Click-code-seq mapping of oxidized guanines in cells exposed to DNMT1 inhibitor GSK-3484862. Click-code-seq mapping of oxidized guanines and abasic sites in plasmids with site-specific DNA modifications.
By relating the numbers of oxidized guanines in different sequence contexts to the abundance of these contexts in the human genome, we observed that the probability of guanine to be or remain oxidized is low if this guanine is preceded by cytosine (CpG sites) compared to other nucleotides. As CpG sites are substrates of epigenetic cytosine methylation, we investigated the influence of cytosine methylation status on guanine oxidation level in CpG sites. For this, we exposed HAP1 and U2OS cells for three days to GSK-3484862, a novel DNA methyltransferase 1 (DNMT1) inhibitor causing the degradation of this enzyme within 24 hours and having low cellular toxicity. Using Infinium MethylationEPIC v2.0 array, we observed a drastic hypomethylation after the exposure in both cell lines such that the peak of highly methylated CpG sites (beta values 0.8–1) found in vehicle (DMSO) exposed cells is absent in GSK-3484862-exposed cells. In contrast, the oxidation level of guanines in the CpG sites profiled by the array did not change in response to the inhibitor and was virtually constant across CpG sites with different methylation levels. In addition, on the level of all CpG sites in the genome, guanine-oxidation did not differ between DMSO and GSK-3484862 exposures. Thus, in CpG sites, guanine oxidation level likely does not depend on cytosine methylation status. As a control for the click-code-seq protocol, we successfully called 8-oxoG incorporated at specific sites in a plasmid (~25 fmol) that was mixed with ~28-times bigger amount of the unmodified vector. As a control for click-code-seq detection of abasic sites, we inserted uracils in a plasmid, converted them to abasic sites by uracil-DNA glycosylase (UDG) and successfully called them in the expected locations. Overall design: Single-nucleotide-resolution genome-wide mapping click-code-seq of guanine oxidation in HAP1 or U2OS wild-type cells exposed to GSK-3484862 or DMSO (vehicle), with each cell line - exposure condition in 3 biological replicates. Single-nucleotide-resolution genome-wide mapping click-code-seq of guanine oxidation in a plasmid with site-specific 8-oxoguanine insertion and a plasmid vector without the insertion; FPG was used to recognize guanine oxidation in plasmid DNA. Single-nucleotide-resolution genome-wide mapping click-code-seq of abasic sites in a plasmid with site-specific uracil insertion and a plasmid vector without the insertion; UDG was used to convert uracils to abasic sites in plasmid DNA.