O6-MeG has an MGMT-independent strand bias towards the non-transcribed strand in expressed genes. (A–H) Gene-specific analysis of O6-MeG distribution in three times 1 mM TMZ-exposed LN-229 WT (A, C, E and G) and LN-229 +MGMT (B, D, F and H) cells with respect to gene expression. O6-MeG abundance was normalized by gene G abundance (A, B, C and D) and corrected by O6-MeG abundance of TMZ-exposed naked DNA (E, F, G and H). (A, B, E and F) O6-MeG abundance compared to gene expression. Left panels show O6-MeG abundance in gene expression tiers in one replicate. The asterisks indicate the average abundance. Right panels show the means of O6-MeG abundance in gene expression tiers of three replicates. (C,D,G andH) Gene-body profiles of O6-MeG abundance. Means and 95% confidence interval of three replicates are shown. TSS: transcription start site. TES: transcription end site. For gene bodies, 5% of the gene length was used as bin size (2.2 kb average) while 2.5 kb bin size was used outside the gene body. (I and J) O6-MeG abundance per gene was normalized by read depth and G abundance and replicates were averaged. Left panels show LN-229 WT and +MGMT while right panels show the difference of LN-229 +MGMT and WT. Analysis was done for all genes (I) or oncogenes only (J).
