Extended Data Fig. 1: RNAPII levels at DSBs and control loci.
From: Transcriptional repression facilitates RNA:DNA hybrid accumulation at DNA double-strand breaks
(a) Distribution of 80 best AsiSI-induced DSBs. There are 15 ‘silent’ DSBs (which comprise intergenic DSBs and DSBs falling within transcriptionally silent genes) and 65 TC-DSBs (top panel). Most TC-DSBs fall within 1 kb of the TSS (88%, bottom left panel) and are distributed across promoters, exons and introns (respectively 41, 25 and 34%, bottom right panel). (b) Average profile and heatmap of BLESS signal after break induction on −/+ 5 kb around silent and TC-DSBs. (c) Average profile and heatmap of RNAPII ChIP-seq signal (using 405 A and D8L4Y antibodies) on all genes −/+ 2 kb (scaled read count). (d) Browser tracks (hg19) of RNAPII ChIP-seq (using 405 A and D8L4Y antibodies) before (-DSB) and after DSB induction (+DSB) and Log2 fold change ratio (+DSB/-DSB) at the CDKN1A (encoding p21) DDR gene. (e) Average profile and heatmap of RNAPII ChIP-seq signals (using 405 A and D8L4Y antibodies) on −/+ 5 kb around silent and TC-DSBs (scaled read count). (f) Average profile and heatmap of RNAPII ChIP-seq signals (using 405 A and D8L4Y antibodies) on −/+ 5 kb around the 80 best DSBs classified according to RNAPII level before breakage (high, medium, low). (g) Quantification of RNAPII ChIP-seq signals on a −/+ 1 kb window around DSBs in exons (n = 19) or introns (n = 26). Centre line: median; Box limits: 1st and 3rd quartiles; Whiskers: Maximum and minimum without outliers; Points: outliers. P values, paired two-sided nonparametric Wilcoxon tests. (h) Genomic tracks (hg19) of RNAPII ChIP-seq and RNA-seq Log2 fold change ratio +DSB/-DSB at a TC-DSB in the RBMXL1 gene (DSB 526). Source numerical data are available in source data.
