Edited by Eric R. FearonType II collagen ␣1 is specific for cartilaginous tissues, and mutations in its gene are associated with skeletal diseases. Its expression has been shown to be dependent on SOX9, a master transcription factor required for chondrogenesis that binds to an enhancer region in intron 1. However, ChIP sequencing revealed that SOX9 does not strongly bind to intron 1, but rather it binds to intron 6 and a site 30 kb upstream of the transcription start site. Here, we aimed to determine the role of the novel SOX9-binding site in intron 6. We prepared reporter constructs that contain a Col2a1 promoter, intron 1 with or without intron 6, and the luciferase gene. Although the reporter constructs were not activated by SOX9 alone, the construct that contained both introns 1 and 6 was activated 5-10-fold by the SOX9/SOX5 or the SOX9/SOX6 combination in transient-transfection assays in 293T cells. This enhancement was also observed in rat chondrosarcoma cells that stably expressed the construct. CRISPR/Cas9-induced deletion of intron 6 in RCS cells revealed that a 10-bp region of intron 6 is necessary both for Col2a1 expression and SOX9 binding. Furthermore, SOX9, but not SOX5, binds to this region as demonstrated in an electrophoretic mobility shift assay, although both SOX9 and SOX5 bind to a larger 325-bp fragment of intron 6 containing this small sequence. These findings suggest a novel mechanism of action of SOX5/6; namely, the SOX9/5/6 combination enhances Col2a1 transcription through a novel enhancer in intron 6 together with the enhancer in intron 1.SOX9 is a major transcription factor that regulates chondrocyte differentiation (1-3). The role of SOX9 in chondrogenesis was suggested first by the identification of heterozygous mutations in and around the SOX9 gene in the human genetic disease campomelic dysplasia, which is a cartilage disease that causes severe skeletal malformations and is often associated with XY female sex reversal (4, 5). Furthermore, site-and stage-specific down-regulation of SOX9 mRNA by mutations in a noncoding region near the SOX9 gene have been shown to cause Pier-Robinson syndrome, which is characterized by the abnormal positioning of the jaw, cleft palate, and airway obstruction (1).During chondrocyte differentiation, SOX9 regulates each step, from mesenchymal condensation and chondrocyte differentiation to the formation of hypertrophic chondrocytes (6). Many genes have been shown to be direct targets of this transcription factor, including genes encoding extracellular matrix (ECM) 4 proteins, membrane proteins, other transcription factors, and signaling molecules (7-9). Some of the ECM proteins that are regulated by SOX9 include COL2A1, COL9A2, ACAN, PRELP, and MATN 3.The expression of one of these ECM proteins, type II collagen ␣1 (COL2A1) is necessary for chondrocyte differentiation (10). Type II collagen ␣1 is specific for cartilaginous tissues and necessary for the normal embryonic development of the skeleton. Mutations in this gene cause achondrogenesis, chondrodys...