Quantitative profiling of initiating ribosomes in vivo (original) (raw)

• Aitken, C.E. & Lorsch, J.R. A mechanistic overview of translation initiation in eukaryotes. Nat. Struct. Mol. Biol. 19, 568–576 (2012).
  Article CAS PubMed Google Scholar
• Gray, N.K. & Wickens, M. Control of translation initiation in animals. Annu. Rev. Cell Dev. Biol. 14, 399–458 (1998).
  Article CAS PubMed Google Scholar
• Gebauer, F. & Hentze, M.W. Molecular mechanisms of translational control. Nat. Rev. Mol. Cell Biol. 5, 827–835 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Sonenberg, N. & Hinnebusch, A.G. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136, 731–745 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Spriggs, K.A., Bushell, M. & Willis, A.E. Translational regulation of gene expression during conditions of cell stress. Mol. Cell 40, 228–237 (2010).
  Article CAS PubMed Google Scholar
• Liu, B. & Qian, S.B. Translational reprogramming in cellular stress response. Wiley Interdiscip. Rev. RNA 5, 301–315 (2014).
  Article CAS PubMed Google Scholar
• Jackson, R.J., Hellen, C.U. & Pestova, T.V. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 11, 113–127 (2010).
  Article CAS PubMed PubMed Central 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. Science 324, 218–223 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Ingolia, N.T. Ribosome profiling: new views of translation, from single codons to genome scale. Nat. Rev. Genet. 15, 205–213 (2014).
  CAS PubMed Google Scholar
• Plotkin, J.B. & Kudla, G. Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet. 12, 32–42 (2011).
  Article CAS PubMed Google Scholar
• Shah, P., Ding, Y., Niemczyk, M., Kudla, G. & Plotkin, J.B. Rate-limiting steps in yeast protein translation. Cell 153, 1589–1601 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Morris, D.R. & Geballe, A.P. Upstream open reading frames as regulators of mRNA translation. Mol. Cell. Biol. 20, 8635–8642 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Sanz, E. et al. Cell-type-specific isolation of ribosome-associated mRNA from complex tissues. Proc. Natl. Acad. Sci. USA 106, 13939–13944 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Heiman, M. et al. A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738–748 (2008).
  Article CAS PubMed PubMed Central 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. USA 109, E2424–E2432 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Schneider-Poetsch, T. et al. Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin. Nat. Chem. Biol. 6, 209–217 (2010).
  Article CAS PubMed PubMed Central 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).
  Article CAS PubMed PubMed Central Google Scholar
• Blobel, G. & Sabatini, D. Dissociation of mammalian polyribosomes into subunits by puromycin. Proc. Natl. Acad. Sci. USA 68, 390–394 (1971).
  Article CAS PubMed PubMed Central Google Scholar
• David, A. et al. Nuclear translation visualized by ribosome-bound nascent chain puromycylation. J. Cell Biol. 197, 45–57 (2012).
  Article CAS PubMed PubMed Central 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. Cell 147, 789–802 (2011).
  Article CAS PubMed PubMed Central 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. USA 106, 7507–7512 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Kozak, M. Pushing the limits of the scanning mechanism for initiation of translation. Gene 299, 1–34 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Dorokhov, Y.L. et al. Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry. Proc. Natl. Acad. Sci. USA 99, 5301–5306 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Gilbert, W.V., Zhou, K., Butler, T.K. & Doudna, J.A. Cap-independent translation is required for starvation-induced differentiation in yeast. Science 317, 1224–1227 (2007).
  Article CAS PubMed Google Scholar
• Meyuhas, O. Synthesis of the translational apparatus is regulated at the translational level. Eur. J. Biochem. 267, 6321–6330 (2000).
  Article CAS PubMed Google Scholar
• Hamilton, T.L., Stoneley, M., Spriggs, K.A. & Bushell, M. TOPs and their regulation. Biochem. Soc. Trans. 34, 12–16 (2006).
  Article CAS PubMed Google Scholar
• Hinnebusch, A.G. Translational regulation of GCN4 and the general amino acid control of yeast. Annu. Rev. Microbiol. 59, 407–450 (2005).
  Article CAS PubMed Google Scholar
• Sidrauski, C. et al. Pharmacological brake-release of mRNA translation enhances cognitive memory. Elife 2, e00498 (2013).
  Article PubMed PubMed Central Google Scholar
• Sherman, M.Y. & Goldberg, A.L. Cellular defenses against unfolded proteins: a cell biologist thinks about neurodegenerative diseases. Neuron 29, 15–32 (2001).
  Article CAS PubMed Google Scholar
• Vabulas, R.M. & Hartl, F.U. Protein synthesis upon acute nutrient restriction relies on proteasome function. Science 310, 1960–1963 (2005).
  Article CAS PubMed Google Scholar
• Suraweera, A., Munch, C., Hanssum, A. & Bertolotti, A. Failure of amino acid homeostasis causes cell death following proteasome inhibition. Mol. Cell 48, 242–253 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Hilbe, J.M. Negative Binomial Regression 2nd edn. (Cambridge Univ. Press, 2011).
• Dillies, M.A. et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief. Bioinform. 14, 671–683 (2013).
  Article CAS PubMed Google Scholar
• Bailey, T.L. et al. MEME Suite: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).
  CAS PubMed PubMed Central Google Scholar
• Sun, J., Conn, C.S., Han, Y., Yeung, V. & Qian, S.B. PI3K-mTORC1 attenuates stress response by inhibiting cap-independent Hsp70 translation. J. Biol. Chem. 286, 6791–6800 (2011).
  Article CAS PubMed Google Scholar
• Liu, B., Han, Y. & Qian, S.B. Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol. Cell 49, 453–463 (2013).
  Article CAS PubMed PubMed Central Google Scholar