Ribo-Seq (a.k.a. Ribosome Profiling) is a high-throughput sequencing technology that provides genome-wide information on protein synthesis. It was developed in 2009 by the Weissman lab in the University of California, San Francisco (1).
While RNA-Seq quantifies mRNA abundance transcriptome-wide, Ribo-Seq additionally provides transcriptome-wide information on protein synthesis by identifying the exact locations of translating ribosomes on mRNAs. Although global determination of steady state proteins levels (proteome) is the holy grail of gene expression analysis, until the sensitivity of proteomics significantly increases, a combination of Ribo-Seq and RNA-Seq will likely remain the best proxy for the proteome.
Under certain conditions (drug treatment, development, stress etc.) a particular mRNA may not change in abundance, yet protein synthesis can be altered dramatically. Conversely, conditions that change the levels of a particular mRNA may have little impact on its protein synthesis. Therefore, using a combination of RNA-Seq and Ribo-Seq technologies in parallel can provide a more complete “map” of gene expression leading to improved biological interpretation and diagnostics.
1. Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. and Weissman, J.S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.
2. Andreev, D.E., O’Connor, P.B., Fahey, C., Kenny, E.M., Terenin, I.M., Dmitriev, S.E., Cormican, P., Morris, D.W., Shatsky, I.N. and Baranov, P.V. (2015) Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression. Elife, 4, e03971.
3. Andreev, D.E., O’Connor, P.B., Zhdanov, A.V., Dmitriev, R.I., Shatsky, I.N., Papkovsky, D.B. and Baranov, P.V. (2015) Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes. Genome Biol, 16, 90.