Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations
Figure 4
Examples of predicted impact of methylation on gene activity.
(A) Predicted impact of methylation on the accessibility of transcription factors. The black line corresponds to the experimental population of nucleosomes (data from Deniz et al. [45]) in a portion of the yeast XV chromosome (close to the putative transcription start site of a gene, located at base pair 201879). The blue line represents the theoretical nucleosome probability, predicted from the elastic deformation energy for un-methylated DNA, and the red line shows the resulting nucleosome probability after CpG methylation. A vertical box highlights the binding position of the ABF1 transcription factor. (B) Example of the impact of methylation in nucleosome phasing. The blue line corresponds to the probability to wrap a nucleosome in a region of yeast chromosome VIII, where we have experimentally detected a stable nucleosome (Deniz et al. [45]) next to the PHD1 recognition box. The red line illustrates the nucleosome probability profile found when the sequence is methylated. We have depicted the associated change in translational positioning in the cartoons embedded in the figure: minor groove facing the histones in green, major groove facing the histones in red, and the PHD1 recognition box as yellow balls.