title: Ribosomal profiling adds new coding sequences to the proteome.
abstract: Next generation sequencing (NGS) has enabled an in-depth look into genes, transcripts and their translation at the genomic scale. The application of NGS sequencing of ribosome footprints (Ribo-Seq) reveals translation with single nucleotide (nt) resolution, through the deep sequencing of ribosome-bound fragments (RBFs). Some results of Ribo-Seq challenge our understanding of the protein-coding potential of the genome. Earlier bioinformatic approaches had shown the presence of hundreds of thousands of putative small ORFs (smORFs) in eukaryotic genomes, but they had been largely ignored due to their large numbers and difficulty in determining their translation and function. Ribo-Seq has revealed that hundreds of putative smORFs within previously assumed long non-coding RNAs (lncRNAs) and UTRs of canonical mRNAs are associated with ribosomes, appearing to be translated. Here we review some of the approaches used to define translation within Ribo-Seq experiments and the challenges in defining translation of these novel smORFs in lncRNAs and UTRs. We also look at some of the bioinformatic and biochemical approaches used to independently corroborate these exciting new findings and elucidate real translation events.
authors.affiliation: School of Life Sciences, JMS Building, University of Sussex, Brighton BN1 9QG, U.K.
authors.forename: Muhammad Ali S
authors.initials: MA
authors.lastname: Mumtaz
authors.affiliation: School of Life Sciences, JMS Building, University of Sussex, Brighton BN1 9QG, U.K. j.p.couso@sussex.ac.uk.
authors.forename: Juan Pablo
authors.initials: JP
authors.lastname: Couso
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008957:Models, Genetic; D016366:Open Reading Frames / Q000235:genetics*; D011132:Polyribosomes / Q000235:genetics / Q000378:metabolism; D014176:Protein Biosynthesis / Q000235:genetics*; D020543:Proteome / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics; D012270:Ribosomes / Q000235:genetics* / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D020543:Proteome; D062085:RNA, Long Noncoding
keywords: NGS sequencing of footprints from polysome fractions (Poly-Ribo-Seq); long non-coding ribonucleic acid (ncRNA); proteome; ribosome profiling; small open reading frames (smORFs); translation