DNA Methylation in Arabidopsis shows evidence of local adaptation

In a new paper in eLife, researchers from the lab of Magnus Nordborg provide the first direct evidence between adaptation to the local environment and DNA methylation. Combining Genome Wide Association Studies (GWAS) and analysis of methylation through Next Generation Sequencing (NGS), the authors demonstrate a global increase in CG gene body methylation in plants originating from Northern Sweden as compared to plants from Southern Sweden. This difference is largely due to trans-acting factors that lie withing genomic regions previously shown to have been under strong selective pressure for adaptation to the colder environments found in the North of Sweden.


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.

Press Release (DE)

Original Publication

Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M. (2015) DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 2015;4:e05255.