Work

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

Year: 2016

Type: preprint

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 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.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.1101/039511

Authors: Tim Stuart, Steven R. Eichten, Jonathan Cahn, Yuliya Karpievitch, Justin Borevitz, Ryan Lister

Institutions: The University of Western Australia, ARC Centre of Excellence in Plant Energy Biology, Australian National University

Language: English

Topic: Chromosomal and Genetic Variations

Subfield: Plant Science

Field: Agricultural and Biological Sciences

Domain: Life Sciences

Open Access status: green

Funder: Australian Research Council

Awards: Beyond genes: How the extended genotype of plants facilitates adaptation, ARC Centre of Excellence in Plant Energy Biology, Deciphering the regulation and function of the epigenome in eukaryotic development and stress response