Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage

DNA damage results in increased expression of antisense promoter upstream transcripts (PROMPTs). (A) mNET-seq metagene profiles showing sense and antisense transcription near the TSS of down-regulated PCGs from Y1P-damage and no-damage samples. (B) Box plot indicates mNET-seq read coverage across PROMPTs of down-regulated PCGs from Y1P-damage and no-damage samples. A two-sample Wilcoxon test is used to compute statistical significance of difference in PROMPT expression for down-regulated genes between the Y1P-damage and Y1P-nondamage samples. (C) IGV profile of mNET-seq signal across a representative down-regulated gene showing increased PROMPT expression. (D) mNET-seq metagene profiles showing sense and antisense transcription near the TSS of up-regulated PCGs from Y1P-damage and no-damage samples. (E) Box plot indicates mNET-seq read coverage across PROMPTs of up-regulated PCGs from Y1P-damage and no-damage samples. (F) Cumulative distribution plot showing the log₂FC of PROMPTs upon IR between up-regulated and down-regulated PCGs from Y1P samples. The Mann–Whitney U test is used for statistically testing the medians between the log₂FC of PROMPT distribution between up-regulated and down-regulated PCGs upon IR from Y1P samples. (G) Volcano plots of differentially expressed PROMPTs from Y1P upon IR.