Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages [RNA-seq and ChIP-seq]

The enteric nervous system (ENS) predominantly originates from vagal neural crest cells (VNC) that emerge from the caudal hindbrain, invade the foregut and populate the gastrointestinal tract. However, the gene regulatory network (GRN) orchestrating the early specification of VNC remains unknown. Using an EdnrB enhancer, we generated a comprehensive temporal map of the chromatin and transcriptional landscape of VNC in the avian model, revealing three VNC cell clusters (neural, neurogenic and mesenchymal), each predetermined epigenetically prior to neural tube delamination. We identify and functionally validate regulatory cores (Sox10/Tfap2B/SoxB/Hbox) mediating each programme and elucidate their combinatorial activities with other spatiotemporally-specific transcription factors (bHLH/NR). Our global deconstruction of the VNC-GRN in vivo sheds light on critical early regulatory mechanisms that may influence the divergent neural phenotypes in enteric neuropathies. Overall design: Transcriptomic and TF binding of avian neural crest cells isolated from their in vivo context at HH12, HH18 and HH25 Authors' note: [1] We electroporated out TF tagged with Avi with a BirA. Then we pulled down with Streptavidin beads. Therefore, no antibodies were used. Plasmids are available on Addgene and deposited appropriately [2] The RNA_featurecount.txt also contains the data from RNA samples in the other subseries (included in the GSE125711 superseries).