Extended Data Fig. 1: Distinct motif enrichment patterns in dynamically shifting Runx binding sites, comparison with PU.1 site stability, and efficient detection of direct Runx binding sites by CUT&RUN.
From: Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms
a, Heatmap illustrates PU.1 binding profiles in immortalized HSPC, DN1, DN2a, and DN2b cells. b, Top motifs enriched in Runx binding sites from indicated regions of Fig. 1b are shown. Statistical significance was computed using Homer de novo motif discovery algorithm. c, Scatter plots and Area-proportional Venn diagrams compare Runx1 and Runx3 binding sites in Phase 1 and Phase 2 pro-T cells, as measured by ChIP-seq cross-linked with DSG + FA1 vs. by CUT&RUN (C&R). Numbers in the Venn diagram indicate number of differential peaks compared between DSG-crosslinked ChIP-seq vs. C&R (fold enrichment > 2, Poisson enrichment P < 0.001). d, Violin plots show Runx motif quality position weight matrix (PWM) score in non-promoter Runx peaks detected similarly by ChIP-seq and C&R (purple) or preferentially detected by different technique (green; more efficiently detected by C&R, red; more efficiently detected by ChIP-seq). The horizontal dotted black line shows threshold PWM score to be recognized as a Runx motif. Thin vertical black bars mark minima and maxima values and thick vertical black lines indicate 25th to 75th percentiles range. The red lines with white circles show median values. e, Motif frequencies for Runx, bHLH, ETS, and PU.1 or TCF1 (Tcf7) factors within each peak are displayed.
