Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
- The University of Western Australia, Australia
- 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.
Data availability
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Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variationAvailable at Dryad Digital Repository under a CC0 Public Domain Dedication.
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Patterns of population epigenomic diversityPublicly available at the NCBI Short Read Archive (accession no: SRA012474).
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Patterns of population epigenomic diversityPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE43858).
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Patterns of population epigenomic diversityPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE43857).
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Reference-guided assembly of four diverse Arabidopsis thaliana genomesAvailable at the 1001 Genomes Project.
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Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutationsPublicly available at the NCBI Short Read Archive (accession no: SRP045804).
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Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thalianaPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE53322).
Article and author information
Author details
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
- Daniel Zilberman, University of California, Berkeley, United States
Version history
- Received: August 18, 2016
- Accepted: December 1, 2016
- Accepted Manuscript published: December 2, 2016 (version 1)
- 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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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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