Fig. 3

Global CHH methylation is diversely regulated during the initiation of three root types. A Box plots indicate the methylation ratios at the CHH context across the genome. Methylation of each 100 kb was summarized. Two biological replicates are shown for each sample. The 25 th and 75 th percentiles (box), median and highest and lowest values are shown. Double asterisks indicate significant differences, P-value < 0.01 (Student’s t-test). B Metaplots showing the average CHH methylation levels on genes, transposon elements, and their flanking regions. C Upper panel, histograms showing numbers of differentially CHH methylated regions (DMR) identified in indicated comparisons. Lower panel, genomic distribution of DMRs. TE, transposon elements. D Venn diagram shows the overlap of hypo-CHH DMRs identified in the initials of three root types. E Box plots summarizing the length distribution of CHH DMRs associated transposon elements. Random selected genomic 50 bp windows were used as control. F Metaplot showing enrichment of short transposon elements (< 500 bp) across the genic regions in the rice genome