title: Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse.
abstract: In order to find evidence for translation of alternatively spliced transcripts, especially those that result in a change in reading frame, we collected exon-skipping cases previously found by RNA-Seq and applied a computational approach to screen millions of mass spectra. These spectra came from seven human and six mouse tissues, five of which are the same between the two organisms: liver, kidney, lung, heart, and brain. Overall, we detected 4 percent of all exon-skipping events found in RNA-seq data, regardless of their effect on reading frame. The fraction of alternative isoforms detected did not differ between out-of-frame and in-frame events. Moreover, the fraction of identified alternative exon-exon junctions and constitutive junctions were similar. Together, our results suggest that both in-frame and out-of-frame translation may be actively used to regulate protein activity or localization.
authors.forename: Rodrigo F
authors.initials: RF
authors.lastname: Ramalho
authors.forename: Sujun
authors.initials: S
authors.lastname: Li
authors.forename: Predrag
authors.initials: P
authors.lastname: Radivojac
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Hahn
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D005091:Exons; D006801:Humans; D013058:Mass Spectrometry; D051379:Mice; D020033:Protein Isoforms / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D016364:Reading Frames
chemical_list: D020033:Protein Isoforms