Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

Abstract

Using a new bioinformatic method to analyze ribosome profiling data, we show that 40% of lncRNAs and pseudogene RNAs expressed in human cells are translated. In addition, ~35% of mRNA coding genes are translated upstream of the primary protein-coding region (uORFs) and 4% are translated downstream (dORFs). Translated lncRNAs preferentially localize in the cytoplasm, whereas untranslated lncRNAs preferentially localize in the nucleus. The translation efficiency of cytoplasmic lncRNAs is nearly comparable to that of mRNAs, suggesting that cytoplasmic lncRNAs are engaged by the ribosome and translated. While most peptides generated from lncRNAs may be highly unstable byproducts without function, ~9% of the peptides are conserved in ORFs in mouse transcripts, as are 74% of pseudogene peptides, 24% of uORF peptides and 32% of dORF peptides. Analyses of synonymous and nonsynonymous substitution rates of these conserved peptides show that some are under stabilizing selection, suggesting potential functional importance.DOI: http://dx.doi.org/10.7554/eLife.08890.001

Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

“…Several groups have recently applied machine-learning algorithms to mammalian Ribo-seq data to detect AUG uORFs (Fields et al 2015;Ji et al 2015;Calviello et al 2016). Although these studies identified hundreds of uORFs, they did not test them for function or address NCC uORFs.…”

Decoding sORF translation – from small proteins to gene regulation

“…41 Apart from allosteric regulation, it is also feasible that short proteins could negatively regulate enzyme activities by competing with enzymatic substrates for binding to the active site. While direct evidence is still missing, it is intriguing to speculate that pseudogenes, about one-third of which were recently shown to be translated into proteins of various lengths in human cells, 15 might provide a source for such competitive inhibitory peptides. 60 Future work might also reveal that some of the newly discovered proteins have specific enzymatic activities themselves.…”

“…New translated regions have not only been identified in transcripts thought to be non-coding, but also upstream of a large fraction of protein-coding ORFs (so-called upstream ORFs, uORFs). 4,[13][14][15][16][17][18][19][20][21] These usually short translated ORFs were likely missed in previous mutagenesis screens due to their small size, and remained un-annotated in genome annotations due to their small size and lack of evidence for codingness. [22][23][24] In analogy to the term 'pervasive transcription', 25 this unforeseen prevalence of short ORF (sORF) translation has spurred the notion of 'pervasive translation'.…”

Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis

“…There are additional pipelines that include 3-nt periodicity as part of the analysis (18,19). The 3-nt periodicity of Ribo-seq has been leveraged to identify novel small ORFs in zebrafish embryos and mouse/human cells (6,15,18,19).…”

“…Furthermore, computational pipelines have been developed to identify translated ORFs by interrogating 3-nt periodicity specifically, including "ORF score" (a summary statistic that tests if one particular reading frame is enriched in Ribo-seq by comparing to a uniform distribution) (6) and "RiboTaper" (a spectrum analysis that determines whether footprints on a transcript display 3-nt periodicity) (15). There are additional pipelines that include 3-nt periodicity as part of the analysis (18,19). The 3-nt periodicity of Ribo-seq has been leveraged to identify novel small ORFs in zebrafish embryos and mouse/human cells (6,15,18,19).…”