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

Manana Melikishvili; Julia H. Chariker; Eric C. Rouchka; Yvonne N. Fondufe-Mittendorf

doi:10.1038/celldisc.2017.43

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

Manana Melikishvili, Julia H. Chariker, Eric C. Rouchka, Yvonne N. Fondufe-Mittendorf

Molecular and Cellular Biochemistry

Research output: Contribution to journal › Article › peer-review

35 Scopus citations

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.

Original language	English
Article number	17043
Journal	Cell Discovery
Volume	3
DOIs	https://doi.org/10.1038/celldisc.2017.43
State	Published - Nov 28 2017

Bibliographical note

Funding Information:
This work used the Vincent J Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303 for PAR-CLIP sequencing and University of Louisville for poly-A RNA sequencing. We also thank Dr Louis Hersh for critical review of the manuscript, Dr Fried for help with EMSA analyses. We would like to thank the Markey Cancer Center’s Research Communications Office for manuscript editing and assistance with graphic design. His-tagged PARP-1 expression vectors were a kind gift from the Pascal laboratory (University of Montreal). This research was supported by NIH grants P20 GM103436 (ECR): 1RO1ES024478 and NSF MCB-1517986 (YNF-M).

Funding Information:
This work used the Vincent J Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303 for PARCLIP sequencing and University of Louisville for poly-A RNA sequencing. We also thank Dr Louis Hersh for critical review of the manuscript, Dr Fried for help with EMSA analyses. We would like to thank the Markey Cancer Center's Research Communications Office for manuscript editing and assistance with graphic design. His-tagged PARP-1 expression vectors were a kind gift from the Pascal laboratory (University of Montreal). This research was supported by NIH grants P20 GM103436 (ECR): 1RO1ES024478 and NSF MCB-1517986 (YNF-M).

Publisher Copyright:
© 2017 The Author(s).

Keywords

PAR-CLIP
PARP1
RNA-binding proteins
alternative splicing
transcription

ASJC Scopus subject areas

Biochemistry
Molecular Biology
Genetics
Cell Biology

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

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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author = "Manana Melikishvili and Chariker, {Julia H.} and Rouchka, {Eric C.} and Fondufe-Mittendorf, {Yvonne N.}",

note = "Funding Information: This work used the Vincent J Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303 for PAR-CLIP sequencing and University of Louisville for poly-A RNA sequencing. We also thank Dr Louis Hersh for critical review of the manuscript, Dr Fried for help with EMSA analyses. We would like to thank the Markey Cancer Center{\textquoteright}s Research Communications Office for manuscript editing and assistance with graphic design. His-tagged PARP-1 expression vectors were a kind gift from the Pascal laboratory (University of Montreal). This research was supported by NIH grants P20 GM103436 (ECR): 1RO1ES024478 and NSF MCB-1517986 (YNF-M). Funding Information: This work used the Vincent J Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303 for PARCLIP sequencing and University of Louisville for poly-A RNA sequencing. We also thank Dr Louis Hersh for critical review of the manuscript, Dr Fried for help with EMSA analyses. We would like to thank the Markey Cancer Center's Research Communications Office for manuscript editing and assistance with graphic design. His-tagged PARP-1 expression vectors were a kind gift from the Pascal laboratory (University of Montreal). This research was supported by NIH grants P20 GM103436 (ECR): 1RO1ES024478 and NSF MCB-1517986 (YNF-M). Publisher Copyright: {\textcopyright} 2017 The Author(s).",

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AU - Chariker, Julia H.

AU - Rouchka, Eric C.

AU - Fondufe-Mittendorf, Yvonne N.

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N2 - 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.

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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