Four putative SWI2/SNF2 chromatin remodelers have dual roles in regulating DNA methylation in Arabidopsis

Abstract

DNA methylation is a conserved epigenetic mark that is critical for many biological processes in plants and mammals. In Arabidopsis, the antagonistic activities of RNA-directed DNA methylation (RdDM) and ROS1-dependent active DNA demethylation are key for the dynamic regulation of locus-specific DNA methylation. However, the molecular factors that coordinate RdDM and active demethylation are largely unknown. Here we report that CLSY4 and its three paralogous SWI2/SNF2-type chromatin-remodeling proteins function in both RdDM and DNA demethylation in Arabidopsis. We initially identified CLSY4 in a genetic screen for DNA demethylation factors and subsequently demonstrated that it also is important in RdDM. Comprehensive genetic analyses using single and high order mutants of CLSY family proteins revealed their roles as double agents in the balance between methylation and demethylation reactions. The four CLSY proteins collectively are necessary for the canonical RdDM pathway; at the same time, each CLSY likely mediates DNA demethylation at specific loci where DNA methylation depends on RdDM. These results indicate that the four chromatin-remodeling proteins have dual functions in regulating genomic DNA methylation, and thus provide new insights into the dynamic regulation of DNA methylation in a model multicellular eukaryotic organism.

DNA methylation in Marchantia polymorpha

“…ROS1 is involved in establishing boundaries between TEs and genes at thousands of loci by preventing the spread of DNA methylation and DNA hypermethylation as it counteracts RdDM through a postulated mechanism based on the ability of ROS1 to demethylate its own promoter from RdDM hypermethylation (Zhang et al ., ). Recently, in addition to its role in the generation of 24‐nucleotide siRNAs (Zhou et al ., ), CLSY4 was found to function in DNA demethylation in the same genetic pathway of the ROS1 family (Yang et al ., ).…”

Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

“…Pol IV activity depends on a family of four CLSY putative chromatin remodeling proteins (Greenberg et al, 2013;Smith et al, 2007;Zhou et al, 2018). Simultaneous loss of CLSY1 and CLSY2 has the same effect as loss of SHH1, whereas CLSY3 and CLSY4 mediate RdDM at a largely distinct set of loci (Yang et al, 2018;Zhou et al, 2018). Mutations of SHH1 and CLSY1/2 preferentially reduce mCHH and sRNA at DRM TEs and increase mCHH at CMT TEs (Figure 3C).…”

Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants

“…Mass spectrometry found that CLASSY proteins, a subfamily of SWI2/SNF2-like ATPases related to chromatin remodelers, copurify with the Pol IV complex in A. thaliana and maize [36,62]. The biochemical activity of CLSY proteins has not been elucidated, but genetic screens have isolated clsy mutations that disrupt gene silencing in both these plant species [63][64][65]. The four A. thaliana proteins, CLSY1 through CLSY4, facilitate the association of Pol IV at about 90% of loci that give rise to 24 nt siRNAs [66].…”