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PMID: 22056041 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes.

Cell ·Vol. 147 ·No. 4 ·2011-11-11 ·Pages 789-802

Ingolia NT, Lareau LF, Weissman JS

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.

MeSH Terms
Algorithms Animals Artificial Intelligence Embryoid Bodies/cytology,metabolism Embryonic Stem Cells/metabolism Genomics/methods Harringtonines/pharmacology High-Throughput Nucleotide Sequencing/methods Kinetics Mice Open Reading Frames Peptide Chain Initiation, Translational Protein Biosynthesis RNA/analysis Ribosomes/chemistry,drug effects Sequence Analysis, RNA/methods
Chemicals
Harringtonines harringtonine RNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ingolia Nicholas T
Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. [email protected]
Lareau Liana F
Weissman Jonathan S
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Article Info
Journal
Cell
Abbr.
Cell
ISSN
1097-4172
DOI
10.1016/j.cell.2011.10.002
Email
[email protected]
Published
2011-11-11
Epub
2011-00-03
Pages
789-802
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC3225288
Subset
IM
Grants
NIGMS NIH HHS · F32 GM080853 · United States
NIA NIH HHS · P01 AG10770 · United States
NIA NIH HHS · P01 AG010770 · United States
Howard Hughes Medical Institute · United States
NIGMS NIH HHS · F32 GM080853-03 · United States
NIGMS NIH HHS · GM080853 · United States
Databases
GEO
GSE30839
External Links
PubMed source DOI: 10.1016/j.cell.2011.10.002 PMC Full Text View journal details
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