Supplementary Figure 1: Deregulated MYCN binding at active promoters and enhancers in neuroblastoma. | Nature Genetics

Supplementary Figure 1: Deregulated MYCN binding at active promoters and enhancers in neuroblastoma.

From: Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma

Supplementary Figure 1

a, Cell-normalized steady-state mRNA transcript levels of MYCN in human neuroblastoma cell lines. b, Line plots of quantified western blot bands from increasing cell-number-normalized cropped western blots of MYCN protein levels. Error bars denote ±s.d. for four replicate blots. c, Scatterplots of average ranked MYCN occupancy across four cell lines (x axis) versus ranked MYCN occupancy in each respective cell line (y axis). Contour lines illustrate the density of correlation of MYCN occupancy and are color-coded from high density (red) to low density (yellow). d, Meta track representation of MYCN and H3K27ac ChIP–seq signal (RPM/bp) across four neuroblastoma cell lines at the RPL22 locus. e, Meta track representation of MYCN and H3K27ac ChIP–seq signal (RPM/bp) across four neuroblastoma cell lines at an upstream ID2 enhancer. f, Heatmap of MYCN (red) signal at promoters (left) and enhancers (right) in each respective neuroblastoma cell line. Each row shows the ±5-kb region centered on the TSS ranked by average H3K27ac signal. Color scaled intensities are in units of RPM/bp. g, Heatmap of H3K27ac (blue) signal at promoters (left) and enhancers (right) in each respective neuroblastoma cell line. Each row shows the ±5-kb region centered on the enhancer ranked by average H3K27ac signal. Color scaled intensities are in units of RPM/bp. h, Clustering of the indicated ChIP–seq signal at promoters in the BE(2)-C cell line. Color scaled intensities reflect pairwise similarity via Pearson correlation. i, Top, MYCN signal contribution in the BE(2)-C cell line at the top 20,000 promoters. Bottom, line plots of signal contribution at the top 20,000 promoters of the indicated marks. Error bars represent 95% confidence intervals of the mean. j, Line plots showing the correlation of ranked MYCN-enriched regions (x axis) versus average ChIP–seq signal (top), percentage overlap with a given genomic feature (middle), or E-box density (bottom) on the y axis. Error bars represent 95% confidence intervals of the mean.

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