Sphingolipid metabolism is spatially regulated in the developing embryo bySOXEgenes

During epithelial-to-mesenchymal transition (EMT), significant rearrangements occur in plasma membrane protein and lipid content that are important for membrane function and acquisition of cell motility. To gain insight into how neural crest cells regulate their lipid content at the transcriptional level during EMT, here we identify critical enhancer sequences that regulate the expression of SMPD3 , a gene responsible for sphingomyelin hydrolysis to produce ceramide, which is necessary for neural crest EMT. We uncovered three enhancer regions within the first intron of the SMPD3 locus that drive reporter expression in distinct spatial and temporal domains, together collectively recapitulating the expression domains of endogenous SMPD3 within the ectodermal lineages. We further dissected one enhancer that is specifically active in the migrating neural crest. By mutating putative transcriptional input sites or knocking down upstream regulators, we find that the SoxE-family transcription factors Sox9 and Sox10 regulate the expression of SMPD3 in migrating neural crest cells. Together these results shed light on how core components of developmental gene regulatory networks interact with metabolic effector genes to control changes in membrane lipid content. Highlights SMPD3 is expressed in the neural tube, neural crest, and notochord during early development SMPD3 expression is regulated by at least three intronic enhancers Sox10 and its binding sites are required for expression by a migratory neural crest-specific SMPD3 enhancer Sox10 is a positive regulator of endogenous SMPD3 expression during neural crest migration