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Analysis of eukaryotic lincRNA sequences reveals signatures of repressed translation in species under strong selection

View ORCID ProfileAnneke Brümmer, Rene Dreos, Ana Claudia Marques, Sven Bergmann
doi: https://doi.org/10.1101/737890
Anneke Brümmer
1Department of Computational Biology (DBC), University of Lausanne, Lausanne, Switzerland
3Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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  • ORCID record for Anneke Brümmer
Rene Dreos
2Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland
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Ana Claudia Marques
1Department of Computational Biology (DBC), University of Lausanne, Lausanne, Switzerland
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Sven Bergmann
1Department of Computational Biology (DBC), University of Lausanne, Lausanne, Switzerland
3Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
4Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
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  • For correspondence: sven.bergmann@unil.ch
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Abstract

Long intergenic non-coding RNAs (lincRNAs) represent a large fraction of transcribed loci in eukaryotic genomes. Although classified as non-coding, most lincRNAs contain open reading frames (ORFs), and it remains unclear why cytoplasmic lincRNAs are not or very inefficiently translated.

Here, we analysed signatures of repressed translation in lincRNA sequences from six eukaryotes. In species under stronger selection, i.e. fission yeast and worm, we detected significantly shorter ORFs than in intronic and non-transcribed control regions, a suboptimal sequence context around start codons for translation initiation, and trinucleotides (“codons”) corresponding to less abundant tRNAs than codons in control regions, potentially impeding translation elongation.

We verified that varying tRNA expression levels affect ribosome-binding to lincRNAs by analyzing data from five human cell lines. Notably, for three cell lines, codons in abundant cytoplasmic lincRNAs corresponded to lower expressed tRNAs than control codons, substantiating cell type-specific repression of lincRNA translation in human. Finally, comparing non-coding with peptide-encoding ORFs suggested that codon usage at the start of ORFs to be of particular relevance for ribosome-binding.

The identified sequence signatures may assist distinguishing peptide- from real non-coding lincRNAs in a cell.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 20, 2021.
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Analysis of eukaryotic lincRNA sequences reveals signatures of repressed translation in species under strong selection
Anneke Brümmer, Rene Dreos, Ana Claudia Marques, Sven Bergmann
bioRxiv 737890; doi: https://doi.org/10.1101/737890
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Analysis of eukaryotic lincRNA sequences reveals signatures of repressed translation in species under strong selection
Anneke Brümmer, Rene Dreos, Ana Claudia Marques, Sven Bergmann
bioRxiv 737890; doi: https://doi.org/10.1101/737890

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