Frac-seq reveals isoform-specific recruitment to polyribosomes
- Timothy Sterne-Weiler1,
- Rocio Teresa Martinez-Nunez2,
- Jonathan M Howard1,
- Ivan Cvitkovic1,
- Sol Katzman1,
- Muhammad A Tariq1,
- Nadar Pourmand1 and
- Jeremy R Sanford1,3
- ↵* Corresponding author; email: jsanfor2{at}ucsc.edu
Abstract
Pre-mRNA splicing is required for the accurate expression of virtually all human protein coding genes. However, splicing also plays important roles in coordinating subsequent steps of pre-mRNA processing such as polyadenylation and mRNA export. Here we test the hypothesis that nuclear pre-mRNA processing influences the polyribosome association of alternative mRNA isoforms. By comparing isoform ratios in cytoplasmic and polyribosomal extracts we determined that the alternative products of approximately 30% (597/1,954) of mRNA processing events are differentially partitioned between these subcellular fractions. Many of the events exhibiting isoform-specific polyribosome association are highly conserved across mammalian genomes, underscoring their possible biological importance. We find that differences in polyribosome association may be explained, at least in part by the observation that alternative splicing alters the cis-regulatory landscape of mRNAs isoforms. For example, inclusion or exclusion of upstream open reading frames (uORFs) in the 5' UTR as well as Alu-elements and microRNA target sites in the 3' UTR have a strong influence on polyribosome association of alternative mRNA isoforms. Taken together, our data demonstrate for the first time the potential link between alternative splicing and translational control of the resultant mRNA isoforms.
- Received September 11, 2012.
- Accepted June 5, 2013.
- © 2013, Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.
