Extended Data Fig. 3: OTS964 and pladi B globally disrupt splicing in a similar way.

a, IGV genome browser view of Brd2 and Ddx47 genes from RNA-seq treated with 30 nM OTS964 or DMSO (control) for 4 h. b, Box plots showing ratio of spliced reads over total unspliced and spliced reads in RNA-seq after treatment with DMSO (control) or 30 nM OTS964 for 4 h. First, middle and last introns in selected 6222 isoforms were considered. 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 extend the box by 1.5 times the inter-quartile range. n=2 biologically independent experiments. c, Graph shows change in expression of transcripts of five genes in WT or CDK11 G579S HCT116 cells either treated with DMSO or 200 nM flavopiridol for 4 h. mRNA levels were normalized to Ppia mRNA expression and expression in DMSO was set as 1. n = 4 biologically independent experiments, error bars=SEM. E-E=primers spanning exon-exon junctions; E-In=primers spanning exon-intron junctions. d, Box plots showing the ratio of intronic reads over total intronic and exonic reads in 4SU–seq after treatment with DMSO, 50 nM OTS964 and 186 nM pladi B in pulse (upper) and chase (lower) experiment. Two biological replicates (REP1, REP2) are shown. 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 extend the box by 1.5 times the inter-quartile range. e, IGV genome browser view of Dusp4 and Fosl1 genes from pulse and chase 4SU–seq experiments. f, Scatterplots comparing intron ratios in individual genes between DMSO (control) and either OTS964 (left) or pladi B (right) treated HCT116 cells in 4SU–seq pulse experiment. g, Scatterplots comparing intron ratios in individual genes between OTS964 and pladi B treated HCT116 cells in 4SU–seq pulse (left) and chase (right) experiments. h, Boxplots showing distribution of log₂ fold changes of intron ratios for individual genes in OTS964 over DMSO and pladi B over DMSO in 4SU–seq chase experiment. 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 −2 and 4.

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