Extended Data Fig. 7: DNA damage-induced coding strand bias detection control, related to Fig. 4.
From: Genome-wide RNA polymerase stalling shapes the transcriptome during aging
a, Bar diagram representing the coding strand bias in total RNAPII ChIP-seq data 1 hour and 6 hours after irradiating MCF7 cells with 55 J/m2 UVB (data from76). All genes (n = 18224), short genes (10–22 kb) and long genes (>110 kb). Data are mean ± SEM. Note that the strand bias is only present in MCF7 cells 1 hour after UVB treatment, when RNAPII is still stalled on DNA lesions and DNA repair is ongoing. After 6 hours, most of the stalled RNAPII has been removed from the DNA lesions. This shows that i) the protocol used is able to detect a bias towards the coding strand and therefore can be used to analyze aging samples, ii) the coding strand bias is a transient phenotype after UVB. Based on published amounts of coding strand bias after a known UVC-induced DNA lesion density38, we estimate that livers from wildtype aged mice display a coding strand bias fraction in the range of 0.05–0.10. b–f, Mean local DNA methylation coverage (b) and (c–f) local nucleotide composition status in template strands of 50 genes with that exhibit the highest coding strand bias in general. The intragenic intronic region is chosen with the highest coding strand bias (high strand bias loci). This loci gene set is compared t i) random selected intragenic loci of similar size: 6 times 50 random intronic locations in the template strand, and ii) the complete intronic transcriptome; all introns from transcriptome (including high strand bias locations). Average of n = 50 / group shown. Data are mean ± SD.
