Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo

Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors, and cis-signatures allowing reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation. [Display omitted] •Profiling chromatin dynamics uncovers complete repertoire of neural crest (NC) enhancers•NC super-enhancers act additively to sustain network robustness•Enhancer clustering reveals early split between neural-NC and canonical NC programs•Global construction of cranial NC gene regulatory network Using chromatin and transcriptional profiling of cranial neural crest (NC) at population and single-cell levels, Williams et al. reverse engineer and functionally validate global cranial NC gene regulatory network. Interrogation of a full cohort of NC enhancers and upstream inputs reveals distinct regulatory codes governing neural and canonical NC programs.