Fig. 4: G2 genes that show high-level expression from the sense strand and low-level expression from the antisense strand exhibit greater increases of antisense transcription in the Spt5p and Bur1p mutants.

Boxplots represent PRO-seq intensity ratios of each quartile for Spt5p-AID* (a) and Bur1p-IS (b) cells. Quantiles are grouped from left to right by decreasing sense RPKM (Q1~Q4) (left) and decreasing antisense RPKM (q1~q4) (right). Genes of S. cerevisiae (n = 1807) (c) and human DLD-1 (n = 8622) (f) are scattered according to their sense (x axis) and antisense (y axis) expression levels. The gene expression levels are presented as RPKM for mRNA-seq (c) and intragenic density for PRO-seq (f). The top or bottom 30% genes of each quadrant are grouped as G1 (black; high sense, high antisense), G2 (orange; high sense, low antisense), G3 (light blue; low sense, high antisense), and G4 (green; low sense, low antisense). The number of genes in each group is presented. The remaining genes are designated ‘No’ (white). d Boxplots represent log₂FC of antisense PRO-seq signal for each group. The signals from Spt5p-AID* cells treated for 1 h with IAA and Bur1p-IS cells treated with CMK for 20 min as compared with their respective control S. cerevisiae cells. e Boxplots depict the signal density at the early GB for each mutant. g Boxplots represent log₂FC of antisense PRO-seq results for each group. The signals from SPT5-AID cells treated with auxin plus a VCP inhibitor and in NELF-C-AID cells treated with auxin and/or FP are compared with their respective human cells. Human PRO-seq data were downloaded using the appropriate accession number (SPT5-AID, GSE168827 and NELF-C-AID, GSE144786).