Fig. 7
Methylation level in highly sequence-variable HOT regions associated with Col SR, SVs and 24sRC are contributed via RdDM pathway. a Ratio and length of features covering HOT region. b Bar graphs showing permutation test-derived log2(observed/expected) significance for association between HOT regions and each of features tested. Randomization was conducted for merged CR, merged Col SR, each category of SV types, and 24sRC-Total. Permutation was conducted 1000 times (P < 0.001). c,d Expression levels of 24sRCs (c), and methylation levels in CR and SR (d) that are overlapped with HOT regions. “Col SR (CG|CHG|CHH)” indicates genomic loci covered by at least one of three types of cytosine methylation context windows in Col SR, whereas “Col SR (CG∩CHG∩CHH)” indicates loci covered by all three types of cytosine methylation context windows in Col SR. The height of box and the error bar in d represent mean and standard deviation, and P-value in d was calculated with unpaired t-test with Welch’s correction. (****: P < 0.0001). e An example of HOT region covered by 24sRCs and overlapped by Col SR. 24-nt small RNA expression displayed as CP10M-normalized log-scale value. Levels of methylation on each cytosine base displayed as heatmap-style