1. Genetics and Genomics
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Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

  1. Rafik Neme
  2. Diethard Tautz  Is a corresponding author
  1. Max-Planck Institute for Evolutionary Biology, Germany
Research Article
  • Cited 39
  • Views 3,115
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Cite this article as: eLife 2016;5:e09977 doi: 10.7554/eLife.09977

Abstract

Deep sequencing analyses have shown that a large fraction of genomes is transcribed, but the significance of this transcription is much debated. Here, we characterize the phylogenetic turnover of poly-adenylated transcripts in a comprehensive sampling of taxa of the mouse (genus Mus), spanning a phylogenetic distance of 10 Myr. Using deep RNA sequencing we find that at a given sequencing depth transcriptome coverage becomes saturated within a taxon, but keeps extending when compared between taxa, even at this very shallow phylogenetic level. Our data show a high turnover of transcriptional states between taxa and that no major transcript-free islands exist across evolutionary time. This suggests that the entire genome can be transcribed into poly-adenylated RNA when viewed at an evolutionary time scale. We conclude that any part of the non-coding genome can potentially become subject to evolutionary functionalization via de novo gene evolution within relatively short evolutionary time spans.

Article and author information

Author details

  1. Rafik Neme

    Max-Planck Institute for Evolutionary Biology, Plön, Germany
    Competing interests
    No competing interests declared.
  2. Diethard Tautz

    Max-Planck Institute for Evolutionary Biology, Plön, Germany
    For correspondence
    tautz@evolbio.mpg.de
    Competing interests
    Diethard Tautz, Senior editor, eLife.

Ethics

Animal experimentation: All mice were obtained from the mouse collection at the Max Planck Institute for Evolutionary Biology, following standard rearing techniques which ensure a homogeneous environment for all animals. Mice were maintained and handled in accordance to FELASA guidelines and German animal welfare law (Tierschutzgesetz {section sign} 11, permit from Veterinäramt Kreis Plön: 1401-144/PLÖ-004697).

Reviewing Editor

  1. Thomas R Gingeras, Cold Spring Harbor Laboratory, United States

Publication history

  1. Received: July 8, 2015
  2. Accepted: February 1, 2016
  3. Accepted Manuscript published: February 2, 2016 (version 1)
  4. Version of Record published: March 7, 2016 (version 2)
  5. Version of Record updated: October 14, 2016 (version 3)

Copyright

© 2016, Neme & Tautz

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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