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Published Online February 12, 2009
Science DOI: 10.1126/science.1168978

Research Articles

Submitted on November 25, 2008
Accepted on January 30, 2009

Genome-Wide Analysis In Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Nicholas T. Ingolia 1*, Sina Ghaemmaghami 2, John R. S. Newman 1, Jonathan S. Weissman 1

1 Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA.
2 Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA.; Present address: Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA 94158, USA.

* To whom correspondence should be addressed.
Nicholas T. Ingolia , E-mail: ingolia{at}cmp.ucsf.edu

Techniques for systematically monitoring protein translation have lagged far behind methods for measuring mRNA levels. Here, we present a ribosome profiling strategy, based on deep sequencing of ribosome protected mRNA fragments, that enables genome-wide investigation of translation with sub-codon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control both for determining absolute protein abundance and for responding to environmental stress. We also observed distinct phases during translation involving a large decrease in ribosome density going from early to late peptide elongation as well as widespread, regulated initiation at non-AUG codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.


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