Fig. 8: Non-CG DNA methylation is affected in the absence of NDX.

a Circos plot showing the genomic distribution of differentially methylated regions (DMRs) in CG/CHG/CHH nucleotide contexts. Red and blue spots indicate hyper- and hypomethylated DMRs in the ndx1–4 mutant. Outer circle represents the five chromosomes and the mitochondrial and plastid genomes. Color and black-and-white heatmaps show gene density and transposon (TE) density. b Overlap of flag-NDX ChIP peaks with hyper- and hypo-DMRs. Cells contain observed/expected ratios for peak counts. Warmer colors represent higher enrichment. c Anchor plot of flag-NDX ChIP signal over hypo CHH and CHG DMRs (red line) and random sites (blue, green, yellow lines). The NDX signal is enriched in the middle of the CHH DMRs and near the center of hypo CHG DMRs. d, e Annotation of hyper- and hypo-DMRs on d functional genomic features and e chromatin states. Cells contain observed/expected ratios for peak counts. Warmer colors represent higher enrichment. f CMT2 TEs and RdDM TEs were classified by chromosomal location as pericentromeric and arm associated. Metaplots show average DNA methylation levels in CHH/CHG/CG contexts in Col-0 (black) and ndx1–4 (red) plants. CHH and CHG methylation is significantly decreased CMT2 TEs regardless of their arm- or pericentromeric location (mCG levels do not change). CHG methylation levels show reduction at RdDM TEs located in chromosome arms. (mCHH and mCG levels do not change.).