Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation

The specification of cartilage requires Sox9, a transcription factor with broad roles for organogenesis outside the skeletal system. How Sox9 gains selective access to cartilage-specific cis-regulatory regions during skeletal development had remained unclear. By analyzing chromatin accessibility during the differentiation of neural crest cells into chondrocytes of the zebrafish head, we find that cartilage-associated chromatin accessibility is dynamically established. Cartilage-associated regions that become accessible after neural crest migration are co-enriched for Sox9 and Fox transcription factor binding motifs. In zebrafish lacking Foxc1 paralogs, we find a global decrease in chromatin accessibility in chondrocytes, consistent with a later loss of dorsal facial cartilages. Zebrafish transgenesis assays confirm that many of these Foxc1-dependent elements function as enhancers with region- and stage-specific activity in facial cartilages. We propose that Foxc1-dependent chromatin accessibility helps directs the versatile Sox9 protein to a chondrogenic program in the face. HighlightsO_LIDynamic chromatin accessibility across facial cartilage development C_LIO_LICo-enrichment of Fox- and Sox-binding motifs in accessible regions C_LIO_LIFoxc1 establishes accessibility in a subset of facial cartilage enhancers C_LIO_LIModular activity of Foxc1-dependent cartilage enhancers in zebrafish C_LI