Post-transcriptional gene regulation: from genome-wide studies to principles

Abstract

Post-transcriptional regulation of gene expression plays important roles in diverse cellular processes such as development, metabolism and cancer progression. Whereas many classical studies explored the mechanistics and physiological impact on specific mRNA substrates, the recent development of genome-wide analysis tools enables the study of post-transcriptional gene regulation on a global scale. Importantly, these studies revealed distinct programs of RNA regulation, suggesting a complex and versatile post-transcriptional regulatory network. This network is controlled by specific RNA-binding proteins and/or non-coding RNAs, which bind to specific sequence or structural elements in the RNAs and thereby regulate subsets of mRNAs that partly encode functionally related proteins. It will be a future challenge to link the spectra of targets for RNA-binding proteins to post-transcriptional regulatory programs and to reveal its physiological implications.

Figure 1

Gene expression is controlled at multiple steps. See text for details.

Figure 2

Global approaches to study post-transcriptional gene regulation. (a) Determining the translation status of each mRNA for the mapping of translational programs. Cell-extracts are fractionated through a sucrose-density gradient and the absorbance at 254 nm is monitored. RNA is isolated from fractions containing ‘free’ RNA and ribosomal subunits, monosomes (80S) and polysomes, and analyzed with DNA microarrays. The relative position of a message in this profile is an indicator for its translational activity. (b) Systematic identification of RNAs associated with specific RNA-binding proteins. In this so-called ‘ribonomics’ approach, RBPs are immunoprecipitated or affinity-purified via a tag from cellular extracts. RNAs associated with RBPs are isolated, cDNA copies are fluorescently labeled and hybridized to DNA microarrays. The Cy5/Cy3 fluorescence ratio for each locus reflects its enrichment by affinity for the cognate protein.