Mutation Bias, rather than Binding Preference, Underlies the Nucleosome-Associated G+C% Variation in Eukaryotes

The effects of genetic content on epigenetic status have been extensively studied, but how epigenetic status affects genetic content is not well understood. As a key epigenetic factor the nucleosome structure is highly correlated with local G+C% in eukaryotic genomes. The prevailing explanation to the pattern is that nucleosome occupancy favors higher G+C% sequences more than lower G+C% sequences. However, recent observation of a biased mutation spectrum caused by nucleosome occupancy suggests that the higher G+C% of nucleosomal DNA might be the evolutionary consequence of nucleosome occupancy. To distinguish the two explanations, we examined data from an in vitro nucleosome reconstitution experiment in which histones are incubated with yeast Saccharomyces cerevisiae and Escherichia coli genomic DNA, the former has been shaped by nucleosome structure while the latter has not. There is a strong positive correlation between nucleosome density and G+C% for the yeast DNA, an observation consistent with in vivo data, and such a pattern nearly vanishes for E. coli genomic DNA, suggesting that biased mutation, rather than biased occupancy, explains the most nucleosome-associated G+C% variation in eukaryotic genomes.