chase Cancer Center) for advice on ChIP-seq data analysis. The research was supported by grants from the National Institutes of Health (R01 DK082623) to A.V.T.

References

  1. 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 342:249–268PubMedCrossRefGoogle Scholar
  2. 2.
    Nosseri C, Coppola S, Ghibelli L (1994) Possible involvement of poly(ADP-ribosyl) polymerase in triggering stress-induced apoptosis. Exp Cell Res 212:367–373PubMedCrossRefGoogle Scholar
  3. 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 409:493–510PubMedCrossRefGoogle Scholar
  4. 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 94:7303–7307PubMedCrossRefGoogle Scholar
  5. 5.
    Tulin A, Spradling A (2003) Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science 299:560–562PubMedCrossRefGoogle Scholar
  6. 6.
    Petesch SJ, Lis JT (2008) Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell 134:74–84PubMedCrossRefGoogle Scholar
  7. 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 22:832–853PubMedCrossRefGoogle Scholar
  8. 8.
    Tulin A, Chinenov Y, Spradling A (2003) Regulation of chromatin structure and gene activity by poly(ADP-ribose) polymerases. Curr Top Dev Biol 56:55–83PubMedCrossRefGoogle Scholar
  9. 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 284:33926–33938PubMedCrossRefGoogle Scholar
  10. 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 282:32511–32519PubMedCrossRefGoogle Scholar
  11. 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 319:819–821PubMedCrossRefGoogle Scholar
  12. 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 19:24–32PubMedCrossRefGoogle Scholar
  13. 13.
    Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502PubMedCrossRefGoogle Scholar
  14. 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 4:1–7CrossRefGoogle Scholar
  15. 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 132:887–898PubMedCrossRefGoogle Scholar
  16. 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 19:1361–1373PubMedCrossRefGoogle Scholar
  17. 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 27:66–75PubMedCrossRefGoogle Scholar
  18. 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 26:1293–1300PubMedCrossRefGoogle Scholar
  19. 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 36:5221–5231PubMedCrossRefGoogle Scholar
  20. 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 18:1906–1917PubMedCrossRefGoogle Scholar
  21. 21.
    Nix DA, Courdy SJ, Boucher KM (2008) Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinform 9:523CrossRefGoogle Scholar
  22. 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 5:829–834PubMedCrossRefGoogle Scholar
  23. 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: 2344–2349PubMedCrossRefGoogle Scholar
  24. 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:R137PubMedCrossRefGoogle Scholar
  25. 25.
    Collas P and Dahl JA (2008) Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front Biosci 13:929–943PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Niraj Lodhi
    • 1
  • Alexei V. Tulin
    • 2
  1. 1.Epigenetics and Progenitor Cells ProgramFox Chase Cancer CenterPhiladelphiaUSA
  2. 2.Epigenetics and Progenitor Cells Program, Cancer Biology ProgramFox Chase Cancer CenterPhiladelphiaUSA

Personalised recommendations