De novo gene evolution: How do we transition from non-coding to coding?
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Abstract
Recent years have witnessed the discovery of protein–coding genes which appear to have evolved de novo from previously non-coding sequences. This has changed the long-standing view that coding sequences can only evolve from other coding sequences. However, there are still many open questions regarding how new protein-coding sequences can arise from non-genic DNA.
Two prerequisites for the birth of a new functional protein-coding gene are that the corresponding DNA fragment is transcribed and that it is also translated. Transcription is known to be pervasive in the genome, producing a large number of transcripts that do not correspond to conserved protein-coding genes, and which are usually annotated as long non-coding RNAs (lncRNA). Recently, sequencing of ribosome protected fragments (Ribo-Seq) has provided evidence that many of these transcripts actually translate small proteins. We have used mouse non-synonymous and synonymous variation data to estimate the strength of purifying selection acting on the translated open reading frames (ORFs). Whereas a subset of the lncRNAs are likely to actually be true protein-coding genes (and thus previously misclassified), the bulk of lncRNAs code for proteins which show variation patterns consistent with neutral evolution. We also show that the ORFs that have a more favorable, coding-like, sequence composition are more likely to be translated than other ORFs in lncRNAs. This study provides strong evidence that there is a large and ever-changing reservoir of lowly abundant proteins; some of these peptides may become useful and act as seeds for de novo gene evolution.
Cite this as
2017. De novo gene evolution: How do we transition from non-coding to coding? PeerJ Preprints 5:e3031v2 https://doi.org/10.7287/peerj.preprints.3031v2Author comment
Oral presentation for the Molecular Innovation symposium of SMBE 2017
The title has been changed to match that one that appears in the SMBE 2017 program.
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Competing Interests
The authors declare that they have no competing interests
Author Contributions
Jorge Ruiz-Orera conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
José Luis Villanueva-Cañas conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.
William Blevins conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.
M.Mar Albà conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
Description of datasets is not part of the article (Abstract for a conference).
Funding
The work was funded by grants BFU2012-36820 and BFU2015-65235-P from Ministerio de Economía e Innovación (Spanish Government) and co-funded by FEDER (EC). We also received funding from Agència de Gestió d'Ajuts Universitaris i de Recerca Generalitat de Catalunya (AGAUR), grant number 2014SGR1121. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
