Fig. 6. Sequence-level distribution of oxidized thymines in permanganate-treated human cells.

(A) Trinucleotide sequence specificity. Forty-eight trinucleotide contexts were analyzed, but the gapped reads occurred chiefly at trinucleotides with central thymine. Different enzymes (Endo III and NEIL1 in combination and alone) were used to excise the oxidized bases. (B) Sequence context of thymine oxidation by permanganate using logo plot analysis. Position 11 represents the permanganate-oxidized thymine base. At each base position, the height of each letter represents the relative frequency of that nucleic acid base. Note the enrichment of A or C 3′ to the thymine.