Fig. 2

Common applications of ribosome profiling. (A) The broadest application of ribosome profiling is the quantitative estimation of protein synthesis. The amounts of footprints or RPFs reflects the amounts of ribosomes binding to mRNA, which is believed to be proportional to the translational speed that shows the amount of newly synthesized protein; (B) Footprints reflect the position where ribosomes bind to, suggesting the presence of ORFs. Many noncanonical ORFs, such as uORFs, dORFs, lncRNA ORFs, microRNA ORFs and circRNA ORFs, have been discovered through ribosome profiling; (C) The positional information of ribosomes also provides insights into diverse translational regulatory mechanisms, which encompass multiple events through the whole process of translation including ribosome recruitment and scanning, ORF truncation and extension, translation cessation, defects in translation termination, and stop codon read-through. (D) Since translation is an intermediate process converting RNA to protein, translatomics can serve as a bridge between RNomics and proteoics. Therefore, ribo-seq can be combined with several transcriptome or proteome techniques, such as RIP-seq, MeRIP-seq, acRIP-seq, phosphoproteome analysis, and ubiquitinome analysis, to reveal more hidden information on RNA and protein interactions and modifications