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

Recent discoveries 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 that play central roles in gene expression, DNA damage response, and epigenetic regulation. Both proteins possess RNA-binding properties, but the mechanism by which PARP1 and MeCP2 recognize RNA-binding sites remains unclear. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach with a random 70-mer RNA library, we uncovered that PARP1 preferentially binds guanine-rich RNAs, while MeCP2 favors cytosine-rich targets. However, neither protein recognizes a consensus (linear) RNA sequence motif. Instead, PARP1 targets RNAs with long stems and small loops, while MeCP2 targets RNAs with large loops or bulges and intricate multi-stem structures. These findings suggest that both proteins rely on distinct RNA structural features, highlighting the structural versatility of RNA as a regulatory element.