Figure 7Figure 7a. Longer genes tend to have a larger fraction of differentially used exons. Box plot shows the fraction of exons significantly differentially used for 9026 expressed genes grouped into deciles based on the genomic length (including exons and introns) of their longest transcripts. n=3 replicates. Figure 7b. Genes with differentially used exons tend to be longer. Box plots show length of genes with no differentially used exons, or at least one exon differentially up-regulated (DEXSeq log2 fold-change≥0, p<0.01) or down-regulated (log2 fold-change ≤0, p<0.01). P-value from a two-sided Wilcoxon rank sum test comparing median lengths between genes with either up- or down-regulated exons is indicated on top. n=3 replicates. Figure 7c. Down-regulated genes tend to be longer than not-regulated genes, while up-regulated genes show little difference. Box plots show length of genes with no differential expression (-0.10.01), up-regulated (log2 fold-change≥0, p<0.01) or down-regulated (log2 fold-change ≤0, p<0.01) as determined by DESeq2. P-values from two-sided Wilcoxon rank sum tests comparing median lengths for up- and down-regulated genes, respectively, to non-regulated genes are indicated on top. n=3 replicates. Figure 7d. RNAPII processivity is affected not close to but at some distance from the TSS after CDK12 inhibition. The graphs compares the relative distance from the TSS where 10, 50 and 90% of read coverage is identified (=:x% distance) in control (x-axis) against CDK12 inhibited (y-axis) cells. Figure 7e. Transcripts of longer genes are more often impacted by shortening and lose a larger proportion of their length in comparison to shorter genes. The plot shows on the x axis the relative change in the 90% distance (relative Δ90% distance = (90% distance in control - 90% distance in CDK12 inhibited cells) / gene length) and on the y axis the percentage of genes showing a Δ90% distance equal or greater than the value on the x axis. Positive and negative relative Δ90% distances on the x axis indicate a shortening or extension of transcripts, respectively, after CDK12 inhibition. Genes were divided into quintiles according to gene length and curves for quintiles are shown separately. Dotted and dashed horizontal lines indicate the percentage of genes in each quintile with a transcript shortening of at least 10 and 20%, respectively. Figure 7f. Shortening of transcripts is evidenced by down-regulated poly(A) sites (PAS) in the 3' end RNA-seq data and accompanied by up-regulated upstream PAS for the majority of genes. The plot shows the fraction of genes with shortened (relative Δ90% distance ≥0.2), extended (absolute Δ90% distance <-50bp) or unaffected transcripts (|absolute Δ90% distance| ≤25bp) with down-, up- and non-regulated PAS according to the 3'end RNA-seq data. For genes with shortened transcripts and down-regulated PAS in a 3' UTR, the percentage of genes with upstream up-regulated PAS is indicated on the right. In case of multiple identified PAS, the order of preference was as indicated in the legend from top to bottom. Figure 7g. DNA replication and repair genes are longer than other protein coding genes. Box plots show the length for the indicated groups of genes (according to GO annotations). Median gene lengths for each GO category were compared against all other protein-coding genes using a one-sided Wilcoxon rank sum test (p-values provided in figure, n.s.: p>0.001).