Polarized regulatory landscape and Wnt responsiveness underlie Hox activation in embryos

Sequential 3’ to 5’ activation of the Hox gene clusters in early embryos is a most fascinating issue in developmental biology. Neither the trigger nor the regulatory elements involved in the transcriptional initiation of the 3’-most Hox genes have been unraveled in any organism. We demonstrate that a series of enhancers, some of which Wnt-dependent, is located within a HoxA 3’ subTAD. This subTAD forms the structural basis for multiple layers of 3’-polarized features, including DNA accessibility and enhancer activation. Deletion of the cassette of Wnt-dependent enhancers proves its crucial role in initial transcription of HoxA at the 3’ side of the cluster. Overall design: ChIP-sequencing for several antibodies, ATAC-seq and 4C on epiblast stem cells (EpiSCs). Additionally, we performed ATAC-seq on different early stage mouse embryos.