DNA damage reflected in the evolution of G-runs in genomes

DNA oxidation is one of the main types of damage to the genetic material of living organisms. Of the many dozens of oxidative lesions, the most abundant is 8-oxoguanine (8-oxoG), a premutagenic base that leads to G→T transversions during replication. Double-stranded DNA can conduct holes through the π system of stacked nucleobases. Such electron vacancies are ultimately localized at the 5'-terminal nucleotides of polyguanine runs (G-runs), making these positions characteristic sites of 8-oxoG formation. While such properties of G-runs have been studied in vitro at the level of chemical reactivity, the extent to which they can influence mutagenesis spectra in vivo remains unclear. Here, we have analyzed the nucleotide context of G-runs in a representative set of 62 high-quality prokaryotic genomes and in the human telomere-to-telomere genome. G-runs were, on average, shorter than polyadenine runs (A- runs), and the probability of a G-run being elongated by one nucleotide is lower than in the case of A-runs. The representation of T in the position 5'-flanking G-runs is increased, especially in organisms with aerobic metabolism, which is consistent with the model of preferential G→T substitutions at the 5'-position with 8-oxoG as a precursor. Conversely, the frequency of G and C is increased and the frequency of T is decreased in the position 5'-flanking A- runs. A biphasic pattern of G-run expansion is observed in the human genome: the probability of sequences longer than 8-9 nucleotides being elongated by one nucleotide increases significantly. An increased representation of C in the 5'-flanking position to long G-runs was found, together with an elevated frequency of 5'-G→A substitutions in telomere repeats. This may indicate the existence of mutagenic processes whose mechanism has not yet been characterized but may be associated with DNA polymerase errors during replication of the products of further oxidation of 8-oxoG.