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. Author manuscript; available in PMC: 2022 Apr 20.
Published in final edited form as: Curr Biol. 2020 Dec 3;31(3):591–600.e4. doi: 10.1016/j.cub.2020.10.098

Figure 3. Ectopic CHG methylation in cell cultures.

Figure 3.

(A) Heatmap representation of CHG methylation levels at 95 hypermethylated mCHG DMRs in cells (G1 Cells vs WT Leaf), which partially overlap with hypermethylation in ibm1 and ddm1 mutant leaves. The majority of hyper mCHG DMRs is specific to cell cultures, and corresponds to gains in H3K9me2 and 24-nt siRNAs. H3K9me2 levels are plotted as a heatmap showing enrichment over normalized H3 levels, and siRNA bar plot shows the number of reads per million mapping to each DMR. In cells, 62 hypermethylated mCHG DMRs show enriched levels of H3K9me2 (H3K9me2/H3 >= 1.5) and 74 DMRs accumulate 24-nt siRNA (RPM>=5), while only 8 DMRs show enriched levels of H3K9me2 and 5 DMRs accumulate siRNAs in WT leaf. (B) Genome browser tracks show ectopic CHG methylation at four Arabidopsis genes in cells (G1 sample), as compared to WT, met1, ddm1, ibm1 and rdd mutant leaf. Gains of CHG methylation in cell cultures matches H3K9me2 and siRNA peaks. (C) Small RNA profiling shows preferential accumulation of siRNAs of 24-nt in length. RPM - Reads Per Million. (D) Average methylation over the 95 DMRs is plotted in CG, CHG and CHH contexts, and (E) Venn diagram is used to show that hypermethylated DMRs in cells overlap partially with ectopic mCHG DMRs observed in ddm1 and ibm1 mutants. See also Figure S3, and Data S1 and S2.