Fig. 3: Phosphorylation of the Spt5p CTR is crucial for suppressing antisense transcription.

Median PRO-seq intensity of sense (a) and antisense (c) strand signals across all filtered genes (n = 1819) in Bur1p-IS cells. CMK at 20 μM was used to inhibit Spt5p CTR phosphorylation. Three conditions are illustrated in the plots, based on the time after initation of CMK treatment: control (DMSO, red), short (5 min, blue), and long (20 min, violet). Heatmaps depicting the log₂FC of PRO-seq (b, left; d) and ChIP-seq (b, right) signal intensities ranked by gene length for the sense (b) and antisense (d) strands. The TSS and TES of each gene is represented by black dots. e Boxplots show the log₂FC for PRO-seq signal intensity for the sense and antisense strands in intragenic regions. p-values were calculated using the Wilcox test. f Boxplots depict the log₂FC of PRO-seq signal intensity for each cryptic transcript under Bur1p inhibition. The number at the top of the boxplot presents the median value of log₂FC. g Scatter plots compare the log₂FC of sense PRO-seq signal intensity in the early GB versus antisense PRO-seq signal intensity in the TSS upstream, PR, and GB. The antisense data are distributed on the y axis, while the sense PRO-seq data are distributed on the x axis. The blue line denotes the trend line. Pearson correlation coefficient (ρ) is positioned at the top left. h Representative example genome browser track showing a sense transcription wave in FMP27 and elevated antisense PRO-seq signal in BDF1 upon Bur1p inhibition. The antisense signal is represented reversely to the sense transcription. Transcription changes upon Spt5p depletion in FMP27 and BDF1 are represented in Supplementary Fig. 3g.