Analysis of Eukaryotic lincRNA Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure.

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License: CC BY 4.0
Serval ID
serval:BIB_480A22B18475
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Analysis of Eukaryotic lincRNA Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure.
Journal
Molecular biology and evolution
Author(s)
Brümmer A., Dreos R., Marques A.C., Bergmann S.
ISSN
1537-1719 (Electronic)
ISSN-L
0737-4038
Publication state
Published
Issued date
03/02/2022
Peer-reviewed
Oui
Volume
39
Number
2
Pages
msab356
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
Long intergenic noncoding RNAs (lincRNAs) represent a large fraction of transcribed loci in eukaryotic genomes. Although classified as noncoding, most lincRNAs contain open reading frames (ORFs), and it remains unclear why cytoplasmic lincRNAs are not or very inefficiently translated. Here, we analyzed signatures of hindered translation in lincRNA sequences from five eukaryotes, covering a range of natural selection pressures. In fission yeast and Caenorhabditis elegans, that is, species under strong selection, we detected significantly shorter ORFs, a suboptimal sequence context around start codons for translation initiation, and trinucleotides ("codons") corresponding to less abundant tRNAs than for neutrally evolving control sequences, likely impeding translation elongation. For human, we detected signatures for cell-type-specific hindrance of lincRNA translation, in particular codons in abundant cytoplasmic lincRNAs corresponding to lower expressed tRNAs than control codons, in three out of five human cell lines. We verified that varying tRNA expression levels between cell lines are reflected in the amount of ribosomes bound to cytoplasmic lincRNAs in each cell line. We further propose that codons at ORF starts are particularly important for reducing ribosome-binding to cytoplasmic lincRNA ORFs. Altogether, our analyses indicate that in species under stronger selection lincRNAs evolved sequence features generally hindering translation and support cell-type-specific hindrance of translation efficiency in human lincRNAs. The sequence signatures we have identified may improve predicting peptide-coding and genuine noncoding lincRNAs in a cell type.
Keywords
Animals, Caenorhabditis elegans/genetics, Cell Line, Eukaryota/genetics, Humans, Open Reading Frames, RNA, Long Noncoding/genetics, RNA, Untranslated, Schizosaccharomyces/genetics, Selection, Genetic, codon usage, computational sequence analysis, evolutionary selection pressure, noncoding RNA, ribosome binding, tRNA abundance
Pubmed
Web of science
Open Access
Yes
Create date
08/04/2022 16:52
Last modification date
23/01/2024 8:24
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