Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
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 loca...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2016-12-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/20777 |
| _version_ | 1818019431503101952 |
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| author | Tim Stuart Steven R Eichten Jonathan Cahn Yuliya V Karpievitch Justin O Borevitz Ryan Lister |
| author_facet | Tim Stuart Steven R Eichten Jonathan Cahn Yuliya V Karpievitch Justin O Borevitz Ryan Lister |
| author_sort | Tim Stuart |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-14T07:52:01Z |
| format | Article |
| id | doaj.art-b9938a4b115e4a21acf5bf95c30f171b |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:52:01Z |
| publishDate | 2016-12-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-b9938a4b115e4a21acf5bf95c30f171b2022-12-22T02:05:10ZengeLife Sciences Publications LtdeLife2050-084X2016-12-01510.7554/eLife.20777Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variationTim Stuart0https://orcid.org/0000-0002-3044-0897Steven R Eichten1https://orcid.org/0000-0003-2268-395XJonathan Cahn2https://orcid.org/0000-0002-5006-741XYuliya V Karpievitch3Justin O Borevitz4Ryan Lister5https://orcid.org/0000-0001-6637-7239ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, AustraliaARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, AustraliaARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, AustraliaARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, AustraliaARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, AustraliaARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, AustraliaVariation 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.https://elifesciences.org/articles/20777epigeneticstransposable elementsArabidopsisDNA methylationgenomics |
| spellingShingle | Tim Stuart Steven R Eichten Jonathan Cahn Yuliya V Karpievitch Justin O Borevitz Ryan Lister Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation eLife epigenetics transposable elements Arabidopsis DNA methylation genomics |
| title | Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation |
| title_full | Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation |
| title_fullStr | Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation |
| title_full_unstemmed | Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation |
| title_short | Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation |
| title_sort | population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation |
| topic | epigenetics transposable elements Arabidopsis DNA methylation genomics |
| url | https://elifesciences.org/articles/20777 |
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