Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in the regulation of different cellular mechanisms, ranging from DNA repair to regulation of gene expression. The different PARP1 domains have been shown to influence PARP1 binding pattern to chromatin. However, which loci bound by PARP1 are affected in the absence of a specific domain is not known. To determine the binding pattern of the different PARP1 domains, we used a ChIP-seq approach on different GFP-tagged versions of PARP1. Here, we described how to perform and analyze ChIP-seq performed with a GFP antibody in Drosophila melanogaster third instar larvae.
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References
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(Pt 2):249–268
Ji Y, Tulin AV (2010) The roles of PARP1 in gene control and cell differentiation. Curr Opin Genet Dev 20(5):512–518
Lodhi N, Kossenkov AV, Tulin AV (2014) Bookmarking promoters in mitotic chromatin: poly(ADP-ribose)polymerase-1 as an epigenetic mark. Nucleic Acids Res 42(11):7028–7038
Ray Chaudhuri A, Nussenzweig A (2017) The multifaceted roles of PARP1 in DNA repair and chromatin remodelling. Nat Rev Mol Cell Biol 18(10):610–621
Thomas C, Tulin AV (2013) Poly-ADP-ribose polymerase: machinery for nuclear processes. Mol Asp Med 34(6):1124–1137
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
Tulin A, Spradling A (2003) Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science 299(5606):560–562
Weaver AN, Yang ES (2013) Beyond DNA repair: additional functions of PARP-1 in cancer. Front Oncol 3:290
Buki KG, Bauer PI, Hakam A, Kun E (1995) Identification of domains of poly(ADP-ribose) polymerase for protein binding and self-association. J Biol Chem 270(7):3370–3377
Kirsanov KI, Kotova E, Makhov P, Golovine K, Lesovaya EA, Kolenko VM et al (2014) Minor grove binding ligands disrupt PARP-1 activation pathways. Oncotarget 5(2):428–437
Kotova E, Jarnik M, Tulin AV (2010) Uncoupling of the transactivation and transrepression functions of PARP1 protein. Proc Natl Acad Sci U S A 107(14):6406–6411
Rudolph J, Mahadevan J, Dyer P, Luger K (2018) Poly(ADP-ribose) polymerase 1 searches DNA via a ‘monkey bar’ mechanism. elife 7:e37818
Alemasova EE, Lavrik OI (2019) Poly(ADP-ribosyl)ation by PARP1: reaction mechanism and regulatory proteins. Nucleic Acids Res 47(8):3811–3827
Thomas C, Ji Y, Wu C, Datz H, Boyle C, MacLeod B et al (2019) Hit and run versus long-term activation of PARP-1 by its different domains fine-tunes nuclear processes. Proc Natl Acad Sci U S A 116(20):9941–9946
Li N, Chen J (2014) ADP-ribosylation: activation, recognition, and removal. Mol Cells 37(1):9–16
Manasaryan G, Suplatov D, Pushkarev S, Drobot V, Kuimov A, Svedas V et al (2021) Bioinformatic analysis of the nicotinamide binding site in poly(ADP-ribose) polymerase family proteins. Cancers (Basel) 13(6):1201
Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M et al (2018) The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 46(W1):W537–WW44
Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884–ii90
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359
Barnett DW, Garrison EK, Quinlan AR, Stromberg MP, Marth GT (2011) BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics 27(12):1691–1692
Ramirez F, Ryan DP, Gruning B, Bhardwaj V, Kilpert F, Richter AS et al (2016) deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 44(W1):W160–W165
Feng J, Liu T, Qin B, Zhang Y, Liu XS (2012) Identifying ChIP-seq enrichment using MACS. Nat Protoc 7(9):1728–1740
Khan A, Mathelier A (2017) Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinf 18(1):287
Dahmann C (2009) Drosophila: methods and protocols. Methods in molecular biology, vol 420. Humana Press, New York
Ashburner M, Golic KG, Hawley RS (2004) Drosophila: a laboratory handbook. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
Acknowledgments
Funding for this project was provided by the National Science Foundation MCB-1616740 and the Department of Defense grant PC160049 to AVT. Funding agencies had no role in study design, data collection, data analysis, interpretation, or writing of the report.
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Bordet, G., Bamgbose, G., Bhuiyam, S.H., Johnson, S., Tulin, A.V. (2023). Chromatin Immunoprecipitation Approach to Determine How PARP1 Domains Affect Binding Pattern to Chromatin. In: Tulin, A.V. (eds) Poly(ADP-Ribose) Polymerase. Methods in Molecular Biology, vol 2609. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2891-1_17
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DOI: https://doi.org/10.1007/978-1-0716-2891-1_17
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