title: Long non-coding RNAs as a source of new peptides.
abstract: Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs are lineage-specific and do not yet have a known function. In this study, we test the hypothesis that they may act as a repository for the synthesis of new peptides. We find that a large fraction of the lncRNAs expressed in cells from six different species is associated with ribosomes. The patterns of ribosome protection are consistent with the translation of short peptides. lncRNAs show similar coding potential and sequence constraints than evolutionary young protein coding sequences, indicating that they play an important role in de novo protein evolution.
authors.affiliation: Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Ruiz-Orera
authors.affiliation: Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Messeguer
authors.affiliation: Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Subirana
authors.affiliation: Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: M Mar
authors.initials: MM
authors.lastname: Alba
mesh_terms: D000818:Animals; D017360:Arabidopsis; D004331:Drosophila melanogaster; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D016366:Open Reading Frames / Q000235:genetics*; D010455:Peptides / Q000235:genetics*; D014176:Protein Biosynthesis; D040901:Proteomics; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D015027:Zebrafish
chemical_list: D010455:Peptides; D062085:RNA, Long Noncoding
keywords: de novo gene evolution; eukaryote; evolutionary biology; genomics; human; lncRNA; ribosome profiling