Fig. 4. SOX2/β-catenin co-occupancy correlates with cell-type-specific gene expression.
a, SOX2/β-catenin co-occupancy at a CRE shaded blue upstream of the transcriptional start site of Meis3 correlates with its cell-type-specific expression in CEpiLCs. b, Differentially expressed genes associated with cluster 1 CREs are most highly expressed in CEpiLCs. c, SOX2/β-catenin co-occupancy at an upstream of the transcriptional start site of Nodal correlates with its cell-type-specific expression in SOX2-OFF cells. d, Differentially expressed genes associated with cluster 2 CREs are most highly expressed in SOX2-OFF. e, SOX2/β-catenin co-occupancy at a CRE upstream of the pluripotency marker Klf2 correlates with its cell-type-specific expression in SOX2-ON cells. f, Differentially expressed genes associated with cluster 3 CREs are most highly expressed in SOX2-ON. g, Reduced SOX2/β-catenin co-occupancy at multiple CREs upstream of the transcriptional start site of T/Bra in SOX2-ON and naive ESCs correlates with the absence of T/Bra expression in those cell states. h, Differentially expressed genes associated with cluster 4 CREs are expressed at lowest levels in SOX2-ON. Differential expression criterion for genes analysed in b, d, f and h is FDR <0.05, as determined by DESeq2 padj metric from n = 3 biological replicates. Data are represented by Tukey box plots (centre line is median, box limits are upper and lower quartiles, whiskers are 1.5× interquartile range and points are outliers). Source numerical data are available in source data.