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. SOURCE: Nicholas,T,Ingolia (nick@ingolia.org) - Weissman UCSF

Pluto Bioinformatics

GSE30839: RibosomeProfilingof Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes