Identification of Wnt regulated genes that are repressed by, or independent of, β-catenin

Wnt signaling regulates metazoan development and homeostasis, in part by {beta}-catenin dependent activation and repression of a large number of genes. However, Wnt signaling also regulates genes independent of {beta}-catenin, genes that are less well characterized. In this study, using a pan-Wnt inhibitor we performed a comprehensive transcriptome analysis in a Wnt-addicted orthotopic cancer model to delineate the {beta}-catenin-dependent and independent arms of Wnt signaling. We find that while a large percentage of Wnt-regulated genes are regulated by {beta}-catenin, ten percent of these genes are regulated independent of {beta}-catenin. Interestingly, a large proportion of these {beta}-catenin independent genes are Wnt-repressed. Among the {beta}-catenin dependent genes, more than half are repressed by {beta}-catenin. We used this dataset to investigate the mechanisms by which Wnt/{beta}-catenin signaling represses gene expression, revealing the role of a cis-regulatory motif, the negative regulatory element (NRE). The NRE motif is enriched in the promoters of {beta}-catenin repressed genes and is required for their repression. This provides a comprehensive analysis of the {beta}-catenin independent arm of the Wnt signaling pathway in a cancer model and illustrates how a cis-regulatory grammar can determine Wnt-dependent gene activation versus repression.