SOX9 is sufficient to drive endothelial cells towards a mesenchymal fate by altering the chromatin landscape.

The transcription factor SOX9 is expressed in multiple tissues during embryogenesis and directs developmental processes. SOX9 is activated upon epithelial-to-mesenchymal transition (EMT) and the closely related process, endothelial-to-mesenchymal transition (EndMT), but its role in regulating these processes is less clear. Both EMT and EndMT are fundamental processes in normal development and cancer progression. Here, we show that SOX9 expression alone is sufficient to activate mesenchymal enhancers and steer endothelial cells towards a mesenchymal fate. By genome-wide mapping of the chromatin landscape, we show that SOX9 acts as a pioneer transcription factor, having the ability to open the chromatin structure and increase enrichment of active histone marks at a specific subset of target enhancers with an associated SOX motif. SOX9 also displays widespread chromatin pausing that is not associated with SOX motifs. This leads to a switch in enhancer activity states resulting in activation of mesenchymal genes and concurrent suppression of endothelial genes to drive EndMT. Moreover, SOX9 induced widespread changes in chromatin states throughout the genome without SOX9 binding. Our study highlights the crucial developmental role of SOX9 and provides new insight into key molecular functions of SOX9 in regulating the chromatin landscape and mechanisms of EndMT.