Conditional GWAS of non-CG transposon methylation inArabidopsis thalianareveals major polymorphisms in five genes

Abstract

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.

MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data

“…In the CHH context, our finding of a recurrent association at Chr5:10417744 (Figure 5b,e) confirms a recent study that identified natural alleles of CHROMOMETHYLASE2 (CMT2) as determinants of CHH methylation (Sasaki et al, 2019). Similarly, associations of transposon methylation in CHG context and the miR823 and MSI1 loci were recently reported (Sasaki et al, 2022). The association signal in CHH emerged from 120 DMRs, showing a general trend of lower methylation in accessions carrying the alternative allele, with the exception of two regions of overall low CHH methylation (Figure 5h).…”

Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

“…Natural accessions also vary substantially in their methylome, transcriptome, and mobilome (transposable element, TE) landscapes [14][15][16][17]. Largescale structural variation along with methylome variation at TEs is influenced by genetic variation at loci encoding components of the methylation machinery, suggesting that the methylation machinery is a target of selection during adaptation to the environment [15,16,[18][19][20][21]. Substantial variation in methylation is also apparent in genic regions, functioning as a storehouse of epialleles, some of which can impact key developmental processes and fitness under new environments [22,23].…”