Increased Enhancer—Promoter Interactions during Developmental Enhancer Activation in Mammals

Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here, we investigate the 3D conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. 61% of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer–promoter and enhancer–enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer–promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general significance of enhancer–promoter physical proximity for developmental gene activation in mammals. (capture hic) We generated high-resolution enhancer interactome maps across 10 mouse embryonic tissues for 935 bona fide developmental enhancers with characterized in vivo activity at mid-gestation, using enhancer-capture HiC. (RNA-seq) Tissues were collected from E11.5 wildtype or enhancer-knockout embryos to perform differential expression analysis.