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

Tim Stuart, Steven R. Eichten, Jonathan Cahn, Yuliya V. Karpievitch, Justin O. Borevitz, Ryan Lister

Research output: Contribution to journalArticlepeer-review

138 Citations (Scopus)

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.

Original languageEnglish
Article numbere20777
Number of pages27
JournaleLife
Volume5
DOIs
Publication statusPublished - 2 Dec 2016

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