Extended Data Fig. 4: CDK11 inhibition alters total and modified RNAPII occupancies on genes.
From: CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1
a, Immunoblot of proteins after treatment of HCT116 cells with indicated concentrations of pladi B for indicated times. b, Metagene analyses of RNAPII ChIP-seq occupancies of the 7500 protein-coding genes with highest RNAPII occupancy in DMSO treated control. Only genes separated by ≥5,000 nt from other genes are included. Dotted lines indicate transcription start site (TSS), 1,500 nucleotides downstream of TSS, 1,500 nucleotides upstream of transcription termination site (TTS) and TTS. The colour track at the bottom indicates the significance of paired two-sided Wilcoxon tests comparing DMSO treated control cells and cells treated with 30 nM OTS964 for 4 h. Colour code: red = adjusted P-value ≤ 10−15, orange = adjusted P-value ≤ 10−10, yellow = adjusted P-value ≤ 10−3. c, d, Metagene analyses of RNAPII ChIP-seq occupancies over down-, up- and non-regulated genes in RNA-seq (c) and over transcripts with indicated lengths (d) upon 30 nM OTS964 or control DMSO treatment in HCT116 cells for 4 h. e, Scatter plot comparing PI between OTS964 and control DMSO treatment. Genes in red have ≥ 2-fold increase in PI, in green have ≥ 2-fold decrease and in blue are within the 2-fold range. This analysis includes only well-expressed genes with an RPKM ≥ 1 either on the promoter or gene body in control DMSO treatment. f, Pie chart showing proportion of genes with indicated increases or decreases in PI or with no change. g, Boxplots showing the distribution of gene body RPKM (reads per kilo base per million mapped reads) for control DMSO and OTS964 treatment for genes with either a decrease or increase in PI. n = 2 biologically independent experiments. Boxes represent the range between the first and third quartiles for each condition. Black horizontal lines in boxes show the median. The ends of the whiskers (vertical lines) extend the box by 1.5 times the inter-quartile range. Data points outside this range (outliers) are shown as small circles. The y-axis was limited to the range between 0 and 2. h, i, Metagene analyses of P-Ser5 (h) and P-Ser7 (i) occupancies over 7,500 genes upon 30 nM OTS964 or control DMSO treatment for 4 h in HCT116 cells.
