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.
Highlights
(ADP-ribose) polymerase 1 (PARP1) or ADPribosyl transferase 1, a multifunctional nuclear protein, belongs to the PARP family of proteins
To ensure that only Poly (ADP-ribose) polymerase 1 (PARP1) protein-bound RNAs were used for further analysis, gels were transferred onto nitrocellulose membranes, visualized by autoradiography (Figure 1c), and the presence of PARP1-bound RNAs was confirmed by western blot analysis (Figure 1d)
Within mRNAs, we find that PARP1 associates mainly with intronic sequences (Figure 2)
Summary
(ADP-ribose) polymerase 1 (PARP1) or ADPribosyl transferase 1, a multifunctional nuclear protein, belongs to the PARP family of proteins. Besides its DNA damage response, PARP1 plays a crucial role in regulating numerous molecular processes, such as gene transcription and chromatin remodeling [2,3,4]. PARP1 regulates components of the mitotic apparatus, such as centromeres and centrosomes, to control microtubule organization during mitosis and chromosome segregation [10]. Taken together, these studies show that PARP1
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