title: Frac-seq reveals isoform-specific recruitment to polyribosomes.
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 ∼30% (597/1954) 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.
authors.affiliation: Biomolecular Engineering Department, Jack Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA;
authors.forename: Timothy
authors.initials: T
authors.lastname: Sterne-Weiler
authors.forename: Rocio Teresa
authors.initials: RT
authors.lastname: Martinez-Nunez
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Howard
authors.forename: Ivan
authors.initials: I
authors.lastname: Cvitovik
authors.forename: Sol
authors.initials: S
authors.lastname: Katzman
authors.forename: Muhammad A
authors.initials: MA
authors.lastname: Tariq
authors.forename: Nader
authors.initials: N
authors.lastname: Pourmand
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Sanford
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D017398:Alternative Splicing; D003593:Cytoplasm / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010802:Phylogeny; D011132:Polyribosomes / Q000235:genetics / Q000378:metabolism*; D059368:RNA Isoforms / Q000235:genetics / Q000378:metabolism*; D012322:RNA Precursors / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D017423:Sequence Analysis, RNA
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D059368:RNA Isoforms; D012322:RNA Precursors