Skip to main content
Fig. 3 | BMC Genomics

Fig. 3

From: Contribution of RdDM to the ecotype-specific differential methylation on conserved as well as highly variable regions between Arabidopsis ecotypes

Fig. 3

Assessment of 24-nt siRNA clusters (24sRC) enrichment for genomic features and ecotype-specific DMRs (eDMRs). a Composition of genes and transposable elements (TE) overlap with e24sRC-Col (red), e24sRC-Cvi (blue), e24sRC-1/2 (pink, 24sRCs exhibiting differential expression between ecotypes in one or two stages) and non-e24sRC (grey). Features that did not overlap with any of the 24sRCs are represented as grey. Numbers near the colored part of the bar graph represent numbers of features that overlap with each category of 24sRCs. b Composition of 24sRCs, e24sRC-Col, and e24sRC-Cvi overlap with genomic features, including gene, TE, and intergenic region (IGR). c Numbers and compositional ratio of ecotype-specific differentially methylated regions (eDMRs) overlapping e24sRCs (left panel), and that of e24sRCs overlapping eDMRs (right panel). Hyper: hypermethylated region in Col; Hypo: hypermethylated region in Cvi. d Randomization-based permutation test results. e24sRC loci (red-boxed) were 1000-times randomly re-distributed across the Arabidopsis genome, and to measure the numbers of overlaps between them, each randomly re-distributed feature set was compared with eDMR loci (black-boxed). Green dashed line represents the average distribution for numbers of overlaps between randomly re-distributed e24sRC loci and eDMR loci. Red solid line represents observed overlaps with e24sRC loci and eDMR loci. The X-axis represents the numbers of overlaps between e24sRC loci and eDMR loci, and the Y-axis represents the density value for distribution

Back to article page