A genome-wide assessment of the ancestral neural crest gene regulatory network

• Published in: Nature communications Vol. 10; no. 1; pp. 4689 - 15
• Main Authors: Hockman, Dorit, Chong-Morrison, Vanessa, Green, Stephen A., Gavriouchkina, Daria, Candido-Ferreira, Ivan, Ling, Irving T. C., Williams, Ruth M., Amemiya, Chris T., Smith, Jeramiah J., Bronner, Marianne E., Sauka-Spengler, Tatjana
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16-10-2019; Nature Publishing Group; Nature Portfolio
• Subjects: 13/1; 14; 14/1; 14/19; 14/32; 38; 38/23; 38/39; 42; 45; 45/41; 45/91; 49; 631/181/2806; 631/208/177; 631/208/212/2019; 631/553/2711; 64; 64/116; Animals; AP-2 protein; Cell adhesion; Cell adhesion molecules; Cell Adhesion Molecules - genetics; Cell Differentiation - genetics; Cell Movement - genetics; Cluster analysis; Conservation; Embryos; Enhancers; Epigenesis, Genetic; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Regulatory Networks; Genomes; Homeodomain Proteins - genetics; Homology; Humanities and Social Sciences; multidisciplinary; Nervous system; Neural crest; Neural Crest - metabolism; Peripheral nervous system; Petromyzon; Regulatory sequences; Science; Science (multidisciplinary); SOX Transcription Factors - genetics; Transcription Factor AP-2 - genetics; Transcription factors; Transcription Factors - genetics; Vertebrates
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-12687-4

The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of
cis
-regulatory elements, including enhancers of
Tfap2B, SoxE1
and
Hox-
α
2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey
SoxE1
enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.
An understanding of the ancestral state of the neural crest (NC) gene regulatory network (GRN) gives insight into vertebrate evolution. Here, the authors use transcriptomic and chromatin accessibility analyses of the lamprey NC, as well as cross-species enhancer assays, to identify GRN elements conserved throughout vertebrates.