Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control

Tahmasebi, S., Khoutorsky, A., Mathews, M. B. & Sonenberg, N. Translation deregulation in human disease. Nat. Rev. Mol. Cell Biol. 19, 791–807 (2018).

CAS  PubMed  Article  Google Scholar 

Kronstad, L. M. & Glaunsinger, B. A. Diverse virus–host interactions influence RNA-based regulation during γ-herpesvirus infection. Curr. Opin. Microbiol. 15, 506–511 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009).

CAS  PubMed  PubMed Central  Article  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. Nat. Protoc. 7, 1534–1550 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Janich, P., Arpat, A. B., Castelo-Szekely, V., Lopes, M. & Gatfield, D. Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames. Genome Res. 25, 1848–1859 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Chotewutmontri, P., Stiffler, N., Watkins, K. P. & Barkan, A. Ribosome profiling in maize. Maize. Methods Mol. Biol. 1676, 165–183 (2018).

CAS  PubMed  Article  Google Scholar 

Mohammad, F., Green, R. & Buskirk, A. R. A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution. eLife 8, e42591 (2019).

PubMed  PubMed Central  Article  Google Scholar 

Gelsinger, D. R. et al. Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution. Nucleic Acids Res. 48, 5201–5216 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Jensen, B. C. et al. Extensive stage-regulation of translation revealed by ribosome profiling of Trypanosoma brucei. BMC Genomics 15, 911 (2014).

PubMed  PubMed Central  Article  Google Scholar 

Ingolia, N. T., Hussmann, J. A. & Weissman, J. S. Ribosome profiling: global views of translation. Cold Spring Harb. Perspect. Biol. 11, a032698 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Shirokikh, N. E., Archer, S. K., Beilharz, T. H., Powell, D. & Preiss, T. Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination. Nat. Protoc. 12, 697–731 (2017).

CAS  PubMed  Article  Google Scholar 

Archer, S. K., Shirokikh, N. E., Beilharz, T. H. & Preiss, T. Dynamics of ribosome scanning and recycling revealed by translation complex profiling. Nature 535, 570–574 (2016).

CAS  PubMed  Article  Google Scholar 

Sen, N. D. et al. Functional interplay between DEAD-box RNA helicases Ded1 and Dbp1 in preinitiation complex attachment and scanning on structured mRNAs in vivo. Nucleic Acids Res. 47, 8785–8806 (2019).

CAS  PubMed  PubMed Central  Google Scholar 

Wagner, S. et al. Selective translation complex profiling reveals staged initiation and co-translational assembly of initiation factor complexes. Mol. Cell 79, 546–560.e7 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Bohlen, J., Fenzl, K., Kramer, G., Bukau, B. & Teleman, A. A. Selective 40S footprinting reveals cap-tethered ribosome scanning in human cells. Mol. Cell 79, 561–574.e5 (2020).

CAS  PubMed  Article  Google Scholar 

Jackson, V. Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent. Cell 15, 945–954 (1978).

CAS  PubMed  Article  Google Scholar 

Toews, J., Rogalski, J. C. & Kast, J. Accessibility governs the relative reactivity of basic residues in formaldehyde-induced protein modifications. Anal. Chim. Acta 676, 60–67 (2010).

CAS  PubMed  Article  Google Scholar 

Solomon, M. J. & Varshavsky, A. Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc. Natl. Acad. Sci. USA 82, 6470–6474 (1985).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Valášek, L., Szamecz, B., Hinnebusch, A. G. & Nielsen, K. H. In vivo stabilization of preinitiation complexes by formaldehyde cross-linking. Methods Enzym. 429, 163–183 (2007).

Article  CAS  Google Scholar 

Oh, E. et al. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147, 1295–1308 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Wong, C. C., Traynor, D., Basse, N., Kay, R. R. & Warren, A. J. Defective ribosome assembly in Shwachman–Diamond syndrome. Blood 118, 4305–4312 (2011).

CAS  PubMed  Article  Google Scholar 

Liu, B. & Qian, S.-B. Characterizing inactive ribosomes in translational profiling. Translation 4, e1138018 (2016).

PubMed  PubMed Central  Article  Google Scholar 

Vaklavas, C., Blume, S. W. & Grizzle, W. E. Translational dysregulation in cancer: molecular insights and potential clinical applications in biomarker development. Front. Oncol. 7, 158 (2017).

PubMed  PubMed Central  Article  Google Scholar 

Baser, A. et al. Onset of differentiation is post-transcriptionally controlled in adult neural stem cells. Nature 566, 100–104 (2019).

CAS  PubMed  Article  Google Scholar 

Luchessi, A. D. et al. Involvement of eukaryotic translation initiation factor 5A (eIF5A) in skeletal muscle stem cell differentiation. J. Cell. Physiol. 218, 480–489 (2009).

CAS  PubMed  Article  Google Scholar 

Sampath, P. et al. A hierarchical network controls protein translation during murine embryonic stem cell self-renewal and differentiation. Cell Stem Cell 2, 448–460 (2008).

CAS  PubMed  Article  Google Scholar 

Holt, C. E. & Schuman, E. M. The central dogma decentralized: new perspectives on RNA function and local translation in. neurons. Neuron 80, 648–657 (2013).

CAS  PubMed  Article  Google Scholar 

Holt, C. E., Martin, K. C. & Schuman, E. M. Local translation in neurons: visualization and function. Nat. Struct. Mol. Biol. 26, 557–566 (2019).

CAS  PubMed  Article  Google Scholar 

Glock, C., Heumüller, M. & Schuman, E. M. mRNA transport & local translation in neurons. Curr. Opin. Neurobiol. 45, 169–177 (2017).

CAS  PubMed  Article  Google Scholar 

Ichihara, K. et al. Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons. Nucleic Acids Res. 49, 7298–7317 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Young, D. J., Meydan, S. & Guydosh, N. R. 40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling. Nat. Commun. 12, 2976 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

McGlincy, N. J. & Ingolia, N. T. Transcriptome-wide measurement of translation by ribosome profiling. Methods 126, 112–129 (2017).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Brar, G. A. & Weissman, J. S. Ribosome profiling reveals the what, when, where and how of protein synthesis. Nat. Rev. Mol. Cell Biol. 16, 651–664 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Gerashchenko, M. V. & Gladyshev, V. N. Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic Acids Res. 42, e134–e134 (2014).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Wu, C. C.-C., Zinshteyn, B., Wehner, K. A. & Green, R. High-resolution ribosome profiling defines discrete ribosome elongation states and translational regulation during cellular stress. Mol. Cell 73, 959–970.e5 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Lareau, L. F., Hite, D. H., Hogan, G. J. & Brown, P. O. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. eLife 3, 01257 (2014).

Article  CAS  Google Scholar 

Becker, A. H., Oh, E., Weissman, J. S., Kramer, G. & Bukau, B. Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes. Nat. Protoc. 8, 2212–2239 (2013).

CAS  PubMed  PubMed Central  Article 

留言 (0)

沒有登入
gif