Figure 4.

Redistribution of the transcriptome during the DNA DSB response. (A–B) Fold-changes in mean production of all cellular transcripts 2.5–3.5 h after NCS treatment in GFP cells (A) and MYC-GFP cells (B) compared with untreated GFP cells. Transcripts with at least 5 reads in each replicate (n = 3) of each cell line/treatment condition are included. Transcripts are ordered by fold-change in mean production. (C–D) Fold-changes in mean production of p53 target transcripts, as identified by Allen et al. (2014), 2.5–3.5 h after NCS treatment in GFP cells (C) and MYC-GFP cells (D) compared with untreated GFP cells. (E) Foldchanges in mean transcription of select p53 target genes and control genes 2.5–3.5 h after NCS treatment in MYC-GFP and GFP cells, compared with untreated GFP cells, as measured by RNA-seq. Data are represented as mean ± SEM (n = 3 for each condition). (F) Density plot of fold-changes in mean production of cellular transcripts in untreated MYC-GFP cells relative to untreated GFP cells as a function of mean production in untreated GFP cells. Spearman correlation coefficient between expression in untreated GFP cells and fold-change due to MYC above its basal level is ρ = 0.155. (G) Density plot of fold-changes in mean production of cellular transcripts in NCS-treated GFP cells relative to untreated GFP cells as a function of mean production in untreated GFP cells. Spearman correlation coefficient between expression in untreated GFP cells and fold-change due to NCS is ρ = −0.151. For (F–G), transcripts of length ≥ 1500 bases with at least 5 reads in each replicate (n = 3) of each cell line/treatment condition are included. Pink lines represent median fold-change in each bin, calculated for bins with at least 40 transcripts. See also Figure S2 and Table S1.