Open Access

Epigenetics and Chromatin, volume 12, issue 1, publication number 15

Coupling of PARP1-mediated chromatin structural changes to transcriptional RNA polymerase II elongation and cotranscriptional splicing

Matveeva Elena A. ¹

Al Tinawi Qamar M H ^{1, 2}

Rouchka Eric C. ^{3, 4}

Fondufe Mittendorf Yvonne N ¹

Hide authors affiliations Show authors affiliations: 4 affiliations

Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, USA |

Alfaisal University, Al Maather’ Riyadh, Saudi Arabia |

Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, USA |

⁴

Department of Computer Engineering and Computer Science, University of Louisville, Louisville, USA |

Publication type: Journal Article

Publication date: 2019-02-18

Springer Nature

Journal: Epigenetics and Chromatin

Quartile SCImago

Quartile WOS

Impact factor: 3.9

ISSN: 17568935

DOI: 10.1186/s13072-019-0261-1

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PubMed ID: 30777121

Molecular Biology

Genetics

Abstract

BackgroundRecently, we showed that PARP1 is involved in cotranscriptional splicing, possibly by bridging chromatin to RNA and recruiting splicing factors. It also can influence alternative splicing decisions through the regulation of RNAPII elongation. In this study, we investigated the effect of PARP1-mediated chromatin changes on RNAPII movement, during transcription and alternative splicing.ResultsWe show that RNAPII pauses at PARP1–chromatin structures within the gene body. Knockdown of PARP1 abolishes this RNAPII pausing, suggesting that PARP1 may regulate RNAPII elongation. Additionally, PARP1 alters nucleosome deposition and histone post-translational modifications at specific exon–intron boundaries, thereby affecting RNAPII movement. Lastly, genome-wide analyses confirmed that PARP1 influences changes in RNAPII elongation by either reducing or increasing the rate of RNAPII elongation depending on the chromatin context.ConclusionsThese studies suggest a context-specific effect of PARP1–chromatin binding on RNA polymerase movement and provide a platform to delineate PARP1’s role in RNA biogenesis and processing.

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Citations by journals

	1 2 3 4
Cells	Cells, 4, 10.53% Cells 4 publications, 10.53%
Wiley interdisciplinary reviews. RNA	Wiley interdisciplinary reviews. RNA, 4, 10.53% Wiley interdisciplinary reviews. RNA 4 publications, 10.53%
Nucleic Acids Research	Nucleic Acids Research, 3, 7.89% Nucleic Acids Research 3 publications, 7.89%
Cellular and Molecular Life Sciences	Cellular and Molecular Life Sciences, 2, 5.26% Cellular and Molecular Life Sciences 2 publications, 5.26%
Genes and Development	Genes and Development, 2, 5.26% Genes and Development 2 publications, 5.26%
Frontiers in Cell and Developmental Biology	Frontiers in Cell and Developmental Biology, 1, 2.63% Frontiers in Cell and Developmental Biology 1 publication, 2.63%
Cancers	Cancers, 1, 2.63% Cancers 1 publication, 2.63%
Genes	Genes, 1, 2.63% Genes 1 publication, 2.63%
Frontiers in Oncology	Frontiers in Oncology, 1, 2.63% Frontiers in Oncology 1 publication, 2.63%
Cell and Bioscience	Cell and Bioscience, 1, 2.63% Cell and Bioscience 1 publication, 2.63%
3 Biotech	3 Biotech, 1, 2.63% 3 Biotech 1 publication, 2.63%
Molecular Genetics and Genomics	Molecular Genetics and Genomics, 1, 2.63% Molecular Genetics and Genomics 1 publication, 2.63%
Cancer Cell International	Cancer Cell International, 1, 2.63% Cancer Cell International 1 publication, 2.63%
Molecular Cell	Molecular Cell, 1, 2.63% Molecular Cell 1 publication, 2.63%
Trends in Cell Biology	Trends in Cell Biology, 1, 2.63% Trends in Cell Biology 1 publication, 2.63%
European Journal of Pharmacology	European Journal of Pharmacology, 1, 2.63% European Journal of Pharmacology 1 publication, 2.63%
DNA Repair	DNA Repair, 1, 2.63% DNA Repair 1 publication, 2.63%
Redox Biology	Redox Biology, 1, 2.63% Redox Biology 1 publication, 2.63%
Cell Reports Methods	Cell Reports Methods, 1, 2.63% Cell Reports Methods 1 publication, 2.63%
Seminars in Cancer Biology	Seminars in Cancer Biology, 1, 2.63% Seminars in Cancer Biology 1 publication, 2.63%
Cell Proliferation	Cell Proliferation, 1, 2.63% Cell Proliferation 1 publication, 2.63%
FEBS Letters	FEBS Letters, 1, 2.63% FEBS Letters 1 publication, 2.63%
BioEssays	BioEssays, 1, 2.63% BioEssays 1 publication, 2.63%
Methods in Molecular Biology	Methods in Molecular Biology, 1, 2.63% Methods in Molecular Biology 1 publication, 2.63%
Advances in Pharmacology	Advances in Pharmacology, 1, 2.63% Advances in Pharmacology 1 publication, 2.63%
Ageing Research Reviews	Ageing Research Reviews, 1, 2.63% Ageing Research Reviews 1 publication, 2.63%
Cell Reports	Cell Reports, 1, 2.63% Cell Reports 1 publication, 2.63%
	1 2 3 4

Citations by publishers

	2 4 6 8 10
Elsevier	Elsevier, 10, 26.32% Elsevier 10 publications, 26.32%
Springer Nature	Springer Nature, 7, 18.42% Springer Nature 7 publications, 18.42%
Wiley	Wiley, 7, 18.42% Wiley 7 publications, 18.42%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 6, 15.79% Multidisciplinary Digital Publishing Institute (MDPI) 6 publications, 15.79%
Oxford University Press	Oxford University Press, 3, 7.89% Oxford University Press 3 publications, 7.89%
Frontiers Media S.A.	Frontiers Media S.A., 2, 5.26% Frontiers Media S.A. 2 publications, 5.26%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 2, 5.26% Cold Spring Harbor Laboratory 2 publications, 5.26%
	2 4 6 8 10

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Matveeva E. A. et al. Coupling of PARP1-mediated chromatin structural changes to transcriptional RNA polymerase II elongation and cotranscriptional splicing // Epigenetics and Chromatin. 2019. Vol. 12. No. 1. 15

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Matveeva E. A., Al Tinawi Q. M. H., Rouchka E. C., Fondufe Mittendorf Y. N. Coupling of PARP1-mediated chromatin structural changes to transcriptional RNA polymerase II elongation and cotranscriptional splicing // Epigenetics and Chromatin. 2019. Vol. 12. No. 1. 15

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TY - JOUR

DO - 10.1186/s13072-019-0261-1

UR - https://doi.org/10.1186%2Fs13072-019-0261-1

TI - Coupling of PARP1-mediated chromatin structural changes to transcriptional RNA polymerase II elongation and cotranscriptional splicing

T2 - Epigenetics and Chromatin

AU - Matveeva, Elena A.

AU - Al Tinawi, Qamar M H

AU - Rouchka, Eric C.

AU - Fondufe Mittendorf, Yvonne N

PY - 2019

DA - 2019/02/18 00:00:00

PB - Springer Nature

IS - 1

VL - 12

PMID - 30777121

SN - 1756-8935

ER -

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@article{2019_Matveeva,

author = {Elena A. Matveeva and Qamar M H Al Tinawi and Eric C. Rouchka and Yvonne N Fondufe Mittendorf},

title = {Coupling of PARP1-mediated chromatin structural changes to transcriptional RNA polymerase II elongation and cotranscriptional splicing},

journal = {Epigenetics and Chromatin},

year = {2019},

volume = {12},

publisher = {Springer Nature},

month = {feb},

url = {https://doi.org/10.1186%2Fs13072-019-0261-1},

number = {1},

doi = {10.1186/s13072-019-0261-1}

}

Found error?

Publisher

Springer Nature

Journal

Epigenetics and Chromatin

Quartile SCImago

Quartile WOS

Impact factor

3.9

ISSN

17568935 (Print)