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

Fig 4. BONSAI hypermethylation in self-pollinated ddm1 mutants is associated with H3K9 methylation.

Fig 4

(A) Genome browser views of CHH and CHG methylation in AT1G73177 (BONSAI) locus. (B) H2K9me detected by chromatin immunoprecipitation (IP). “input” is the sample before IP; “mock” denotes samples after IP procedure without antibody. H3mK9me1 and H3K9me2 are samples after IP with the respective antibodies. Amplified regions around the BONSAI locus are indicated in (A). LINE and ACT2 are used as positive and negative controls, respectively. 11G plants are the ddm1 mutants in the 11th generation. 11G #1 and 11G #3 samples are prepared from progenies of direct sibling of 9G ddm1 #1 and #3 plants (shown in A), respectively. Results for other loci are shown in S6 and S7 Figs. Although the BONSAI locus accumulated both CHG and CHH methylation, some of the CHG hypermethylated loci have less CHH methylation than others (S6A Fig). In our preliminary analyses, H3K9me1 is more prevalent in those loci than H3K9me2 (S6 and S7 Figs).