Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo

Abstract

SummaryPrecise 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.

Molecular Events Controlling Cessation of Trunk Neural Crest Migration and Onset of Differentiation

“…Our findings of upregulated/downregulated genes coincide in larger proportion with their migratory gene profiling. Further support that our array was focused of DRG transition is that we did not observe TFAP2B, Snai2, Zeb2, and Lmo4 (bona fide NC and EMT factors) in our array (Williams et al, 2019).…”

“…Recently, Williams et al (2019) have shown a global NCC GRN profiling of genes involved in their development. Our findings of upregulated/downregulated genes coincide in larger proportion with their migratory gene profiling.…”

Establishing Primary Cultures of Trunk Neural Crest Cells

“…Sox-10 is a member of the SoxE subclass of high-mobility-group domain-containing Sox transcription factors, which plays a critical role in the maintenance of the progenitor/stem cell state of neural crest cells (Hong & Saint-Jeannet, 2005;Weider & Wegner, 2017). It exists in all vertebrates examined so far, from lamprey to human, and it is expressed at all axial levels by neural crest cells at the time of their segregation from the neural tube and during their subsequent migration to their target sites (Hockman et al, 2019;Williams et al, 2019). In culture, Sox-10 shows essentially the same expression pattern in neural crest cells as in the embryo.…”

“…Current Protocols in Cell Biology Numerous other possible markers for neural crest cells have been reportedly used in vivo or in vitro, such as the p75 low affinity nerve growth factor receptor (p75-NGFR), nestin, Msx-1, Twist-1, Pax-3, AP-2α, cMyc, Id-1, or Ets-1, to name a few (Dupin & Sommer, 2012;Soldatov et al, 2019;Williams et al, 2019). Notwithstanding their interest and potential, these markers have been less frequently used or simply cannot be used to characterize avian trunk neural crest cells in culture.…”

“…The last few decades witnessed the emergence of a variety of elaborated techniques, animal models and molecular tools to investigate neural crest cell development in vivo (Baggiolini et al, 2015;Betancur, Bronner-Fraser, & Sauka-Spengler, 2010;Hockman et al, 2019;Li et al, 2019;Soldatov et al, 2019;Williams et al, 2019). These studies are at the origin of considerable progress in our understanding of this cell population.…”