Open Access
Open access
Cell Discovery, volume 3, issue 1, publication number 17043

Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis

Melikishvili Manana 1
Chariker Julia H 2, 3
Rouchka Eric C. 3, 4
Fondufe Mittendorf Yvonne N 1
1
 
Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, USA
2
 
Department of Psychological and Brain Sciences, University of Louisville, Louisville, USA
3
 
Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, USA
4
 
Department of Computer Engineering and Computer Science, University of Louisville, Louisville, USA
Publication typeJournal Article
Publication date2017-11-28
Journal: Cell Discovery
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor33.5
ISSN20565968
Biochemistry
Molecular Biology
Cell Biology
Genetics
Abstract
Recent studies implicate Poly (ADP-ribose) polymerase 1 (PARP1) in alternative splicing regulation, and PARP1 may be an RNA-binding protein. However, detailed knowledge of RNA targets and the RNA-binding region for PARP1 are unknown. Here we report the first global study of PARP1–RNA interactions using PAR–CLIP in HeLa cells. We identified a largely overlapping set of 22 142 PARP1–RNA-binding peaks mapping to mRNAs, with 20 484 sites located in intronic regions. PARP1 preferentially bound RNA containing GC-rich sequences. Using a Bayesian model, we determined positional effects of PARP1 on regulated exon-skipping events: PARP1 binding upstream and downstream of the skipped exons generally promotes exon inclusion, whereas binding within the exon of interest and intronic regions closer to the skipped exon promotes exon skipping. Using truncation mutants, we show that removal of the Zn1Zn2 domain switches PARP1 from a DNA binder to an RNA binder. This study represents a first step into understanding the role of PARP1–RNA interaction. Continued identification and characterization of the functional interplay between PARPs and RNA may provide important insights into the role of PARPs in RNA regulation.

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Melikishvili M. et al. Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis // Cell Discovery. 2017. Vol. 3. No. 1. 17043
GOST all authors (up to 50) Copy
Melikishvili M., Chariker J. H., Rouchka E. C., Fondufe Mittendorf Y. N. Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis // Cell Discovery. 2017. Vol. 3. No. 1. 17043
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Cite this
RIS Copy
TY - JOUR
DO - 10.1038/celldisc.2017.43
UR - https://doi.org/10.1038%2Fcelldisc.2017.43
TI - Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis
T2 - Cell Discovery
AU - Melikishvili, Manana
AU - Chariker, Julia H
AU - Rouchka, Eric C.
AU - Fondufe Mittendorf, Yvonne N
PY - 2017
DA - 2017/11/28 00:00:00
PB - Springer Nature
IS - 1
VL - 3
PMID - 29387452
SN - 2056-5968
ER -
BibTex
Cite this
BibTex Copy
@article{2017_Melikishvili
author = {Manana Melikishvili and Julia H Chariker and Eric C. Rouchka and Yvonne N Fondufe Mittendorf},
title = {Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis},
journal = {Cell Discovery},
year = {2017},
volume = {3},
publisher = {Springer Nature},
month = {nov},
url = {https://doi.org/10.1038%2Fcelldisc.2017.43},
number = {1},
doi = {10.1038/celldisc.2017.43}
}
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