Heterochromatin is a quantitative trait associated with spontaneous epiallele formation

Abstract

Epialleles are meiotically heritable variations in expression states that are independent from changes in DNA sequence. Although they are common in plant genomes, their molecular origins are unknown. Here we show, using mutant and experimental populations, that epialleles in Arabidopsis thaliana that result from ectopic hypermethylation are due to feedback regulation of pathways that primarily function to maintain DNA methylation at heterochromatin. Perturbations to maintenance of heterochromatin methylation leads to feedback regulation of DNA methylation in genes. Using single base resolution methylomes from epigenetic recombinant inbred lines (epiRIL), we show that epiallelic variation is abundant in euchromatin, yet, associates with QTL primarily in heterochromatin regions. Mapping three-dimensional chromatin contacts shows that genes that are hotspots for ectopic hypermethylation have increases in contact frequencies with regions possessing H3K9me2. Altogether, these data show that feedback regulation of pathways that have evolved to maintain heterochromatin silencing leads to the origins of spontaneous hypermethylated epialleles.

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

“…Polymorphism at NRPE1 , a key component of the RdDM pathway, was revealed in univariate GWAS, while variation in CMT3 (and its regulator, MIR823a ) was only found after controlling for mCHH. At the same time, it seems clear that reality is more complex, and that both mCHH and mCHG are regulated by multiple homeostatic mechanisms that also involve factors not included in our model, like histone modifications [ 68 ]. It is therefore not surprising that most of the polymorphisms we have identified seem to affect both traits, albeit not to the same extent (exceptions include the one at MIR823A , which only seems to affect mCHG, and the previously identified CMT2a’ and CMT2b’ polymorphisms, which only affect mCHH on CMT2-targeted transposons; see S2 and S3 Figs).…”

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

“…Polymorphism at NRPE1 , a key component of the RdDM pathway, was revealed in univariate GWAS, while variation in CMT3 (and its regulator, MIR823a ) was only found after controlling for mCHH. At the same time, it seems clear that reality is more complex, and that both mCHH and mCHG are regulated by multiple homeostatic mechanisms that also involve factors not included in our model, like histone modifications (Zhang et al, 2021). It is therefore not surprising that most of the polymorphisms we have identified seem to affect both traits, albeit not to the same extent (exceptions include the one at MIR823A , which only seems to affect mCHG, and the previously identified CMT2a’ and CMT2b’ polymorphisms, which only affect mCHH on CMT2-targeted transposons; see Figs S2, S3).…”

Parental pericentromeric methylation status drives methylome remodelling and heterosis in epigenetic hybrids

“…We performed whole genome bisulphite sequencing (WGBS) for 169 epiHybrids (pooled siblings) and their parents (382 samples in total). The paternal epiRIL methylomes from this experiment were recently published in Zhang et al (2021) but are integrated here. For each sequence context separately (CG, CHG, and CHH), we partitioned the genome into 200bp regions (step size 50bp) and compared the methylation status of each epiHybrid to that of its two parents (Fig.…”

“…Each row represents one epiRIL. Haplotypes were inferred by using 144 segregating DMRs as molecular markers (Zhang et al 2021). For each DMR, a given epiRIL can be either epihomozygous for the wild-type methylated state (MM, blue) or epihomozygous for the ddmi-like state (UU, red).…”

“…All epiHybrids and their parental lines were harvested at 27 DAS in a time frame of 3 hours as described in (Zhang et al, 2021). Rosettes of all 3 replications were pooled together, were immediately frozen in liquid nitrogen, and stored at -80°C until processing.…”