Fig. 2

Overall workflow of this study. First, chromatin accessibility data from DNase-seq, H3K9ac enrichment data from ChIP-seq and DNA methylation data from BS-seq were analysed individually. Second, the data on accessible regions, H3K9ac-enriched regions and low DNA methylated regions were integrated to predict enhancers. Third, the enhancer candidates were ranked based on signal intensity differences of the chromatin accessibility and H3K9ac enrichment data between V2-IST and husk tissue. Finally, enhancer candidates were linked to their putative target genes based on their tissue specificity and on the differential expression of flanking genes determined by RNA-seq data. For shared candidates, adjacent genes being expressed in both tissues were associated