Fig. 2

Mcs6 and Cdk9 impact Pol II at 5′ and 3′ ends of genes. a Western blot analysis of phosphorylated CTD residues (Ser2-P, Ser-5-P, Ser7-P) in relation to total CTD signal. Levels were measured over a time course of cultures treated with 20 μM 3-MB-PP1. b Browser track image from the SPBC1683.05 locus displaying normalized read counts from untreated (green) and treated data (red) for wild-type, mcs6^as5, and cdk9^as strains from top to bottom, respectively (plus strand only). All PRO-seq samples represent treatments for 5 min with 10 μM 3-MB-PP1 (treated) or equivalent volume of DMSO (untreated). c Heat maps depicting the log₂ fold change in normalized PRO-seq signal (treated/untreated) within 10 bp bins from −250 bp to +4000 bp relative to the TSS (“+” indicates downstream and “−” indicates upstream) for wild-type, mcs6^as5, and cdk9^as strains from left to right, respectively. Data used in b and c reflect the results of combined data from two biological replicates for each treatment. Only one replicate was used for 3-MB-PP1-treated mcs6^as5 (see Methods). Genes within each heat map are sorted by increasing length from top to bottom, with black lines representing observed TSS and CPS (n = 3383). d Hypothetical plot for the illustration of the definition of promoter (TSS to +100) early (+150 to +450 from TSS) and late (−300 to 0 from CPS) gene body regions used in e. e Heat maps depicting whether each gene exhibits a significant fold change (adjusted p < 0.01; treated/untreated; DESeq2: Wald test, Benjamini and Hochberg’s correction) in promoter, early, or late gene body regions. Genes were required to be longer than 800 nt (n = 3003) and are sorted from top to bottom by increasing gene length with length quartiles shown on the right. Significant increases and decreases in each region are shown as red and blue, respectively