Pioneering factors and enhancer grammar

In this third lecture, Pr Denis Duboule describes approaches to identifying enhancer sequences using epigenetic profiling and chromatin accessibility analysis. The evolution of these technologies is described, along with a few examples of their application. These approaches raise the question of which enhancer sequences should be assigned to which target genes. To answer this question, technologies for capturing chromosome conformations are also presented, with the description and definition of topological association domains (TADs), which reflect a structural level of chromatin. These domains often correspond to large regulatory domains (regulatory landscapes) comprising both target genes and the enhancers that regulate them, so as to maximize contacts between these different elements. On this occasion, the example of the HoxD architectural gene cluster is presented. This example introduces the notion of long-distance regulation, which is then illustrated by a historical case study, namely the regulation of the sonic hedgehog (Shh) gene by a regulatory sequence (ZRS) located 1 megabase from its target gene and within the intron of another gene (lmbr1). The necessary enhancer-promoter contact occurs in part via the topological domain containing these different sequences, and also via DNA sites bound by the CTCF protein.