Abstract
Ribosome profiling is an emerging approach using deep sequencing of the mRNA part protected by the ribosome to study protein synthesis at the genome scale. This approach provides new insights into gene regulation at the translational level. In this review we describe the protocol to prepare polysomes and extract ribosome protected fragments before to deep sequence them.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS (2012) The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7(8):1534–1550
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218–223
Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS (2012) High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 335(6068):552–557
Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS (2013) Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife 2, e01179
Guydosh NR, Green R (2014) Dom34 rescues ribosomes in 3′ untranslated regions. Cell 156(5):950–962
Michel AM, Choudhury KR, Firth AE, Ingolia NT, Atkins JF, Baranov PV (2012) Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res 22(11):2219–2229
Michel AM, Fox G, M Kiran A, De Bo C, O’Connor PB, Heaphy SM, Mullan JP, Donohue CA, Higgins DG, Baranov PV (2014) GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res 42(Database issue):D859–D864
Smith JE, Alvarez-Dominguez JR, Kline N, Huynh NJ, Geisler S, Hu W, Coller J, Baker KE (2014) Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae. Cell Rep 7(6):1858–1866
Bazzini AA, Lee MT, Giraldez AJ (2012) Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336(6078):233–237
Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15(3):205–213
Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147(4):789–802
Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloe D, Le Gall C, Schaeffer B, Le Crom S, Guedj M, Jaffrezic F (2013) A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform 14(6):671–683
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Baudin-Baillieu, A., Hatin, I., Legendre, R., Namy, O. (2016). Translation Analysis at the Genome Scale by Ribosome Profiling. In: Devaux, F. (eds) Yeast Functional Genomics. Methods in Molecular Biology, vol 1361. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3079-1_7
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3079-1_7
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3078-4
Online ISBN: 978-1-4939-3079-1
eBook Packages: Springer Protocols