What is the translatome
The translatome is the sum of all mRNA protein-coding regions being translated in the cell. Transcription and mRNA degradation determine the transcriptome, the set of all mRNA sequences in the cell. Transcriptome and post-transcriptional control of translation determine the translatome. The translatome, together with protein modification and degradation determine the proteome, the set of all proteins present in a cell.
While the proteome indicates which and how many proteins are present at a given time in the cell, the translatome indicates the amount of protein produced in the cell at a given time.
What is Ribosome Profiling
The ribosome profiling (RIBO-seq) technique, developed at UCSF by Nicholas Ingolia and Jonathan Weissman (2008), is an adaptation of the “ribosome footprinting” technique developed by Joan Steitz (1969) more than 50 years ago, combining it with RNA-seq, a next-generation sequencing technique newly developed at the time (Nagalakshmi et al. 2008) . With RIBO-seq, mRNA fragments protected by the ribosome from digestion (“ribosome footprints”) are collected, and corresponding cDNA is amplified for sequencing by RNA-seq. Mapping ribosome footprints to the whole transcriptome opens a window on exploring the translatome, and on understanding how the translatome changes after treatments or in different environmental conditions.
“The rich and quantitative nature of ribosome profiling data provide an unprecedented opportunity to explore and model complex cellular processes”
Ribosome profiling has been utilized to identify changes in translation caused by environmental stresses, developmental signals, and medical conditions.
Ribosome profiling has been instrumental in understanding mechanisms of translational regulation, and has revealed the existence of:
Why ribosome profiling?
Ribosome profiling can very well prove to be the most cost-effective and powerful tool for functional genomics analysis. It helps identifying features of gene expression that cannot be obtained using RNA-seq, including translational control and usage of alternative translation-initiation sites. It also helps discovering new regulatory peptides and their functional roles.
Ribosome profiling facilitates the discovery of expression of proteins, proteoforms, and peptides, no matter how small, with unprecedented coverage and sensitivity. As a result, monitoring the effect of condition (e.g., cancer) or of treatment (e.g., drug administration) on protein expression is greatly enhanced, as well as targeting protein/peptide biomarkers.
Identification by RIBO-seq of sets of genes with modified ribosome coverage can be of great assistance to MS-based proteomics for focused analysis and confirmation of expression.
“A breakthrough in transcriptome analysis was achieved with the development of ribosome profiling (RIBO-seq) […] [T]his approach could develop into a common practice for next-generation proteomics. […] This study demonstrated the benefits of ribosome profiling for MS-based protein and peptide identification”
“[D]ata of the recently developed ribosome profiling method […] for mass spectrometry-based identification […] increases the overall protein identification rates […] and enables proteome-wide detection of 5′-extended proteoforms, upstream ORF translation and near-cognate translation start sites”