CHH hypermethylation at <i>ONSEN</i> in <i>cmt3</i> is mediated by CMT2.

(A) Genome browser view of CHG and CHH methylation within ONSEN2 (AT3TE92525/AT3G61330), in Col-0. (B) Genome browser view of CHH methylation within ONSEN2 in Col-0, cmt3-11, cmt2-3, cmt2 cmt3, drm1/2, and drm1/2 cmt3. (C) Metaplots showing average CHH methylation of 8 ONSEN copies in the corresponding mutants. -2kb indicates the upstream 2000 bp of the start site, and 2kb indicates the downstream of 2000 bp of the end site. (D) Bisulfite Sanger-sequencing for CHH methylation level of the ORFs of ONSEN2 and ONSEN1, two ONSEN copies highly induced by heat stress, in the corresponding mutants under non-stress (NS) and heat stress (HS). (E) Boxplots showing CWA (CAA and CTA) and non-CWA CHH methylation level in Col-0, cmt2-3, and cmt3-11 of the open reading frame (ORF) of all eight copies of ONSEN. P-values are from Wilcoxon test. (F) RT-qPCR of ONSEN transcripts in the corresponding mutants under NS and HS. All bars represent mean + SD from two biological replicates. The ONSEN transcripts were normalized to 18S rRNA. Student’s t-test, *P < 0.05; **P < 0.01. ns indicates not significant.