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

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

  • Dubin, Manu J Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
  • Zhang, Pei Molecular and Computational Biology, University of Southern California, Los Angeles, United States
  • Meng, Dazhe Molecular and Computational Biology, University of Southern California, Los Angeles, United States
  • Remigereau, Marie-Stanislas Molecular and Computational Biology, University of Southern California, Los Angeles, United States
  • Osborne, Edward J Department of Biology, University of Utah, Salt Lake City, United States
  • Paolo Casale, Francesco European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
  • Drewe, Philipp Memorial Sloan-Kettering Cancer Center, New York, United States
  • Kahles, André Memorial Sloan-Kettering Cancer Center, New York, United States
  • Jean, Geraldine Memorial Sloan-Kettering Cancer Center, New York, United States
  • Vilhjálmsson, Bjarni Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
  • Jagoda, Joanna Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
  • Irez, Selen Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
  • Voronin, Viktor Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
  • Song, Qiang Molecular and Computational Biology, University of Southern California, Los Angeles, United States
  • Long, Quan Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
  • Rätsch, Gunnar Memorial Sloan-Kettering Cancer Center, New York, United States
  • Stegle, Oliver European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
  • Clark, Richard M Center for Cell and Genome Science, University of Utah, Salt Lake City, United States
  • Nordborg, Magnus ORCID Molecular and Computational Biology, University of Southern California, Los Angeles, United States
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  • 2015-5-5
Published in:
  • eLife. - eLife Sciences Publications, Ltd. - 2015, vol. 4
English 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.
Language
  • English
Open access status
gold
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Persistent URL
https://sonar.ch/global/documents/61890
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