Figure 1. Effects of MYCN on gene expression and RNAPII function.

a: Immunoblot documenting MYC and MYCNER levels in SH-EP cells. Cells were treated with 200 nM 4-OHT or EtOH for 3 h. CDK2 is loading control (n=3; in all legends, n indicates the number of independent biological replicates).

b: Correlation between regulation by MYCN measured by nascent and steady-state RNA levels. 18,213 genes were binned and the mean including the 95 % confidence interval is plotted (n=3).

c: Metagene plots of total RNAPII after 4-OHT treatment (3 h) for the 914 most strongly MYCN-activated (top) and 615 repressed genes (bottom). For each genomic bin, the mean is plotted and the shadow illustrates SEM. RPM: reads per million mapped reads (n=4).

d: Metagene plots (mean+SEM as shadow) of RNAPII-pSer2 for MYCN-activated and -repressed genes (n=4).

e: Correlation of transcriptional changes and RNAPII occupancy at promoters and transcriptional end sites (TES) after MYCNER activation. 11,093 expressed genes were binned based on log₂FC. Plots show median with bootstrapped 95 % confidence intervals with 1,000 re-samplings as error bars.

f: Kernel density plot regulation by MYCN of gene with promoters that have different G/C skews (strong:4,003; weak:3,381; no:1,377) (n=3). p-values were calculated with a two-tailed Wilcoxon one-sample signed-rank test with μ=0.