Extended Data Fig. 5: Tle3 recruitment and stabilized binding require Runx3 and Tbet.
a. Principal component analysis (PCA) of Tle3 CUT&RUN sequencing libraries from WT and TRKO early TEFF cells isolated on 4 dpi. b. Venn diagram showing the overlap of Tle3 binding sites identified in WT and TbetKO TEFF cells. Tle3 CUT&RUN was performed on WT (4 replicates) and TbetKO (in 3 replicates) TEFF cells isolated on 6 dpi. Note that a single Tle3 binding site called in one cell type could overlap with more than one sites in the other, and therefore, the sum of common and uniquely identified Tle3 binding sites in the Venn diagram is not necessarily equal to the total site numbers called in a specific cell type. c. Boxplot showing the ratio of Tle3 binding strength in TbetKO to WT TEFF cells for Tle3 binding sites uniquely detected in each cell type (n = 9,926 for WT only sites, and n = 731 for TbetKO only sites). The box center lines denote the median, box edge denotes interquartile range (IQR), and whiskers denote the most extreme data points that are no more than 1.5 × IQR from the edge. d. Cumulative frequency plot showing differential Tle3 binding strength in WT versus TbetKO TEFF cells at the 3,380 Tbet/Runx-dependent Tle3 binding sites (defined in Fig. 5f). Statistical significance of the observed difference was determined with two-sided paired MWU test. e. Sequencing tracks of Tle3 CUT&RUN in WT and TbetKO TEFF cells. Rectangles with solid lines denote differential Tle3 binding sites with TbetKO cells showing ≥1.25-fold decrease in binding strength with FDR < 0.05, while those with dotted lines denote Tle3 binding sites identified in WT but not TbetKO TEFF cells by the same peak calling criteria.
