Fig. 7

Example of data on (a) DICE and (b) b1 repeat enhancer. From the top: AGPv4 annotation and candidate annotation from our prediction (V V2-IST, H husk candidate), DNase I hypersensitivity and H3K9ac enrichment signal (all replicates pooled) and peak position (indicated as blue and green bars, respectively) in V2-IST and in husk tissue, mCG, mCHG and mCHH levels and unique mappability in percentage. The numbers under gene names indicate relative gene expression levels (V2-IST/husk). Although the b1 locus is on chromosome 2, in the current version of the AGPv4 assembly, the b1 gene is located in contig 44 (B, on the right of the grey vertical line). The dark blue bars in the gene annotation tracks indicate previously annotated known enhancers and putative cis-regulatory elements. The vertical red boxes indicate enhancer candidates identified in this study. Peaks at those tracks might not be present in each replicate, affecting enhancer candidate prediction