Extended Data Fig. 5: RdDM controls the recovery of CH methylation in noncoding regions of TEs.

a, Non-coding regions showed the properties of RdDM targets. The levels of CH methylation and matching 24-nt sRNAs were analyzed in TEs with zero, one, or multiple coding regions. The shaded areas represent non-coding regions. The white areas between the shaded areas represent coding regions (center and right panels). For TEs with multiple coding regions (right panel), the values of non-coding regions in the center represent the average of one or more intergenic non-coding regions in each TE, and the values for two terminal coding regions are shown in between the terminal and intergenic non-coding regions. The results of CH methylation and siRNA are from reanalysis of data from previous report on ddm1 and rdr2 mutants⁹ or siRNAs⁶⁵, respectively. The results are consistent with a previous interpretation that short TEs and the edges of long TEs are targets for RdDM⁹, with a modification that intergenic non-coding regions also showed the properties of RdDM targets (right panels). b, Recovery of CHH methylation in coding and non-coding regions. Recovery in the non-coding regions, including intergenic non-coding regions, depends on DRM2, consistent with the results shown in Extended Data Fig. 4c,d.