title: Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals.
abstract: Transcription initiated at alternative sites can produce mRNA isoforms with different 5'UTRs, which are potentially subjected to differential translational regulation. However, the prevalence of such isoform-specific translational control across mammalian genomes is currently unknown. By combining polysome profiling with high-throughput mRNA 5' end sequencing, we directly measured the translational status of mRNA isoforms with distinct start sites. Among 9,951 genes expressed in mouse fibroblasts, we identified 4,153 showed significant initiation at multiple sites, of which 745 genes exhibited significant isoform-divergent translation. Systematic analyses of the isoform-specific translation revealed that isoforms with longer 5'UTRs tended to translate less efficiently. Further investigation of cis-elements within 5'UTRs not only provided novel insights into the regulation by known sequence features, but also led to the discovery of novel regulatory sequence motifs. Quantitative models integrating all these features explained over half of the variance in the observed isoform-divergent translation. Overall, our study demonstrated the extensive translational regulation by usage of alternative transcription start sites and offered comprehensive understanding of translational regulation by diverse sequence features embedded in 5'UTRs.
authors.affiliation: Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
authors.forename: Xi
authors.identifier: 0000-0002-7572-6354
authors.initials: X
authors.lastname: Wang
authors.affiliation: Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
authors.forename: Jingyi
authors.initials: J
authors.lastname: Hou
authors.affiliation: Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Quedenau
authors.affiliation: Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China wei.chen@mdc-berlin.de chenw@sustc.edu.cn.
authors.forename: Wei
authors.identifier: 0000-0003-3263-1627
authors.initials: W
authors.lastname: Chen
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D005786:Gene Expression Regulation; D008322:Mammals / Q000235:genetics; D051379:Mice; D041681:NIH 3T3 Cells; D011132:Polyribosomes / Q000235:genetics*; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D024363:Transcription Initiation Site
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger
keywords: alternative transcription start sites; cis‐regulatory elements; isoform‐divergent translation; translational regulation