Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including transcription, splicing, DNA repair, replication and recombination. It is important to delineate whether PARP1 randomly associates with nucleosomes or is present at specific nucleosome regions throughout the cell genome. We performed genome-wide association studies in breast cancer cell lines to address these questions. Our studies show that PARP1 associates with epigenetic regulatory elements genome-wide, such as active histone marks, CTCF and DNase hypersensitive sites. Additionally, the binding of PARP1 to chromatin genome-wide is mutually exclusive with DNA methylation pattern suggesting a functional interplay between PARP1 and DNA methylation. Indeed, inhibition of PARylation results in genome-wide changes in DNA methylation patterns. Our results suggest that PARP1 controls the fidelity of gene transcription and marks actively transcribed gene regions by selectively binding to transcriptionally active chromatin. These studies provide a platform for developing our understanding of PARP1's role in gene regulation.
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This research was supported by NIH grants P20GM103436 (ECR); 2P20 RR020171 (YNF-M) (from the National Center for Research Resources), 1R01ES024478, NSF1517986 and International Rett Syndrome Foundation grant (YNF-M). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Nalabothula, Narasimharao; Al-Jumaily, Taha; Eteleeb, Abdallah M.; Flight, Robert M.; Xiaorong, Shao; Moseley, Hunter; Rouchka, Eric C.; and Fondufe-Mittendorf, Yvonne N., "Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation" (2015). Molecular and Cellular Biochemistry Faculty Publication. 77.
S1 Fig. Reproducibility of PARP-nuc-ChIP-seq data analyses.
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S2 Fig. ChIP assay and validation.
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S3 Fig. PARP1 binding at specific promoters correlate with active gene transcription.
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S4 Fig. Evaluation of siRNA transfection efficiency in MCF7 cells.
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S5 Fig. Measurement of PARP1 occupancy and activity after 5-aza-cytidine, decitabine and PJ34 treatment.
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S6 Fig. Differential methylated pattern analyses analyzed from the Infinium microarray analyses.
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S7 Fig. PARylation-mediated methylation patterns in MCF7 cells.
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S8 Fig. MSRPE PCR on DPQ treated DNA.
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S9 Fig. Comparison of MNase-seq data (total nucleosome positioning) with PARP1-bound nucleosomes at (A) TSSs (B) CTCF binding sites (C) highly DNA methylated sites.
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S10 Fig. A view of PARP1 correlative binding with several gene regulatory features.
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S1 Table. Pearson correlations and <em>p values</em> of PARP1 and regulation regions genome-wide and at TSSs.
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S2 Table. Hypermethylated genes and genomic regions mediated by PARylation inhibition.
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S3 Table. Hypomethylated genes and genomic regions mediated by PARylation inhibition.
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S4 Table. Pathways of gene targeted by PARylation-mediated methylation.
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S5 Table. Genes that are both hyper- and hypomethylated by PARylation and the genomic regions affected.