Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

  1. Tim Stuart
  2. Steven Eichten
  3. Jonathan Cahn
  4. Yuliya Karpievitch
  5. Justin Borevitz
  6. Ryan Lister  Is a corresponding author
  1. The University of Western Australia, Australia
  2. The Australian National University, Australia

Abstract

Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.

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The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Tim Stuart

    ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
    Competing interests
    The authors declare that no competing interests exist.
  2. Steven Eichten

    ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2268-395X
  3. Jonathan Cahn

    ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5006-741X
  4. Yuliya Karpievitch

    ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
    Competing interests
    The authors declare that no competing interests exist.
  5. Justin Borevitz

    ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
  6. Ryan Lister

    ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
    For correspondence
    ryan.lister@uwa.edu.au
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6637-7239

Funding

Centre of Excellence in Plant Energy Biology, Australian Research Council (CE140100008)

  • Tim Stuart
  • Steven Eichten
  • Jonathan Cahn
  • Yuliya Karpievitch
  • Justin Borevitz
  • Ryan Lister

Australian Research Council

  • Tim Stuart
  • Steven Eichten
  • Jonathan Cahn
  • Yuliya Karpievitch
  • Justin Borevitz
  • Ryan Lister

Sylvia and Charles Viertel Charitable Foundation

  • Ryan Lister

Australian Research Council (FT120100862)

  • Ryan Lister

Australian Research Council (DE150101206)

  • Steven Eichten

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Daniel Zilberman, University of California, Berkeley, United States

Publication history

  1. Received: August 18, 2016
  2. Accepted: December 1, 2016
  3. Accepted Manuscript published: December 2, 2016 (version 1)
  4. Version of Record published: December 19, 2016 (version 2)

Copyright

© 2016, Stuart et al.

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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  1. Tim Stuart
  2. Steven Eichten
  3. Jonathan Cahn
  4. Yuliya Karpievitch
  5. Justin Borevitz
  6. Ryan Lister
(2016)
Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
eLife 5:e20777.
https://doi.org/10.7554/eLife.20777

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