Specification of axial identity by Hoxa2 distinguishes between a phenotypic and molecular ground state in mouse cranial neural crest cells

Hox genes play a key role in head formation by specifying the axial identity of neural crest cells (NCCs) migrating into embryonic pharyngeal arches. In the absence of Hoxa2 , NCC derivatives of the second pharyngeal arch (PA2) undergo a homeotic transformation and duplicate structures formed by first arch (PA1) NCCs. Current models postulate that PA1 represents a NCC ‘ground state’ and loss of Hoxa2 causes a reversion of PA2 NCCs to the PA1 ‘ground state’. We use bulk and single-cell RNAseq to investigate the molecular mechanisms driving this phenotypic transformation in the mouse. In Hoxa2-/- mutants, PA2 NCCs generally maintain expression of the PA2 transcriptional signature and fail to strongly upregulate a PA1 transcriptional signature. Our analyses identify putative HOXA2 targets and suggest that subsets of NCCs may respond to HOXA2 activity in distinct manners. This separation of phenotypic and molecular states has significant implications for understanding craniofacial development. ### Competing Interest Statement IP: Supported by Graduate School of the Stowers Institute for Medical Research and NIH F31. PAT: Employed and research funded by Stowers Institute for Medical Research; Stipend from American Association of Anatomists for being Editor-in-Chief of Developmental Dynamics. RK: Employed and research funded by Stowers Institute for Medical Research; Member of Scientific Review Board of Howard Hughes Medical Institute; Member of the Board of Directors of the Society for Developmental Biology; Co-inventor listed on patents licensed by the Stowers Institute to Amgen for a drug to regulate bone density.