RAPID-SELEX identifies high-affinity RNA targets for chromatin binding proteins PARP1 and MeCP2

Recent studies showed that some chromatin-binding proteins also interact with RNA to regulate gene expression. Poly (ADP-ribose) polymerase 1 (PARP1) and Methyl-CpG Binding Protein 2 (MeCP2) are two chromatin-associated, DNA-binding proteins with central roles in gene expression, DNA damage response, and epigenetic regulation. PARP1 and MeCP2 both have RNA binding properties, but it is still unclear how PARP1 and MeCP2 are recruited to or recognize RNA binding sites. Here, we used a RAPID-SELEX procedure, a random 70-mer RNA library, and 12 rounds of selection to identify high-affinity PARP1 and MeCP2 RNA targets. PARP1 prefers RNA targets enriched in guanine, while MeCP2 shows a preference for targets enriched in cytosine. However, neither protein seems to have a consensus (linear) RNA sequence motif. Instead, high-affinity PARP1 targets contain intrinsic secondary structures characterized by a relatively long stem and small loop. High affinity MeCP2 targets are also intrinsically structured, characterized by a large loop (or bulge) and multiple stems. These data suggest that both proteins target RNAs based on (unique) structural features rather than nucleotide sequence, and that many different RNA sequences can adopt similar structures. Two replicate groups were obtained for PARP1 and MECP2 each. RNA sequences were obtained for 3 RAPID-SELEX rounds (R3, R8, R12) per replicate group for each protein.