Methylation-Dependent DNA Condensation: Its Implications in Chromosome Organization and Epigenetic Gene Control

Abstract

The methylation of CpG sites on genome has been known to play a crucial role in epigenetic gene regulation. We hypothesize that the C5 methyl group modulates the attractive interaction between double stranded DNAs in the presence of biogenic polyamines like spermine and poly-lysine. We designed a set of experiments with sequence-controlled and chemically modified DNAs to test the hypothesis. We made dsDNAs that have TA-rich, CG-rich, CpG-methylated (mCG) - rich, or UA-rich sequence and measured their propensity to form aggregates by precipitation and ensemble FRET measurements. In the presence of spermine, TA-rich or mCG-rich dsDNAs, both having the C5methyl group on T or mC, exhibited significantly stronger affinity than CG-rich or UA-rich ones that do not contain the methyl group. Similar trend was observed in the presence of hexa-lysine, which models the lysine-rich histone tails. These results suggest the critical role of the additional methyl group in determining the attractive potential between dsDNAs. From multi-color single molecule FRET measurements on vesicle-encapsulated pairs of dsDNAs, we found that the DNA binding dynamics is temporally anti-correlated with the DNA bending dynamics, consistent with the methylation-dependent DNA looping previously observed. From all-atom molecular dynamics simulations, we propose the physical mechanism for the methylation-dependent attraction based on the steric repulsion of polyamines by the C5 methyl group. Our findings suggest plausible explanations for the physical origin of the chromosome arrangement and its epigenetic modulation.