Dysfunction of DRE2 causes genome-wide DNA hypermethylation.

(A) Venn diagram showing the numbers of hyper-DMRs that either overlap between or are unique in dre2-4 and ros1-4. Boxplots showing the distribution and the average CG, CHG, or CHH methylation levels calculated from hyper-DMRs in the respective subgroups. Dark horizontal line, median; edges of boxes, 25th (bottom) and 75th (top) percentiles; whiskers, minimum and maximum percentage of DNA methylation. (B) Heat-map showing the methylation levels of dre2-4-associated hyper-DMRs in Col-0, dre2-4, met18-2 and ros1-4. The color key is presented at right. Light yellow indicates low methylation and black indicates high methylation. (C) Locus-specific bisulfite sequencing results showing the DNA methylation levels of the ROS1 promoter in different genotypes. (D) Relative expression levels of ROS1 in the indicated genotypes as determined by RT-qPCR. Asterisks indicate two-tailed Student’s t-test, *P < 0.05, **P < 0.01. Results from the second biological replicate are shown in S5D Fig.