Relations between clusters of oxidatively damaged nucleotides and active or open nucleosomes in the rat Nth 1 gene

The distribution of oxidative damage to bases such as 8-hydroxyguanine (8-OH-Gua), was determined at the nucleotide level of resolution using the ligation-mediated PCR technique. Administration of a renal carcinogen, ferric nitrilotriacetate (Fe-NTA), is known to induce oxidative stress and subsequent formation of 8-OH-Gua in the kidney. Whole genomic DNA was isolated from the rat kidney with or without Fe-NTA treatment and then digested with formamidopyrimidine-DNA glycosylase (Fpg). As a target, we focused on the gene of a DNA repair enzyme for thymine glycol, Nth 1. Cleaved signals were found in exon 1 and exon 3, but not exon 5. Nucleosomes in these regions, enriched in damaged nucleotides, were highly accessible to micrococcal nuclease, especially in the kidney. Taking into account the function of the protein segment encoded by these regions, we discussed the molecular mechanism of the restricted formation of the damaged nucleotides.