Fig. 2 Combined transcriptome profiling, ChIP-seq, and ATAC-seq analysis identifies 14 highly plausible direct targets of Runx. Combined transcriptome.

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Fig. 2 Combined transcriptome profiling, ChIP-seq, and ATAC-seq analysis identifies 14 highly plausible direct targets of Runx. Combined transcriptome profiling, ChIP-seq, and ATAC-seq analysis identifies 14 highly plausible direct targets of Runx. (A) Heat maps showed the antibody-binding pattern around the TSSs region. Each panel represents 3 kb upstream and downstream of the TSSs. Left, IgG control; right, RUNX1 antibody. (B) Circle chart depicted RUNX1-binding site distribution in relation to the nearest annotated TSSs. Numbers represented distance from TSS (kb), and percentages represented percentage of bound regions. (C) Venn diagram showed the overlap of genes among RNA-seq DEGs, ChIP-seq peak, and ATAC-seq peak. For ChIP-seq and ATAC-seq, we consider differential peaks detected within ±20 kb around TSS. (D) Heat map showed the 14 commonly shared genes from Nf1fl/fl;DhhCre and Runx1fl/fl;Runx3fl/fl;Nf1fl/fl;DhhCre tumor RNA-seq. (E) qRT-PCR confirmed the relative mRNA expression of the 14 targets. (F) Representative two genes (Rnf157: up-regulated gene; Ccnd1: down-regulated gene) showed their RNA-seq gene expression (blue: down-regulation; red: up-regulation), RUNX1-binding ChiP-seq peak, and ATAC-seq peak. *P < 0.05, **P < 0.01. Ashley Hall et al. Sci Adv 2019;5:eaau8389 Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).