BioProject

Using whole-transcriptome and whole-epigenome sequencing approaches for wild-type and Sox9-deficient mouse embryo limb buds, we here identify genes specifically expressed and likely involved in precartilaginous condensation. More...

Using whole-transcriptome and whole-epigenome sequencing approaches for wild-type and Sox9-deficient mouse embryo limb buds, we here identify genes specifically expressed and likely involved in precartilaginous condensation. We show that SOX9 directly upregulates these genes and well-known early-cartilage markers, and that its actions in chondrogenic cells have little impact on neighboring cell types. Intriguingly, we find that SOX9 helps remove epigenetic signatures of transcriptional repression and establish active-promoter and active-enhancer marks at precartilage- and cartilage-specific loci, but is not absolutely required to initiate these changes and activate transcription. Altogether, these findings widen our current knowledge of SOX9 targets in early chondrogenesis and call for new studies to identify the pioneer and transactivating factors that act upstream of or along with SOX9 to prompt chromatin remodeling and specific gene activation at the onset of chondrogenesis and other processes. Overall design: RNAs were isolated from 3-4 biological replicates of control and Sox9-deficient mouse limb buds at E11.5 and E12.5 for RNA-seq experiments. Less...