Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes

PLoS Genet. 2022 Sep 9;18(9):e1010345. doi: 10.1371/journal.pgen.1010345. eCollection 2022 Sep.


Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show that CHG-methylation (mCHG) has a similar genetic architecture-once mCHH is statistically controlled for. We identify five key trans-regulators that appear to modulate mCHG levels, and show that they interact with a previously identified modifier of mCHH in regulating natural transposon mobilization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis* / genetics
  • DNA Methylation / genetics
  • DNA Transposable Elements / genetics
  • Gene Expression Regulation, Plant
  • Genome-Wide Association Study


  • DNA Transposable Elements

Grants and funding

MN was funded the European Research Council (ERC), grant AdvG 789037. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.