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. Author manuscript; available in PMC: 2023 Dec 1.
Published in final edited form as: Mol Cell. 2022 Nov 16;82(23):4428–4442.e7. doi: 10.1016/j.molcel.2022.10.025

Figure 5. Comparison of PAX3-FOXO1-regulated and non-regulated binding sites.

Figure 5.

(A) MA plots showing ATAC-seq peak changes; red (up) or blue (down) (dTAG-47/DMSO, n=2). (B) Flow chart showing the identification of high confidence PAX3-FOXO1 regulate genes and their associated enhancers. (C) Motif analysis of the area under all PAX3-FOXO1 DNA binding peaks from the CUT&RUN analysis (left) or under the 115 ATAC-seq sites associated with genes down-regulated after PAX3-FOXO1 degradation. (D) Heatmap of the intensity of CUT&RUN or ChIP-seq signal after K means clustering of each of the indicated factors. (E) Peaks from the clusters in D that were associated with the regulated genes are shown as a bar graph. (F) Histograms of the CUT&RUN signal of the indicated factors around the regulated ATAC-seq peaks versus the remaining cluster 1 & 2 peaks from K means clustering.