RNAcompete-S: complex RNA sequence/structure models derived from a single-step in vitro selection. NA

RNA-binding proteins recognize RNA sequences and structures, but there is currently no systematic and accurate method to derive both types of preferences that are large, complex, and reflect direct binding. To address this absence, we introduce RNAcompete-S, which couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models). RNAcompete-S confirms that HuR, QKI, and SFRS prefer binding sites that are single stranded, but recapitulates known sequence and structure preferences for Vts1, RBMY, and SLBP. The SSM derived for SLBP is 18 bases long, and when scored using CLIP-seq data, it is more accurate than any previous models. Thus, RNAcompete-S enables accurate identification of large, complex, and intrinsic specificities with a uniform assay.