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. 2015 Apr 22;11(4):e1005154. doi: 10.1371/journal.pgen.1005154

Fig 8. Effects of disrupted heterochromatin in the DDM1 wild type background examined at single base resolution.

Fig 8

(A) Methylation level was compared for each transcription unit in CG, CHG, and CHH contexts. The format is as shown in Fig 2A. A globally hypomethylated epiRIL (epiRIL98: plant #3 in Fig 7A and 7B and plant #2 in Fig 7E and 7F) and two epiRILs with lower level of hypomethylation (epiRIL260 and epiRIL480) are shown. Global hypomethylation indexes of epiRIL98, epiRIL260, and epiRIL480 are 0.38, 0.04, and 0.09, respectively. “WT” data are from the parental wild-type Col plant used to generate the epiRILs. (B) CHG methylation levels in the genes that were not methylated in WT but methylated in epiRIL98 (methylation level < 0.1 in WT and ≥ 0.1 in epiRIL98: n = 232). For these transcription units, distributions of the methylation levels were compared among the parental WT, the parental 4G ddm1 plant, and the epiRIL98. (C-D) Ectopic CHG methylation in epiRIL98 compared to wild type. Each gene was assigned to the inferred haplotypes in epiRIL98: WT-like (C) or ddm1-like (D). The ectopic methylation could be detected in genes of the WT-like haplotype. Examples of such genes are shown in S25 Fig.