title: Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes.
abstract: The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and unannotated translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes.
authors: Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. ingolia@ciwemb.edu
authors: Nicholas T
authors: NT
authors: Ingolia
authors: Liana F
authors: LF
authors: Lareau
authors: Jonathan S
authors: JS
authors: Weissman
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D058732:Embryoid Bodies / Q000166:cytology / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism; D023281:Genomics / Q000379:methods*; D006248:Harringtonines / Q000494:pharmacology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007700:Kinetics; D051379:Mice; D016366:Open Reading Frames; D010442:Peptide Chain Initiation, Translational; D014176:Protein Biosynthesis; D012313:RNA / Q000032:analysis*; D012270:Ribosomes / Q000737:chemistry* / Q000187:drug effects; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D006248:Harringtonines; C062500:harringtonin; D012313:RNA