Fig. 3

PKL affects DNA methylation levels at RdDM target loci. a Distribution of hypo differentially methylated regions (hypoDMRs) on genomic features. The Arabidopsis genome (TAIR10) was divided into four non-overlapping features based on the genome annotation. “gene/TE” represents genomics regions annotated as both genes and TEs. b Heatmap showing the DNA methylation levels at hypoDMRs identified in pkl. c Overlaps among CHH hypoDMRs identified in pkl, nrpd1, and nrpe1. The size of the circle is proportional to the number of DMRs identified in each mutant. d Distribution of hyperDMRs on the four non-overlapping genomic features. e Heatmap of the DNA methylation levels at hyperDMRs identified in pkl. f Overlaps among CHH hyperDMRs identified in pkl and CHH hypoDMRs identified in nrpd1 or nrpe1. g Violin plot showing the distribution of CHH methylation levels at the 3608 pkl hyperDMR regions that are also identified as hypoDMRs of nrpd1 and nrpe1 (Fig. 3f). h Violin plot showing the distribution of CHH methylation levels at the 2537 pkl-specific hyperDMR regions (Fig. 3f). i Total lengths of mCHH DMRs identified in the pkl mutant (PKL), the nrpd1 and nrpe1 mutants (RdDM), and the overlapped regions between the two