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

Elife
Authors
Keywords
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.

Year of Publication
2015
Journal
Elife
Volume
4
Pages
e08890
Date Published
2015 Dec 19
ISSN
2050-084X
URL
DOI
10.7554/eLife.08890
PubMed ID
26687005
PubMed Central ID
PMC4739776
Links
Grant list
R01 CA107486 / CA / NCI NIH HHS / United States
CA 107486 / CA / NCI NIH HHS / United States
Howard Hughes Medical Institute / United States