Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes

By Nicholas T. Ingolia, L. Lareau, Jonathan S. Weissman. Cell, 2011

2,080 citations recorded by the source corpus.

SUMMARY 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/14f962568690191f74e724c96bb8d9743c850bc7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. (2014, methodology): “(A) Cumulative length distribution shows 1 nt larger footprints on annotated coding sequences from emetine- versus cycloheximide-treated cells (Ingolia et al., 2011).”
Long noncoding RNAs: Cellular address codes in development and disease (2013, positive): “Ribosome profiling, a method that enumerates transcripts associated with ribosomes, had detected many lncRNAs, but it was unclear whether these lncRNAs are just being scanned similarly to 50 untranslated regions or actually are productively engaged in translation (Ingolia et al., 2011).”
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation (2014, methodology): “However, many of these transcripts (including lincRNAs) (Khalil et al , 2009; Guttman et al , 2010; Ingolia et al , 2011) contain multiple putative small open reading frames (smORFs, ≤ 100 aa) that can potentially be translated and thus might have a coding function (Ingolia et al , 2011; Chew et al…”
Codon Bias as a Means to Fine-Tune Gene Expression (2015, background): “…translation elongation at the coding region’s 5 0 end; these investigators claimed that this earlier observed phenomenon was an artifact either of the ribosome proﬁling experiment (Ingolia et al., 2011) or of the data analysis, because shorter genes have higher initiation rates (Shah et al., 2013).”
LNCcation: lncRNA localization and function (2021, result): “, 2019); however, that lncRNA association with polysomal fractions is indicative of active translation (Ingolia et al., 2011; Ruiz-Orera et al., 2014) is not supported by other studies (Bánfai et al.”
c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells (2012, neutral): “, 2008]), miRNA-binding sites, and 30 UTR (Ingolia et al., 2011; Liu and Levens, 2006; Sampson et al., 2007).”
Toward a Kinetic Understanding of Eukaryotic Translation. (2018, background): “Genome-wide analysis of the translatome indicates that the TE of a large number of different mRNAs is altered in response to changes in environmental conditions and events such as progression through stages of the cell cycle (Ingolia et al. 2011; Brar et al. 2012; Stumpf et al. 2013; Tanenbaum et al”
Identification of protein coding regions in RNA transcripts (2014, background): “Several ribosome profiling studies (12,23–24) raised concerns about the frequent presence of alternative TIS’s located both upstream and downstream of annotated TIS’s confirmed by Ribo-seq experiments.”