Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations
Figure 3
Methylated and non-methylated DNA elastic deformation energies.
(A) Distribution of deformation energies for 147 bp-long random DNA sequences with CpG steps positioned every 10 base steps (one helical turn) in minor (red and dark red) and major (light and dark blue) grooves respectively. The energy values were rescaled by the slope of a best-fit straight line of figure 2, which is 0.23, to map the elastic deformation energies to ΔΔG. Methylation of the DNA causes a higher energetic cost for nucleosome formation, especially when the MeCpG steps are positioned in the minor groove facing the histones (dark red). (B) Correlation between the additional energetic cost due to methylation (〈EMeth〉-〈E〉, kJ/mol) to form a nucleosome and the phasing of CpG steps respect to the histone (the zero is the reference phase position in which the CpG minor groove directly faces the histones). The cartoons illustrate two extreme positions of the methyl groups with respect to the histone core, which translate into a change in the rotational phase: the position of the methyl group, pointing to the solvent in 0 (red dot) and to the histones in 5 (blue dot).