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Fig. 2 | Genome Biology

Fig. 2

From: DNA methylation dynamics during early plant life

Fig. 2

Differential methylation during early development. a Methylation level for each context is shown for a 3-kb window (upper half) of chromosome 1 for early embryo, mature embryo, four-day-old seedling, and ten-day-old seedling for each context separately (CG = red, CHG = blue, CHH = green). siRNA density (violet; ten-day-old seedlings) is indicated below. Gene models are represented in blue and TEs in orange. CHH DMRs are indicated as black horizontal bars for the comparisons of early vs. mature embryos (*) and mature embryos vs. four-day-old seedlings (**) as well as for WT vs. drm1/2 (DRM1/2) and WT vs. cmt2 (CMT2) at the seedling stage [26]. b Venn diagram representing the overlap of annotated loci associated with CG, CHG, and CHH hypermethylation DMRs in the mature embryo vs. four-day-old seedling (RF = representation factor; > 1 = higher than random, < 1 = lower than random with p value < 1.0xe–30). c Meta-TE plot for all TE sequences in the range of 1–2 kb with absolute CHH methylation levels for the four developmental stages analyzed (early and late embryo, four-day-old and ten-day-old seedling). TEs of other size classes are shown in Additional file 2: Figure S8. d Meta-TE representation of CHH-DMR distribution of CHH hypomethylation identified between early and mature embryos over TE annotations. e Distribution of methylation level frequency for CHH sites in mature embryos (dark green) and four-day-old seedlings (light green) within CHH-DMRs identified between mature embryos and four-day-old seedlings

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