Extended Data Fig. 4: MYC target genes and the location of targeted E-boxes.

Genome browser snapshots showing MYC binding at promoters of MYC target genes in three colon cancer cell lines GP5d, LoVo, and COLO320 and ATAC-seq signal for open chromatin in GP5d cells (traces from BAM coverage files are shown for ChIP-nexus tracks from ref. ³⁴ and for GP5d ATAC-seq from ref. ³⁵). The high spatial resolution of the ChIP-nexus peaks was utilized for selecting the MYC binding sites for the CGE experiments; the locations of E-boxes targeted in Fig. 2b are marked with red arrows and the additional MDN1 E-box targeted in Extended Data Fig. 5 is marked with a blue arrow (genome coordinates indicate the position of the first cytosine in the E-box sequence CACGTG in the forward strand; hg19). In addition, ChIP-seq tracks for MYC and H3K27ac as well as BAM coverage track for ATAC-seq from HAP1 cells is shown. Table shows differential gene expression for the selected MYC target genes as log₂(fold change) values upon MYC silencing (siMYC) in LoVo and GP5d cells (RNA-seq data from ref. ³⁴).