Supplementary Figure 2: Dynamic chromatin consequences of direct MYCN shutdown. | Nature Genetics

Supplementary Figure 2: Dynamic chromatin consequences of direct MYCN shutdown.

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

Supplementary Figure 2

a, ChIP-Rx signal (RPM/bp, before scaling) upon MYCN shutdown in the tet-off MYCN SHEP-21N cell line at the NPM1 locus. b, ChIP-Rx signal (RPM/bp) upon MYCN shutdown in the tet-off MYCN SHEP-21 cell line at the NPM1 locus. c, Heatmap and meta plot of MYCN signal at promoters (left) and enhancers (right) upon MYCN shutdown in the tet-off MYCN SHEP-21N cell line. Each row shows the ±5-kb region centered on the TSS or enhancer ranked by average H3K27ac signal. Color scaled intensities are in units of RPM/bp. d, Heatmap and meta plot of H3K27ac signal at promoters and enhancers upon MYCN shutdown in the tet-off MYCN SHEP-21N cell line. Each row shows the ±5-kb region centered on the TSS or enhancer ranked by average H3K27ac signal. Color scaled intensities are in units of RPM/bp. e, Box plots of MYCN and H3K27ac ChIP–seq signal at active promoters. MYCN and H3K27ac signal at 0, 2, and 24 h after MYCN shutdown for standard ChIP–seq; ChIP-Rx before/after scaling. Significant differences are denoted (Welch’s two-tailed t test): ***P < 1 × 10–9, **P < 1 × 10–6. f, Box plots of MYCN and H3K27ac ChIP–seq signal at active enhancers. MYCN and H3K27ac signal at 0, 2, and 24 h after MYCN shutdown for standard ChIP–seq; ChIP-Rx before/after scaling. Significant differences are denoted (Welch’s two-tailed t test): ***P < 1 × 10–9, **P < 1 × 10–6. g, Heatmap and meta plot of H3K4me3, RNA Pol II, and CTCF signal at promoters upon MYCN shutdown in the tet-off MYCN SHEP-21N 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. h, Cropped western blot of total histone H3 and H3K27ac levels at 0, 2, and 24 h after MYCN shutdown. The percentage of H3K27ac remaining versus 0 h is indicated. i, Distribution plots of RNA Pol II traveling ratios (TR) for all active genes in traditional normalized ChIP–seq data. Differences in the TR distribution at 0 h versus 2 h and 0 h versus 24 h are significant; Welch’s two-tailed t test: ***P < 1 × 10–9, **P < 1 × 10–6. j, Box plots of log2 fold changes in active gene expression (traditional normalization) at the indicated time points versus 0 h after MYCN shutdown. Significant differences are denoted (Welch’s two-tailed t test): **P < 1 × 10–6.

Back to article page