Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

Abstract

mRNA half-lives are transcript-specific and vary over a range of more than 100-fold in eukaryotic cells. mRNA stabilities can be regulated by sequence-specific RNA-binding proteins (RBPs), which bind to regulatory sequence elements and modulate the interaction of the mRNA with the cellular RNA degradation machinery. However, it is unclear if this kind of regulation is sufficient to explain the large range of mRNA stabilities. To address this question, we examined the transcriptome of 74 Schizosaccharomyces pombe strains carrying deletions in non-essential genes encoding predicted RBPs (86% of all such genes). We identified 25 strains that displayed changes in the levels of between 4 and 104 mRNAs. The putative targets of these RBPs formed biologically coherent groups, defining regulons involved in cell separation, ribosome biogenesis, meiotic progression, stress responses and mitochondrial function. Moreover, mRNAs in these groups were enriched in specific sequence motifs in their coding sequences and untranslated regions, suggesting that they are coregulated at the posttranscriptional level. We performed genome-wide RNA stability measurements for several RBP mutants, and confirmed that the altered mRNA levels were caused by changes in their stabilities. Although RBPs regulate the decay rates of multiple regulons, only 16% of all S. pombe mRNAs were affected in any of the 74 deletion strains. This suggests that other players or mechanisms are required to generate the observed range of RNA half-lives of a eukaryotic transcriptome.

Author Summary

Messenger RNAs (mRNAs) are the molecules that relay the information from genes (DNA) to proteins. Cells contain different amounts of each mRNA type depending on their function and their situation. The quantity of each mRNA depends on the balance between its production (transcription) and its degradation (mRNA decay). Recent studies have shown that the rate at which each mRNA is degraded is specific for every gene, but little is known about how this is regulated. In this work, we look at the role of a class of proteins that bind to RNA molecules (RNA-binding proteins, or RBPs) in the regulation of RNA decay. By systematically examining cells in which a single RBP has been inactivated we identify those that are important for RNA degradation. We found RBPs that make mRNAs more stable (that is, they are degraded more slowly) and others that make them unstable. These RBPs control the RNAs of genes with common features, suggesting that they provide a way of coordinating the function of groups of genes. However, for many genes we did not find RBPs that control their stability, indicating that other players are important to regulate RNA degradation.