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DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two...

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Autores principales: Dubin, Manu J, Zhang, Pei, Meng, Dazhe, Remigereau, Marie-Stanislas, Osborne, Edward J, Paolo Casale, Francesco, Drewe, Philipp, Kahles, André, Jean, Geraldine, Vilhjálmsson, Bjarni, Jagoda, Joanna, Irez, Selen, Voronin, Viktor, Song, Qiang, Long, Quan, Rätsch, Gunnar, Stegle, Oliver, Clark, Richard M, Nordborg, Magnus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413256/
https://www.ncbi.nlm.nih.gov/pubmed/25939354
http://dx.doi.org/10.7554/eLife.05255
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author Dubin, Manu J
Zhang, Pei
Meng, Dazhe
Remigereau, Marie-Stanislas
Osborne, Edward J
Paolo Casale, Francesco
Drewe, Philipp
Kahles, André
Jean, Geraldine
Vilhjálmsson, Bjarni
Jagoda, Joanna
Irez, Selen
Voronin, Viktor
Song, Qiang
Long, Quan
Rätsch, Gunnar
Stegle, Oliver
Clark, Richard M
Nordborg, Magnus
author_facet Dubin, Manu J
Zhang, Pei
Meng, Dazhe
Remigereau, Marie-Stanislas
Osborne, Edward J
Paolo Casale, Francesco
Drewe, Philipp
Kahles, André
Jean, Geraldine
Vilhjálmsson, Bjarni
Jagoda, Joanna
Irez, Selen
Voronin, Viktor
Song, Qiang
Long, Quan
Rätsch, Gunnar
Stegle, Oliver
Clark, Richard M
Nordborg, Magnus
author_sort Dubin, Manu J
collection PubMed
description Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation. DOI: http://dx.doi.org/10.7554/eLife.05255.001
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spelling pubmed-44132562015-05-06 DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation Dubin, Manu J Zhang, Pei Meng, Dazhe Remigereau, Marie-Stanislas Osborne, Edward J Paolo Casale, Francesco Drewe, Philipp Kahles, André Jean, Geraldine Vilhjálmsson, Bjarni Jagoda, Joanna Irez, Selen Voronin, Viktor Song, Qiang Long, Quan Rätsch, Gunnar Stegle, Oliver Clark, Richard M Nordborg, Magnus eLife Genomics and Evolutionary Biology Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation. DOI: http://dx.doi.org/10.7554/eLife.05255.001 eLife Sciences Publications, Ltd 2015-05-05 /pmc/articles/PMC4413256/ /pubmed/25939354 http://dx.doi.org/10.7554/eLife.05255 Text en © 2015, Dubin et al http://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Genomics and Evolutionary Biology
Dubin, Manu J
Zhang, Pei
Meng, Dazhe
Remigereau, Marie-Stanislas
Osborne, Edward J
Paolo Casale, Francesco
Drewe, Philipp
Kahles, André
Jean, Geraldine
Vilhjálmsson, Bjarni
Jagoda, Joanna
Irez, Selen
Voronin, Viktor
Song, Qiang
Long, Quan
Rätsch, Gunnar
Stegle, Oliver
Clark, Richard M
Nordborg, Magnus
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
title DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
title_full DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
title_fullStr DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
title_full_unstemmed DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
title_short DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
title_sort dna methylation in arabidopsis has a genetic basis and shows evidence of local adaptation
topic Genomics and Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413256/
https://www.ncbi.nlm.nih.gov/pubmed/25939354
http://dx.doi.org/10.7554/eLife.05255
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