Eukaryotic gene expression is a complex process orchestrated by multiple regulatory steps, of which transcription and translation are the two most important ones. Recent genome-wide studies have demonstrated that translation plays critical roles in determining cellular protein abundance. However, our current knowledge about how translation being controlled is still very limited. It remains yet underexplored whether and to what extent the regulation between eukaryotic transcription and translation could be coordinated.

Transcription outputs, mRNA transcripts, consist of not only the coding sequences (CDS) that dictate the encoded peptide sequences, but also 5ʹ and 3ʹ untranslated regions (UTRs),  which are imbedded with various cis-regulatory elements regulating mRNA translation. In the past decades, researches based on single gene or single type of regulatory element have demonstrated that 5’UTRs plays crucial roles in regulating eukaryotic protein synthesis. Yet their global impact on translation is still under investigation. In higher eukaryotes, around half of the protein-coding genes use multiple transcription start sites (TSSs). Given that mRNA isoforms transcribed from alternative TSSs are frequently composed of divergent translational regulatory cis-elements in their distinct 5ʹ UTRs, they could have divergent translational efficiency. However, to what extent the alternative usage of TSS can influence protein synthesis still remains unknown.

To answer these questions, Wei Chen’s group developed a novel sequencing-based method, by combining polysome profiling technology and cap analysis of gene expression (CAGE) technology. This method enabled to determine the 5’UTR for each mRNA isoform, and to directly measure the translational status of mRNA isoforms with distinct start sites.

Using this technology, Wei Chen’s group identified in mouse fibroblasts 4,153 genes with alternative TSSs. 18% of these genes exhibited significant isoform-divergent translation. Systematic analyses of the isoform-specific translation revealed a variety of sequence features repressing translation, including: upstream open-reading frames, cap-adjacent stable RNA secondary structures, 5ʹ-terminal oligopyrimidine (5ʹ TOP) and many novel regulatory sequence motifs. Quantitative models integrating all these features explained over half of the variance in the observed isoform-divergent translation.

Serving as a framework for studying the 5’UTR-mediated translational regulation which can be readily applied to other cell types or cellular conditions, this research offered comprehensive understanding of translational regulation by diverse sequence features embedded in 5ʹUTRs.

Post-doctoral researcher Xi Wang and PhD student Jingyi Hou from Max-Delbrück Center for Molecular Medicine were the co-first authors of this paper.

Full text: http://msb.embopress.org/content/12/7/875