Fig. 6: Rat1p restricts antisense transcription by interacting with Spt5p.

a Co-immunoprecipitation of Spt5p-5xFLAG Rat1p-AID*-6HA cell lysate with anti-FLAG and anti-HA. b Heatmaps depict log₂FC results from antisense PRO-seq (left) and mRNA-seq (right) upon Rat1p depletion, ranked by gene length across all filtered genes (n = 1807). IAA at 1 mM was applied for 1 h to degrade Rat1p. c MA plots illustrating changes observed under treatment with IAA versus EtOH for the antisense PRO-seq signal. Genes are illustrated as dots. Red indicates significantly up-regulated genes with log₂FC >1 and adjusted p-value <0.05; blue indicates significantly down-regulated genes with log₂FC <−1 and adjusted p-value <0.05. The numbers of DEGs are depicted in the plot. d Venn-diagram indicating the number of overlapped genes between DEGs showing significantly increased antisense PRO-seq signals in the PR and GB. Image sizes do not reflect gene numbers. e Boxplots representing the PRO-seq intensity ratios in each quartile for Rat1p-AID* cells. Quantiles are grouped by decreasing sense RPKM from left to right (Q1~Q4) (left) and decreasing antisense RPKM from left to right (q1~q4) (right). p-values were calculated using the Wilcox test. f Boxplots depict the log₂FC for PRO-seq signals (left) and mRNA-seq signals (right) upon Rat1p depletion in each group described in Fig. 4. g Boxplots depict the log₂FC of PRO-seq signals upon Rat1p KD for each cryptic transcript. The number at the top of the boxplot is the median value of log₂FC.