GSE30839
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes
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 novel  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 new class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated  complexity to mammalian proteomes. Overall design: Examination of translation in mouse embryonic stem cells and during differentiation into embryoid bodies