Extended Data Fig. 8: SOX2 and β-catenin co-occupy cell-type specific CREs with T/BRA and CDX2.

(a) SOX2 and β-catenin occupancy is correlated with T/BRA and CDX2 in CEpiLCs at cell-type specific CREs classified in Fig. 3e. Metaplots show mean ± s.e.m. (b) A sub-set of low-affinity SOX2 motifs within Cluster 1 SOX2 bound CREs are located in close proximity to CDX motifs. (c) A sub-set of low-affinity SOX2 motifs within Cluster 2 and Cluster 4 SOX2 bound CREs are located in close proximity to T/BRA motifs. Differential occupancy of (d) SOX2 and (e) β-catenin at T/BRA co-occupied peaks in T/BraKO progenitors compared to CEpiLCs. Differentially occupied peaks coloured red are statistically different between conditions (FDR <0.05). FDR was determined by DESeq2 padj metric from n=3 biological replicates. Labelled peaks are adjacent to genes differentially expressed in T/BraKO progenitors. (f) SOX2 and β-catenin occupancy is specifically reduced at CREs adjacent to paraxial mesoderm determinants in T/BraKO progenitors. Average SOX2 (g), β-catenin (h), and LEF1 (i) occupancy is reduced at cluster 1 CDX2 co-occupied peaks. Average SOX2 (j), β-catenin (k) and LEF1 (l) occupancy at cluster 4 CDX2 occupied peaks. Average (m) SOX2, (n) β-catenin, and (o) LEF1 at T/BRA co-occupied cluster 2 peaks in CEpiLCs and T/BraKO progenitors. Average (p) SOX2, (q) β-catenin, and (r) LEF1 at T/BRA co-occupied cluster 4 peaks in CEpiLCs and T/BraKO progenitors. (s) Average nucleosome occupancy is unchaged compared to CEpiLCs across all clusters of SOX differential peaks in CdxKO and T/BraKO progenitors (reanalysed from³⁵).