Identification of PARP1-RNA binding in-vivo using PAR-CLiP Sequencing. Homo sapiens

Recent studies have implicated PARP1 in alternative splicing regulation. In addition, PARP1 has been shown to bind RNA in vivo suggesting that it is an RNA-binding protein (RBP). However, a detailed knowledge of the RNA-targets as well as the RNA binding region of PARP1 is unknown. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HeLa cells and identified a largely overlapping set ∼22142 of PARP1-RNA binding peaks mapping to mRNAs, of which ∼20484 sites are located in the intronic regions of genes. PARP1 preferentially bound RNA containing a Guanine-rich sequences. Using a bayesian model, we determined positional effects of PARP1 on exon skipping: PARP1 binding upstream and downstream to the skipped exons generally promoted exon inclusion, whereas binding on exons and closer to the skipped exon, promoted exon skipping. Finally, using truncation mutants, we narrowed the PARP1-RNA binding domain to the amino terminus region of the protein. Such studies on transcriptome-wide mapping of RNA-targets by PARP1, present the first step into understanding the role of PARP1 and RNA biogenesis. Our understanding of the role of PARPs and PAR in the transcriptional and post-transcriptional regulation of gene expression through modulation of RNA is still in the early stages. Continued identification and characterization of the functional interplay between PARPs and RNA may provide important insights into the role of PARPs in RNA regulation. Overall design: 1 pooled sample combining PARP1 binding using PAR-CLiP Sequencing from 7 biological replicates