TY - JOUR
T1 - A genome-wide assessment of the ancestral neural crest gene regulatory network
AU - Hockman, Dorit
AU - Chong-Morrison, Vanessa
AU - Green, Stephen A.
AU - Gavriouchkina, Daria
AU - Candido-Ferreira, Ivan
AU - Ling, Irving T.C.
AU - Williams, Ruth M.
AU - Amemiya, Chris T.
AU - Smith, Jeramiah J.
AU - Bronner, Marianne E.
AU - Sauka-Spengler, Tatjana
N1 - Funding Information:
We thank Sebastian Shimeld for access to embryos and genomic DNA of the brook lamprey, Hugo Parker for the lamprey HLC vector, and Sally-Ann Clark at the WIMM FACS Core Facility for assistance with cell sorting. We thank Toros Tasgin and Sarah Meyes for cloning candidate genes for in situ and Justine Van Greenen for amplifying and analysing L. planeri genomic DNA sequences. This work was supported by a Leverhulme Research Grant to T.S.S. (RPG-2015–026), the National Institute of General Medical Sciences of the National Institutes of Health grants to J.J.S. (R01GM104123) and C.T.A. (R24GM095471), a Wellcome Trust Institutional Strategic Support Fund grant (H2RZKC00) to D.H. and T.S.S., a Junior Research Fellowship (Trinity College, Oxford), the Sydney Brenner Fellowship, a Company of Biologists Travelling Fellowship (DEVTF-150403) and an EMBO Short Term Fellowship to D.H., and a Clarendon Fund Fellowship to V.C.M.
Publisher Copyright:
© 2019, The Author(s).
PY - 2019/10/16
Y1 - 2019/10/16
N2 - 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-α2 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.
AB - 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-α2 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.
UR - http://www.scopus.com/inward/record.url?scp=85073423656&partnerID=8YFLogxK
U2 - 10.1038/s41467-019-12687-4
DO - 10.1038/s41467-019-12687-4
M3 - Article
C2 - 31619682
AN - SCOPUS:85073423656
SN - 2041-1723
VL - 10
SP - 1
EP - 15
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 4689
ER -