Figure 4.

EGF driven downregulation of pre-mRNAs and mRNAs in MCF10A cells. (A) Pre-mRNA and mRNA profiles of 364 transcriptionally repressed genes. The left heatmap displays mRNA expression as defined by the gene-level exon FC profiles; genes are grouped first according to the time of their lowest mRNA FC, and within each such group, they are ordered according to the time of their lowest pre-mRNA FC, as reflected by intronic FC (right heatmap). The order of the genes is the same in both heatmaps. Names of genes that were chosen for detailed validation are indicated. Note that mRNA profiles are very poor indicators of shutdown of pre-mRNA production. Heatmaps were normalized as in Figure 2B. (B) qPCR measurements of expression FC profiles of selected downregulated genes in a high-resolution time course following stimulation of MCF10A cells with EGF. Dots represent averages of technical triplicates, solid lines represent best fit (see Materials and methods) of pre-mRNA (red) and mature mRNA (blue). Production profiles (green lines), mRNA half-lives and degradation (gold) were inferred from these measurements as described in Materials and methods.