FOXK1 is a transcriptional repressor of Wnt signalling. (A) Heatmap highlighting the top 20 transcription factors associated with the Wnt signalling pathway enriched in the Foxk1 null D5 EB group from the RNAseq dataset. (B) Wnt6 transcript expression during EB differentiation from D2 to D8 in the presence and absence of FOXK1. Note that the expression of Wnt6 remains high at later stages of differentiation compared to the control group where it is down-regulated. (C) A region upstream of Wnt6 (chr1:74,770,049-74,773,057) that contains a FOXK1 DNA motif, β-catenin-binding site, and decreased chromatin accessibility in the absence of Foxk1 compared to control EBs at D5. (D) qPCR analysis using FOXK1 ChIP demonstrates a significant enrichment at the Wnt6 upstream region compared to the Gapdh control region. (E) β-Catenin transactivates the TOP-flash reporter, which is inhibited by FOXK1. Statistical test: Student’s t-test. Data presented as mean ± SEM.