Fig. 2

Characteristics of MHSs. a Overlaps among MHSs, DHSs, and ATAC-seq peaks. Percentage in each grid represents overlapping rate between the features in rows and the features in columns. The rows of the matrix represent the source features, while the columns represent the linked features. The percentage in each cell at the intersection of a row and column represents the overlapping rate between the source feature and the linked feature. For example, the cell at the intersection of MHS row and the DHS (single cut) column indicates that 61% of MHSs overlapped with DHSs. b Length distribution MHSs and DHSs. Specific MHSs, MHSs that were exclusively identified by MH-seq. Common MHSs: MHSs that are also identified by DNase-seq and ATAC-seq. Common DHSs: DHSs that are also identified by MH-seq and ATAC-seq. c MH-seq profile associated with an intergenic enhancer L3. L3 (chr2: 17722957–18723472) was previously identified by DNase-seq [28]. Gene models are shown at the top of the panel. Several small MH-seq peaks were identified within L3. White rectangles represent intergenic enhancers identified by DNase-seq. Orange and green rectangles mark regions associated with root- and leave-specific enhancer activity, respectively. Black rectangles represent open chromatin regions identified by MH-seq, DNase-seq and ATAC-seq. d Genomic features associated with cMHSs and sMHSs. “intergenic” represents the genomic regions that at least 3 kb away from genes but not overlap with transposable elements. “Transposable elements” represents genomic regions that at least 3 kb away from genes and overlap with transposable elements