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

Elife. 2016 Dec 2:5:e20777. doi: 10.7554/eLife.20777.


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.

Keywords: A. thaliana; Arabidopsis; DNA methylation; chromosomes; epigenetics; evolutionary biology; genes; genomics; transposable elements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / classification*
  • Arabidopsis / genetics*
  • DNA Methylation*
  • DNA Transposable Elements*
  • Epigenomics
  • Gene Expression Regulation*
  • Genetic Variation*
  • Genetics, Population*


  • DNA Transposable Elements

Grants and funding

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