Fig. 2.
TSS-proximal junctions occur in genes that are highly and commonly transcribed in NSPCs and B lymphocytes. (A) Venn diagram illustrating the three classes (1–3) of genes transcribed in WT CSR-activated B lymphocytes and Xrcc4−/−p53−/− NSPCs. (B) Venn diagram showing class 1–3 genes transcribed in WT CSR-activated B lymphocytes and ATM−/−R26I-SceI-GR c-Myc25x I-SceI NSPCs. Class 1 genes are actively transcribed in NSPCs but are inactive in B cells. Class 2 genes are actively transcribed in both NSPCs and B cells. Class 3 genes are transcribed in B cells but not in NSPCs. Gene activity [reads per kilobase of transcript per million reads mapped (RPKM) ≥ 0.05] was determined by GRO-seq analysis. Numbers of genes per category are listed. (C and D) Plots showing the relative distance of junctions from Chr12-sgRNA-1–expressing Xrcc4−/−p53−/− NSPCs (C) or ATM−/−R26I-SceI-GR c-Myc25x I-SceI NSPCs (D) to the closest TSS of class 1 (blue trace), class 2 (red trace), and class 3 (black trace) genes. Figures are organized as described in Fig. 1A. (E) Box-and-whiskers plots of the transcription activity (GRO-seq density) of class 1 (Left) and class 2 (Center) genes and genes in class 2 containing HTGTS junctions located within 2 kb of the TSS from Chr12-sgRNA-1–expressing Xrcc4−/−p53−/− NSPCs or ATM−/−R26I-SceI-GR c-Myc25× I-SceI NSPCs (Right). (F) The number of genes in each group in E is indicated. The upper and lower box edges represent the 25th and 75th percentile, respectively; the horizontal line denotes the median. ****P < 0.0001; **P < 0.01 (Mann–Whitney u test).