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Cell. 2011 Nov 11;147(4):789-802. doi: 10.1016/j.cell.2011.10.002. Epub 2011 Nov 3.

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

Author information

1
Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. ingolia@ciwemb.edu

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.

PMID:
22056041
PMCID:
PMC3225288
DOI:
10.1016/j.cell.2011.10.002
[Indexed for MEDLINE]
Free PMC Article

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