Fig. 4

fie mutant seedlings partially maintain an embryonic RdDM profile. a Methylation ratios over 100-kb windows for CG (red), CHG (blue), and CHH (green) over chromosome 5 as an example in three comparisons. b Genome browser screenshot of a 4-kb region indicating DNA methylation levels in WT mature embryo and four-day-old seedling in WT and fie. Gene models are represented in blue and TEs in orange (bottom). CHH-DMRs are indicated as black horizontal bars; CG methylation is shown in red, CHG in blue, and CHH in green; WT seedling 24-nt siRNA (ten-day-old seedling) abundance shown as blue bars. c Venn diagram showing the overlap of TE annotations with CHH hypermethylation DMRs between mature embryo vs. four-day-old seedling (WT embryo vs. seedling CHH-DMRs) as well as fie vs. WT four-day-old seedling (fie vs. WT seedling CHH-/CHG-DMRs). d Venn diagram comparing fie vs. WT four-day-old seedlings CHH hypermethylation DMRs with DRM1/2- and CMT2-dependent CHH methylation. RF = representation factor; RF > 1 = overlap higher than random, RF < 1 = overlap lower than random, with p value < 1.0xe^–30. e Box plot representing the relative abundance of 24-nt siRNAs from seeds (red) [25] and seedlings (blue) in reads per million (RPM; y-axis) for 100-nt windows throughout the genome (All), DMRs that show both, CG hypomethylation in the endosperm vs. four-day-old seedlings as well as CHH hypermethylation DMRs in the mature embryo vs. four-day-old seedlings (Mature embryo) and for CHH-hyper DMRs found in fie seedlings compared to WT seedlings (fie seedling)