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 in a given interval of time. Thus, the translatome provides a measure of the rate of protein production. In a steady state this rate is proportional to the amount of protein present in the cell.
What is Ribosome Profiling
The translatome has become accessible with the development of ribosome profiling (RIBO-seq), a technology used to translation in vivo through next-generation sequencing. RIBO-seq provides precise quantitative accounts of translation, its regulation, and when and where translation happens.
“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 powerful tool for functional genomics analysis. It provides information on gene expression that cannot be obtained using RNA-seq, including translational control and usage of alternative translation-initiation sites. It also allows discovery of regulatory peptides and their level of expression.
Ribosome profiling allows 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 the chances of finding protein/peptide biomarkers.
Identification by RIBO-seq of sets of proteins with modified expression can be of great assistance to MS-based proteomics for focused analysis and confirmation.
“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”