Deciphering the protein‐RNA recognition code: Combining large‐scale quantitative methods with structural biology

Abstract

RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence-specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross-linking immuno-precipitation (CLIP) and other recently developed high-throughput methods provide comprehensive, genome-wide maps of protein-RNA interactions in the cell. Structural biology gives detailed insights into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high-throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein-RNA recognition in gene regulation, as we review in this article.

Position-dependent interactions of Y-box protein 2 (YBX2) with mRNA enable mRNA storage in round spermatids by repressing mRNA translation and blocking translation-dependent mRNA decay

“…This review considers controversies concerning the identity of this particular Y‐box protein isoform for spermatid development; the binding specificity of Y‐box proteins; the functions of YBX2 in mRNA stability and translational repression; and whether YBX2 targets mRNAs at the level of transcription in the nucleus or mRNA in the cytoplasm. This review also assembles evidence that strong repression by YBX2 in round spermatids requires binding to cis ‐elements at the 3′ terminus of the 3′UTR (3T3U)—a hypothesis that agrees with the current model that RNA‐binding proteins associate with mRNA with little specificity, whereas mRNA‐specific regulation requires cooperative interactions of multiple RNA binding proteins bound to closely spaced cis ‐elements (Hennig and Sattler, ).…”

“…The great variety of sequences than Y‐box proteins can bind illustrates a fundamental dilemma in RNA biology: Individual RNA binding domains, including the cold‐shock domain, commonly bind short sequences with degenerate sites that are often present in multiple copies in many –sometimes thousands–mRNAs, yet proteins containing these domains can be very selective in which individual mRNAs they regulate (Hennig and Sattler, ). One approach that increases mRNA specificity is through the formation of complexes of multiple RNA binding proteins (Leeper et al, ; Alfroz et al, ; Hennig and Sattler, ), as exemplified by the extraordinary observation that one of the five cold‐shock domains in UNR/CSDE5 (upstream of N‐RAS/cold‐shock domain‐containing protein E) and two RNA recognition motifs in sex‐lethal (Sxl) form a ternary complex with a 16‐nt U‐rich segment in the Drosophila melanogaster msl2 3′UTR (Hennig et al, ). Assembly of this ternary complex increases the affinity of UNR/CSDE5 for the msl2 3′UTR by 1,000‐fold relative to that of UNR/CSDE5 alone.…”

A structural perspective of RNA recognition by intrinsically disordered proteins

“…Many RBPs utilise multiple domains to recognise its partner RNA. This multi-domain binding involves cooperative interactions between the RBDs and dictates the dynamics of conformational polymorphism in RNA binding [54]. These interacting domains of RBPs are often linked by a flexible stretch of polypeptides called linkers or spacers.…”

Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15

“…In this genomic era, the imperative to utilize primary sequence data to elucidate the relationship between an RBP, its recognition site, and its function, is only growing [4]. Identifying the binding sites for RBPs is an important task toward unraveling gene regulatory networks [5].…”