Fig. 6: ZNF398 activates transcription in concert with SMAD3 and EP300.
a Top: Hierarchical clustering of 15 genome-wide-binding profiles (available genome-wide binding profiles from CODEX45). Normalised Pointwise Mutual Information (NPMI) between each pair of samples were used to display all pairwise binding overlaps in a clustered heatmap45. Colours in the heatmap show the level of overlap for each pair of samples (red, all binding sites overlapped; yellow, overlap expected by chance; blue, mutually exclusive binding). Bottom: Hierarchical clustering of pairwise Spearman correlation of ZNF398 and ChIP-seq datasets indicated. Colours indicate the level of correlation (red indicates perfect correlation, blue indicates perfect anticorrelation). ZNF398 clusters together with active histone marks. See also Supplementary Fig. 6a for DNA motifs associated with ZNF398 peaks. b Binding plots show the location of ZNF398 (obtained in two hPSC lines, H9 and BG0V1) and H3K27ac, H3K4me3, H3K4me1, SMAD3, EP300, NANOG and OCT4. 5771 sites are displayed within a 10 kb window centred around ZNF398 peaks. Note the presence of ZNF398 both at active enhancers (H3K4me1 positive) and active promoters (H3K4me3 positive). c SMAD3 interacts with ZNF398. Co-IP with antibodies against SMAD3, Avi-Tag-ZNF398 and IgG were performed on nuclear lysates of H9 expressing ZNF398, treated with 25 ng/ml Activin A for 1 h to promote nuclear accumulation of SMAD3. Precipitated complexes were probed for endogenous SMAD3 and Avi-Tag-ZNF398. Representative of two independent experiments. Uncropped gels are provided as a Source Data file.
