title: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation.
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.
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.
authors.forename: Tim
authors.identifier: 0000-0002-3044-0897
authors.initials: T
authors.lastname: Stuart
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia.
authors.forename: Steven R
authors.identifier: 0000-0003-2268-395X
authors.initials: SR
authors.lastname: Eichten
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.
authors.forename: Jonathan
authors.identifier: 0000-0002-5006-741X
authors.initials: J
authors.lastname: Cahn
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.
authors.forename: Yuliya V
authors.initials: YV
authors.lastname: Karpievitch
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia.
authors.forename: Justin O
authors.initials: JO
authors.lastname: Borevitz
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.
authors.forename: Ryan
authors.identifier: 0000-0001-6637-7239
authors.initials: R
authors.lastname: Lister
mesh_terms: D017360:Arabidopsis / Q000145:classification* / Q000235:genetics*; D019175:DNA Methylation; D004251:DNA Transposable Elements; D057890:Epigenomics; D005786:Gene Expression Regulation; D014644:Genetic Variation; D005828:Genetics, Population
chemical_list: D004251:DNA Transposable Elements
keywords: A. thaliana; Arabidopsis; DNA methylation; chromosomes; epigenetics; evolutionary biology; genes; genomics; transposable elements