TCF/LEF dependent and independent transcriptional regulation of Wnt/β‐catenin target genes

During canonical Wnt signalling, the activity of nuclear β‐catenin is largely mediated by the TCF/LEF family of transcription factors. To challenge this view, we used the CRISPR/Cas9 genome editing approach to generate HEK 293T cell clones lacking all four TCF/LEF genes. By performing unbiased whole transcriptome sequencing analysis, we found that a subset of β‐catenin transcriptional targets did not require TCF/LEF factors for their regulation. Consistent with this finding, we observed in a genome‐wide analysis that β‐catenin occupied specific genomic regions in the absence of TCF/LEF. Finally, we revealed the existence of a transcriptional activity of β‐catenin that specifically appears when TCF/LEF factors are absent, and refer to this as β‐catenin‐GHOST response. Collectively, this study uncovers a previously neglected modus operandi of β‐catenin that bypasses the TCF/LEF transcription factors. Synopsis TCF/LEF‐deleted cells are used to challenge the assumption that Wnt/β‐catenin transcription is exclusively mediated by this transcription factor family. Genome‐wide gene expression and β‐catenin DNA binding analyses suggest that alternative transcription factors control a subset of β‐catenin target genes. TCF/LEF quadruple knockout (d4TCF) and β‐catenin knockout (dBcat) HEK 293T cells were generated. d4TCF cells display β‐catenin‐dependent gene regulation upon Wnt pathway activation. β‐catenin binds to specific genomic regions in the absence of TCF/LEF. The transcription factor FOXO4 is a candidate for TCF/LEF‐independent β‐catenin activity. Graphical Abstract Genome‐wide gene expression and β‐catenin DNA binding analyses in TCF/LEF knockout cells reveal a subset of Wnt/β‐catenin target genes that do not depend on these transcription factors.