Fig. 2: No evidence of de novo transcription at DSBs.
From: Transcriptional repression facilitates RNA:DNA hybrid accumulation at DNA double-strand breaks
a, Genomic tracks (hg19) of ChIP-seq against RNAPII CTD phosphorylation on serine 5 (S5P) (3E8 or D9NI antibodies), serine 7 (S7P), tyrosine 1 (Y1P) and serine 2 (S2P) (3E10 or E1Z3G antibodies) before and after DSB induction on two TC-DSBs (DSB 379 and DSB 526). b, Average profile of ChIP-seq against RNAPII phosphorylated forms at silent and TC-DSBs. c, Quantification of ChIP-seq signal of RNAPII CTD phosphorylations at silent (n = 15) and TC-DSBs (n = 65) on a ±500 bp window around DSBs. Centre line shows the median; box limits show first and third quartiles; whiskers show maximum and minimum without outliers; points indicate outliers. P values were calculated using paired two-sided nonparametric Wilcoxon tests. d, Genomic tracks (hg19) of BLESS and TTchem-seq signal at silent and TC-DSBs before (−DSB) and after DSB induction. e, Average profile of TTchem-seq signal at silent and TC-DSBs. The signal was oriented according to gene directionality. f, Quantification of TTchem-seq on a ±500-bp window around silent (n = 15) and TC-DSBs (n = 65). Centre line shows median; box limits show first and third quartiles; whiskers show maximum and minimum without outliers; points indicate outliers. P values were calculated using paired two-sided nonparametric Wilcoxon tests. g, Average profile of TTchem-seq signal on damaged and control genes in −DSB and +DSB conditions. h, Quantification of TTchem-seq signal at damaged (n = 76) and control (n = 73) genes. Centre line shows median; box limits show first and third quartiles; whiskers show maximum and minimum without outliers; points indicate outliers. P values were calculated using paired two-sided nonparametric Wilcoxon tests. i, Genomic tracks (hg19) of ChIP-seq against SPT5 in −DSB and +DSB conditions at two TC-DSBs as in a. j, Average profile of SPT5 ChIP-seq signal on damaged and control genes in −DSB and +DSB conditions.
