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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Artificial Intelligence
  • Embryoid Bodies / cytology
  • Embryoid Bodies / 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*
  • Ribosomes / drug effects
  • Sequence Analysis, RNA / methods*


  • Harringtonines
  • harringtonine
  • RNA

Associated data

  • GEO/GSE30839