Ribosome profiling: new views of translation, from single codons to genome scale (original) (raw)
Brown, P. O. & Botstein, D. Exploring the new world of the genome with DNA microarrays. Nature Genet.21, 33–37 (1999). ArticleCAS Google Scholar
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev. Genet.10, 57–63 (2009). ArticleCAS Google Scholar
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science324, 218–223 (2009). ArticleCAS Google Scholar
Johannes, G., Carter, M. S., Eisen, M. B., Brown, P. O. & Sarnow, P. Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl Acad. Sci. USA96, 13118–13123 (1999). ArticleCAS Google Scholar
Arava, Y. et al. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA100, 3889–3894 (2003). ArticleCAS Google Scholar
Hendrickson, D. G. et al. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol.7, e1000238 (2009). Article Google Scholar
Steitz, J. A. Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA. Nature224, 957–964 (1969). ArticleCAS Google Scholar
Wolin, S. L. & Walter, P. Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J.7, 3559–3569 (1988). ArticleCAS Google Scholar
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol.14, R36 (2013). Article Google Scholar
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol.11, R106 (2010). ArticleCAS Google Scholar
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics26, 139–140 (2010). ArticleCAS Google Scholar
Olshen, A. B. et al. Assessing gene-level translational control from ribosome profiling. Bioinformatics29, 2995–3002 (2013). ArticleCAS Google Scholar
Michel, A. M. et al. GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res.42, D859–D864 (2013). Article Google Scholar
Ingolia, N. T., Lareau, L. F. & Weissman, J. S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell147, 789–802 (2011). ArticleCAS Google Scholar
Shah, P., Ding, Y., Niemczyk, M., Kudla, G. & Plotkin, J. B. Rate-limiting steps in yeast protein translation. Cell153, 1589–1601 (2013). ArticleCAS Google Scholar
Arribere, J. A. & Gilbert, W. V. Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res.23, 977–987 (2013). ArticleCAS Google Scholar
Vogel, C. & Marcotte, E. M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nature Rev. Genet.13, 227–232 (2012). ArticleCAS Google Scholar
Michel, A. M. et al. Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res.22, 2219–2229 (2012). ArticleCAS Google Scholar
Brar, G. A. et al. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science335, 552–557 (2012). ArticleCAS Google Scholar
Chew, G. L. et al. Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs. Development140, 2828–2834 (2013). ArticleCAS Google Scholar
Lee, S., Liu, B., Huang, S. X., Shen, B. & Qian, S. B. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl Acad. Sci. USA109, E2424–E2432 (2012). ArticleCAS Google Scholar
Fritsch, C. et al. Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res.22, 2208–2218 (2012). ArticleCAS Google Scholar
Sonenberg, N. & Hinnebusch, A. G. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell136, 731–745 (2009). ArticleCAS Google Scholar
Starck, S. R. et al. Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science336, 1719–1723 (2012). ArticleCAS Google Scholar
Menschaert, G. et al. Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events. Mol. Cell. Proteomics12, 1780–1790 (2013). ArticleCAS Google Scholar
Fournier, C. T. et al. Amino termini of many yeast proteins map to downstream start codons. J. Proteome Res.11, 5712–5719 (2012). ArticleCAS Google Scholar
Pelechano, V., Wei, W. & Steinmetz, L. M. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature497, 127–131 (2013). ArticleCAS Google Scholar
Sonenberg, N. & Hinnebusch, A. G. New modes of translational control in development, behavior and disease. Mol. Cell28, 721–729 (2007). ArticleCAS Google Scholar
Stern-Ginossar, N. et al. Decoding human cytomegalovirus. Science338, 1088–1093 (2012). ArticleCAS Google Scholar
Schwaid, A. G. et al. Chemoproteomic discovery of cysteine-containing human short open reading frames. J. Am. Chem. Soc.135, 16750–16753 (2013). ArticleCAS Google Scholar
Slavoff, S. A. et al. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nature Chem. Biol.9, 59–64 (2013). ArticleCAS Google Scholar
Kondo, T. et al. Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nature Cell Biol.9, 660–665 (2007). ArticleCAS Google Scholar
Guttman, M., Russell, P., Ingolia, N. T., Weissman, J. S. & Lander, E. S. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell154, 240–251 (2013). ArticleCAS Google Scholar
Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell154, 26–46 (2013). ArticleCAS Google Scholar
Drummond, D. A. & Wilke, C. O. The evolutionary consequences of erroneous protein synthesis. Nature Rev. Genet.10, 715–724 (2009). Article Google Scholar
Carvunis, A. R. et al. Proto-genes and de novo gene birth. Nature487, 370–374 (2012). ArticleCAS Google Scholar
Calvo, S. E., Pagliarini, D. J. & Mootha, V. K. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc. Natl Acad. Sci. USA106, 7507–7512 (2009). ArticleCAS Google Scholar
Plotkin, J. B. & Kudla, G. Synonymous but not the same: the causes and consequences of codon bias. Nature Rev. Genet.12, 32–42 (2011). ArticleCAS Google Scholar
Li, G. W., Oh, E. & Weissman, J. S. The anti- Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature484, 538–541 (2012). ArticleCAS Google Scholar
Qian, W., Yang, J. R., Pearson, N. M., Maclean, C. & Zhang, J. Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet.8, e1002603 (2012). ArticleCAS Google Scholar
Stadler, M. & Fire, A. Wobble base-pairing slows in vivo translation elongation in metazoans. RNA17, 2063–2073 (2011). ArticleCAS Google Scholar
Dana, A. & Tuller, T. Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput. Biol.8, e1002755 (2012). ArticleCAS Google Scholar
Tuller, T. et al. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell141, 344–354 (2010). ArticleCAS Google Scholar
Woolstenhulme, C. J. et al. Nascent peptides that block protein synthesis in bacteria. Proc. Natl Acad. Sci. USA110, E878–E887 (2013). ArticleCAS Google Scholar
Charneski, C. A. & Hurst, L. D. Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol.11, e1001508 (2013). ArticleCAS Google Scholar
Ito, K. & Chiba, S. Arrest peptides: _cis_-acting modulators of translation. Annu. Rev. Biochem.82, 171–202 (2013). ArticleCAS Google Scholar
Pechmann, S., Willmund, F. & Frydman, J. The ribosome as a hub for protein quality control. Mol. Cell49, 411–421 (2013). ArticleCAS Google Scholar
Shalgi, R. et al. Widespread regulation of translation by elongation pausing in heat shock. Mol. Cell49, 439–452 (2013). ArticleCAS Google Scholar
Gerashchenko, M. V., Lobanov, A. V. & Gladyshev, V. N. Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress. Proc. Natl Acad. Sci. USA109, 17394–17399 (2012). ArticleCAS Google Scholar
Liu, B., Han, Y. & Qian, S. B. Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol. Cell49, 453–463 (2013). ArticleCAS Google Scholar
Oh, E. et al. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell147, 1295–1308 (2011). ArticleCAS Google Scholar
Han, Y. et al. Monitoring cotranslational protein folding in mammalian cells at codon resolution. Proc. Natl Acad. Sci. USA109, 12467–12472 (2012). ArticleCAS Google Scholar
Spriggs, K. A., Bushell, M. & Willis, A. E. Translational regulation of gene expression during conditions of cell stress. Mol. Cell40, 228–237 (2010). ArticleCAS Google Scholar
Wang, D. O., Martin, K. C. & Zukin, R. S. Spatially restricting gene expression by local translation at synapses. Trends Neurosci.33, 173–182 (2010). ArticleCAS Google Scholar
Hotamisligil, G. S. Endoplasmic reticulum stress and the inflammatory basis of metabolic disease. Cell140, 900–917 (2010). ArticleCAS Google Scholar
Thoreen, C. C. et al. A unifying model for mTORC1-mediated regulation of mRNA translation. Nature485, 109–113 (2012). ArticleCAS Google Scholar
Hsieh, A. C. et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature485, 55–61 (2012). ArticleCAS Google Scholar
Cho, J. et al. LIN28A is a suppressor of ER-associated translation in embryonic stem cells. Cell151, 765–777 (2012). ArticleCAS Google Scholar
Castello, A. et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell149, 1393–1406 (2012). ArticleCAS Google Scholar
Baltz, A. G. et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell46, 674–690 (2012). ArticleCAS Google Scholar
Guo, H., Ingolia, N. T., Weissman, J. S. & Bartel, D. P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature466, 835–840 (2010). ArticleCAS Google Scholar
Bazzini, A. A., Lee, M. T. & Giraldez, A. J. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science336, 233–237 (2012). ArticleCAS Google Scholar
Stadler, M., Artiles, K., Pak, J. & Fire, A. Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets. Genome Res.22, 2418–2426 (2012). ArticleCAS Google Scholar
Heiman, M. et al. A translational profiling approach for the molecular characterization of CNS cell types. Cell135, 738–748 (2008). ArticleCAS Google Scholar
Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nature Protoc.7, 1534–1550 (2012). ArticleCAS Google Scholar