Rotational Position of a 5-Methylcytosine-containing Cyclobutane Pyrimidine Dimer in a Nucleosome Greatly Affects Its Deamination Rate

Abstract

C to T mutation hotspots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. These mutations are proposed to arise from the insertion of A by DNA polymerase opposite the T that results from deamination of the methylC ( m C) within the CPD. Although the frequency of CPD formation and repair is modestly modulated by its rotational position within a nucleosome, the effect of position on the rate of m C deamination in a CPD has not been previously studied. We now report that deamination of a T m C CPD whose sugar phosphate backbone is positioned against the histone core surface decreases by a factor of 4.7, whereas that of a T m C CPD positioned away from the surface increases by a factor of 8.9 when compared with unbound DNA. Because the m Cs undergoing deamination are in similar steric environments, the difference in rate appears to be a consequence of a difference in the flexibility and compression of the two sites due to DNA bending. Considering that formation of the CPD positioned away from the surface is also enhanced by a factor of two, a T m CG site in this position might be expected to have up to an 84-fold higher probability of resulting in a UV-induced m C to T mutation than one positioned against the surface. These results indicate that rotational position may play an important role in the formation of UV-induced C to T mutation hotspots, as well as in the mutagenic mechanism of other DNA lesions.

Modulation of cyclobutane thymine photodimer formation in T11-tracts in rotationally phased nucleosome core particles and DNA minicircles

“…This is different from what has previously been observed for non-T-tract sequences, where the maximum of CPD formation and HO· cleavage closely coincided (11,29). The frequency of CPD formation in these sequences was found to correlate with the amplitude of nucleotide motion as inferred from temperature factors of the nucleotides in the crystal structures of nucleosomes.…”

UV wavelength-dependent DNA damage and human non-melanoma and melanoma skin cancer

“…The deamination reaction is then followed by ‘correct’ lesion bypass during DNA replication by DNA polymerase eta. We and others have provided evidence that the second pathway, the deamination bypass pathway, may play an important role in UVB mutagenesis in mammalian cells [45, 64, 74–76]. …”

Photoinduced Damage to Cellular DNA: Direct and Photosensitized Reactions†

“…The situation might be more complex in cellular DNA where binding of specific proteins was found to decrease the deamination rate (77) while the presence of a 5¢-end G enhances the reaction (78). Deamination of 5mCyt containing CPDs is also greatly modulated by rotational positioning in nucleosomes (79).…”