Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken

SRY ( sex-determining region Y)-box 9 ( SOX9) is a transcription factor regulating both chondrogenesisand sex determination. Among vertebrates, SOX9’s functions in chondrogenesisare well conserved, while they vary in sex determination. To investigate the conservation of SOX9’s regulatory functions in chondrogenesisand gonaddevelopment among species, we performed chromatin immunoprecipitationsequencing (ChIP-seq) using developing limb budsand male gonadsfrom embryos of two vertebrates, mouse and chicken. In both mouse and chicken, SOX9bound to intronic and distal regions of genes more frequently in limb budsthan in male gonads, while SOX9bound to the proximal upstream regions of genes more frequently in male gonadsthan in limb buds. In both species, SOX palindromicrepeats were identified more frequently in SOX9binding regions in limb budgenes compared with those in male gonadgenes. The conservation of SOX9binding regions was significantly higher in limb budgenes. In addition, we combined RNA expression analysis (RNA sequencing) with the ChIP-seq results at the same stage in developing chondrocytes and Sertoli cellsand determined SOX9target genes in these cells of the two species and disclosed that SOX9targets showed high similarity of targets in chondrocytes, but not in Sertoli cells.