PT - JOURNAL ARTICLE AU - Tim Stuart AU - Steven R. Eichten AU - Jonathan Cahn AU - Yuliya Karpievitch AU - Justin Borevitz AU - Ryan Lister TI - Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation AID - 10.1101/039511 DP - 2016 Jan 01 TA - bioRxiv PG - 039511 4099 - http://biorxiv.org/content/early/2016/08/18/039511.short 4100 - http://biorxiv.org/content/early/2016/08/18/039511.full AB - 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 a burden of 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. Nearly 200 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.