Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs (original) (raw)
Figure 5
Extensive clustering of genes and enhancers highlights a complex regulation network in distal limbs.
A,B. 5C interaction matrix of the HoxA cluster and its upstream regulatory region in distal limb (A) and head (B). The 5C data was generated by 5C-seq using tissues from E12.5 embryos, and is presented in the form of heatmaps according to color scales as described in Figure 2. Heatmaps above the linear diagram of the genomic region show interaction frequencies for each restriction fragment, irrespective of their size. Heatmaps at the bottom show the mean interaction frequencies per 20 kb DNA fragment and were obtained from binning and smoothing of the 5C raw data. Expressed genes within the region are colored in red. The yellow and green shading links the genomic position of HoxA and Evx1 genes, and the enhancer clusters to the corresponding areas in heatmaps. Black arrows point to interactions between the gene sub-TADs and enhancer sub-TADs. White lines delineate the TAD and sub-TADs therein. Dashed white lines are drawn to highlight the sub-TAD interactions. C. Topological organization of the HoxA cluster and Evx1. Genes are organized in three sub-TADs in the limb (top). Interaction enrichment in head tissues compared to the limb (bottom) shows significant increase in interaction between the gene sub-TADs in the head. Smoothing was performed based on distance (8 kb) and heatmap intensities represent the mean of interaction frequency for each 8 kb window. D. Extensive limb-enriched interactions between distal HoxA enhancers suggest that a physical network regulates 5′ HoxA genes in the limb. The interaction matrix of the region containing enhancer e10 to e18 is shown in the form of a heatmap. Limb-enriched contacts are shown in red according to the color scale as described in Figure 2.