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Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation.

Nalabothula N, Al-jumaily T, Eteleeb AM, Flight RM, Xiaorong S, Moseley H, Rouchka EC, Fondufe-Mittendorf YN - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

PARP1-mediated differential methylation profile (after PARylation inhibition) according to: (A) all differential methylated patterns as analyzed on the Infinium HumanMethylation450 BeadChip; (B) differential methylated patterns are mapped to gene regions based on their functional genome distribution; (C) CpG island regions based on CpG content and neighborhood context (TSS: proximal promoter, defined as 200 bp or 1500 bp upstream of the transcription start site; UTR: untranslated region; CpG island: 200+ bp stretch of DNA with a C+G content of >50% and an observed CpG/expected CpG in excess of 0.6; shore: the flanking region of CpG islands, 0–2000 bp; shelf: regions flanking island shores (i.e., covering 2000–4000 bp distant from the CpG island); on the HumanMethylation450 BeadChip (two biological replicates of non-treated and PARylation inhibited samples were used).
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pone.0135410.g005: PARP1-mediated differential methylation profile (after PARylation inhibition) according to: (A) all differential methylated patterns as analyzed on the Infinium HumanMethylation450 BeadChip; (B) differential methylated patterns are mapped to gene regions based on their functional genome distribution; (C) CpG island regions based on CpG content and neighborhood context (TSS: proximal promoter, defined as 200 bp or 1500 bp upstream of the transcription start site; UTR: untranslated region; CpG island: 200+ bp stretch of DNA with a C+G content of >50% and an observed CpG/expected CpG in excess of 0.6; shore: the flanking region of CpG islands, 0–2000 bp; shelf: regions flanking island shores (i.e., covering 2000–4000 bp distant from the CpG island); on the HumanMethylation450 BeadChip (two biological replicates of non-treated and PARylation inhibited samples were used).

Mentions: To determine the PARP1-mediated methylation regions, MCF7 cells were treated with PJ34, the genomic DNA purified and subjected to the Infinium HumanMethylation450 BeadChip microarray analyses. This microarray method allows the interrogation of 485,000 methylation sites per sample at single CpG site resolution [77,78]. After analyses, we detected differential methylation in 1,201 CpG sites, of which 869 were hypermethylated and 333 were hypomethylated (Fig 5A; S6 Fig, S2 and S3 Tables). These differentially methylated regions were non-randomly distributed (Fig 5A and 5D) in relationship to gene annotations and CpG density.


Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation.

Nalabothula N, Al-jumaily T, Eteleeb AM, Flight RM, Xiaorong S, Moseley H, Rouchka EC, Fondufe-Mittendorf YN - PLoS ONE (2015)

PARP1-mediated differential methylation profile (after PARylation inhibition) according to: (A) all differential methylated patterns as analyzed on the Infinium HumanMethylation450 BeadChip; (B) differential methylated patterns are mapped to gene regions based on their functional genome distribution; (C) CpG island regions based on CpG content and neighborhood context (TSS: proximal promoter, defined as 200 bp or 1500 bp upstream of the transcription start site; UTR: untranslated region; CpG island: 200+ bp stretch of DNA with a C+G content of >50% and an observed CpG/expected CpG in excess of 0.6; shore: the flanking region of CpG islands, 0–2000 bp; shelf: regions flanking island shores (i.e., covering 2000–4000 bp distant from the CpG island); on the HumanMethylation450 BeadChip (two biological replicates of non-treated and PARylation inhibited samples were used).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4549251&req=5

pone.0135410.g005: PARP1-mediated differential methylation profile (after PARylation inhibition) according to: (A) all differential methylated patterns as analyzed on the Infinium HumanMethylation450 BeadChip; (B) differential methylated patterns are mapped to gene regions based on their functional genome distribution; (C) CpG island regions based on CpG content and neighborhood context (TSS: proximal promoter, defined as 200 bp or 1500 bp upstream of the transcription start site; UTR: untranslated region; CpG island: 200+ bp stretch of DNA with a C+G content of >50% and an observed CpG/expected CpG in excess of 0.6; shore: the flanking region of CpG islands, 0–2000 bp; shelf: regions flanking island shores (i.e., covering 2000–4000 bp distant from the CpG island); on the HumanMethylation450 BeadChip (two biological replicates of non-treated and PARylation inhibited samples were used).
Mentions: To determine the PARP1-mediated methylation regions, MCF7 cells were treated with PJ34, the genomic DNA purified and subjected to the Infinium HumanMethylation450 BeadChip microarray analyses. This microarray method allows the interrogation of 485,000 methylation sites per sample at single CpG site resolution [77,78]. After analyses, we detected differential methylation in 1,201 CpG sites, of which 869 were hypermethylated and 333 were hypomethylated (Fig 5A; S6 Fig, S2 and S3 Tables). These differentially methylated regions were non-randomly distributed (Fig 5A and 5D) in relationship to gene annotations and CpG density.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus