Nuclear poly(A)-binding protein and nucleolin utilize their RNA recognition motifs to read PAR chains

Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification mediated by ADP-ribosyltransferases, known as PARPs, which attach ADP-ribose units onto proteins, forming negatively charged multimeric chains. This modification relaxes chromatin at DNA damage sites, facilitating repair machinery access. Additionally, PAR polymers serve as docking platforms for effector proteins, termed PAR "readers", commonly involved in DNA repair. The recruitment of these proteins is mediated through conserved protein domains, including RNA recognition motifs (RRMs). Using an array of hundreds of recombinant RNA-binding domains, we systematically examined RRM interactions with PAR chains of varying lengths. Despite their chemical similarity to RNA, only a small subset of RRMs binds PAR. We identified the RRMs of poly(A)-binding protein (PABPN1) and nucleolin (NCL) as readers of short- and long-chain PAR, respectively. PABPN1 binds short chains via a single RRM unit, while NCL engages long chains using three of its four RRMs. Both proteins are recruited to DNA damage sites marked by PARP activity in a laser micro-irradiation assay, and their RRMs exhibit competitive binding to PAR and RNA. These findings highlight the capacity of specific RRMs to recognize structurally similar ribonucleotide and ADP-ribose polymers, expanding our understanding of RRM versatility and the functional interplay between PARylation and RNA binding.