SOX9 and TCF transcription factors associate to mediate Wnt/β-catenin target gene activation in colorectal cancer

Activation of the Wnt/beta-catenin pathway regulates gene expression by promoting the formation of a beta-catenin-T-cell factor (TCF) complex on target enhancers. In addition to TCFs, other transcription factors interact with the Wnt/beta-catenin pathway at different levels to produce tissue-specific patterns of Wnt target gene expression. The transcription factor SOX9 potently represses many Wnt target genes by downregulating beta-catenin protein levels. Here, we find using colony formation and cell growth assays that SOX9 surprisingly promotes the proliferation of Wnt-driven colorectal cancer (CRC) cells. In contrast to how it indirectly represses Wnt targets, SOX9 directly co-occupies and activates multiple Wnt-responsive enhancers in CRC cells. Our examination of the binding site grammar of these enhancers shows the presence of TCF and SOX9 binding sites that are necessary for transcriptional acti-vation. In addition, we identify a physical interaction between the DNA-binding domains of TCFs and SOX9 and show that TCF-SOX9 interactions are important for target gene regula-tion and CRC cell growth. Our work demonstrates a highly context-dependent effect of SOX9 on Wnt targets, with the presence or absence of SOX9-binding sites on Wnt-regulated enhancers determining whether they are directly activated or indirectly repressed by SOX9.

Automated summary

Activation of the Wnt/beta-catenin pathway leads to the formation of a beta-catenin-TCF complex, regulating gene expression. SOX9, a transcription factor, can repress many Wnt target genes by downregulating beta-catenin protein levels. Interestingly, SOX9 also directly activates multiple Wnt-responsive enhancers in colorectal cancer cells, promoting cell proliferation.