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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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. This research was supported by NIH grants P20 GM103436 (ECR): 1RO1ES024478 and NSF MCB-1517986 (YNF-M).
RNA-seq data are deposited in GEO (GSE91051) along with the PAR-CLIP data (GSE95360). The processed files for the PARCLIP peaks, differential gene expression, and alternative splicing analysis are provided as Supplementary Data 1. Visualization tracks for PARCLIP and RNASeq data are provided as a track hub on the UCSC Genome Browser (http://bit.ly/2l7f5OY).
Supplementary information is linked to the online version of the paper on the Cell Discovery website.
Melikishvili, Manana; Chariker, Julia H.; Rouchka, Eric C.; and Fondufe-Mittendorf, Yvonne N., "Transcriptome-Wide Identification of the RNA-Binding Landscape of the Chromatin-Associated Protein PARP1 Reveals Functions in RNA Biogenesis" (2017). Molecular and Cellular Biochemistry Faculty Publications. 125.