Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

Abstract

RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. We identified specific sequences or predicted structures significantly enriched in target mRNAs of 16 RBPs. These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3′-untranslated regions, others in 5′-untranslated regions, some in coding sequences, and many in two or more of these features. Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation. These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.

Author Summary

Regulation of gene transcription has been extensively studied, but much less is known about how the fates of the resulting mRNA transcripts are regulated. We were intrigued by the fact that while most eukaryotic genomes encode hundreds of RNA-binding proteins (RBPs), the targets and regulatory roles of only a small fraction of these proteins have been characterized. In this study, we systematically identified the RNAs associated with a select sample of 40 of the approximately 600 predicted RBPs in the budding yeast, Saccharomyces cerevisiae. We found that most of these RBPs bound specific sets of mRNAs whose protein products share physiological themes or similar locations within the cell. For 16 of the 40 RBPs, we identified sequence motifs significantly enriched in their RNA targets that presumably mediate recognition of the target by the RBP. The intricate, overlapping patterns of mRNAs associated with RBPs suggest an extensive combinatorial system for post-transcriptional regulation, involving dozens or even hundreds of RBPs. The organization and molecular mechanisms involved in this regulatory system, including how RBP–mRNA interactions are integrated with signal transduction systems and how they affect the fates of their RNA targets, provide abundant opportunities for investigation and discovery.

Abstract

A systematic study of the RNA targets of 40 known or predicted RNA-binding proteins in yeast suggests that an extensive system of dozens or hundreds of specific RNA-binding proteins may act to regulate the post-transcriptional fate of most or all RNAs in the yeast cell.