Fig. 5

The dynamic activities of TF-bound dOCRs contribute to tissue-specific gene expression. a Number of total tissue-active dOCRs and tissue-active dOCRs that are involved in dOCR-gene loops in ear and tassel. b The percentages of tissue-enriched genes involved in tissue-active dOCR-gene loops are significantly higher than those of tissue-enriched genes involved in total dOCR-gene loops (background) in ear and tassel. c Comparison of the percentages of tissue-enriched genes looped with tissue-active dOCRs shows that ear-active dOCRs tend to interact with ear-enriched genes, while tassel-active dOCRs tend to interact with tassel-enriched genes. d A schematic diagram of 3 types of TFs based on their binding to the anchors of dOCR-gene loops. dOCR TF, TF with binding sites on only dOCRs; Local TF, TF with binding sites on only the local OCRs of gene anchors; Joint TF, TF with binding sites on both loop anchors. e The percentages of different types of TF binding sites (TFBSs) involved in dOCR-gene loops. dOCR TFBSs, TF binding sites in only the dOCR anchors of dOCR-gene loops; Local TFBSs, TF binding sites in only the gene anchors of dOCR-gene loops; Joint TFBSs, TF binding sites on both anchors of dOCR-gene loops. f Example of ear-active dOCRs looping with the TB1 gene, which is highly expressed in ear but lowly expressed in tassel. Chromatin interaction map (top panel) with obvious loops marked by arrowheads. TAD-separation scores and TADs, chromatin loops, tissue-active dOCRs, RNA levels, epigenetic features, ChIP-seq, and DAP-seq peaks around the dOCRs and TB1 in ear and tassel are shown. g A proposed model for TB1 regulation showing a de-repression status in ear compared to tassel. The distal cis-regulatory element (CRE) of TB1 is more open with less H3K27me3 modifications, leading to easier access of multiple TFs in ear than that in tassel, which could drive an increased expression of TB1. The hexagons with different colors represent different TFs, which might show a sequential and differential binding to CRE in ear and tassel. h Case of tassel-active dOCRs looping to a JA response gene, ZmZIM15, which has a higher expression in tassel. Chromatin loops, tissue-active dOCRs, RNA levels, epigenetic features, and ChIP-seq data (5 tassel-enriched TFs) around ZmZIM15 and its dOCRs in ear and tassel are shown. The chromatin interaction map around ZmZIM15 is shown on the left of the gene track, with loops marked by arrowheads