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

Qian Song,Vincent J Cannistraro,John-Stephen Taylor

doi:10.1074/jbc.m110.183178

Qian Song, Vincent J Cannistraro + Show 1 more

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https://doi.org/10.1074/jbc.m110.183178

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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 η 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.

Highlights

Occur at methylated 5Ј-PyCG sites (10 –12)
UV preferentially induces the formation of cyclobutane pyrimidine dimer (CPD) in nucleosomes at sites where the phosphodiester backbone is positioned away from the histone surface and DNA bending is toward the major groove [32, 33]
When DNA containing randomly distributed CPDs is assembled into nucleosomes, the CPDs favor positions away from the surface [37], which is consistent with the 30° bend that they make toward the major grove of DNA [38]

Summary

Introduction

Occur at methylated 5Ј-PyCG sites (10 –12). It has been found that 5-methylcytosine is involved in 25– 40% of sunlight-induced mutations of the cII and lacI transgenes as well as the p53 gene in skin tumors and that CPDs are responsible for a significant fraction of these mutations [6, 13]. The frequency of C to T and CC to TT mutations will depend, on the rate of formation of C-containing dimers, their rate of repair, deamination, and bypass by polymerases All of these processes are expected to be modulated by sequence context, protein interactions, as well as the secondary and tertiary structure of DNA. UV preferentially induces the formation of CPDs in nucleosomes at sites where the phosphodiester backbone is positioned away from the histone surface and DNA bending is toward the major groove [32, 33]. In an earlier study with a 5S rRNA gene, no correlation was observed with rotational positioning of the CPD [45]

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