Cytosine Methylation Enhances DNA Condensation Revealed by Equilibrium Measurements Using Magnetic Tweezers

Abstract

CpG methylation of DNA is common in mammalian cells. In sperm, the DNA has the highest level of CpG methylation and is condensed into toroidal structures. How CpG methylation affects DNA structures and interactions is important to understand its biological roles but is largely unknown. Using an RNA−DNA−RNA structure, we observed the equilibrium hopping dynamics between the condensed and extended states of DNA in the presence of polyamines or polylysine peptide as a reduced model of histone tails. Combing with the measured DNA elasticities, we report that CpG methylation of each cytosine nucleotide substantially increases DNA−DNA attraction by up to 0.2 k B T. For the DNA with 57% GC content, the relative increase caused by CpG methylation is up to 32% for the spermine-induced DNA−DNA attraction and up to 9% for the polylysine-induced DNA−DNA attraction. These findings help us to evaluate the energetic contributions of CpG methylation in sperm development and chromatin regulation.

A molecular view of DNA flexibility

“…Finally, cytosine methylation has also been studied in the context of DNA condensation by polycations, the phenomenon by which highly positively charged ions mediate DNA compaction by stabilizing inter-helical interactions (Bloomfield, 1997). smFRET, MT, and MD simulations coincide that cytosine methylation enhances DNA condensation (Yoo et al ., 2016; Kang et al ., 2018; Yang et al ., 2020). Importantly, this effect appears consistent when using different condensing polycations (spermidine 3+ , CoHex 3+ , spermine 4+ , and polylysine 6+ ), and DNA sequences.…”

Cytosine methylation regulates DNA bendability depending on the curvature

“…17 Recently, due to the importance of the effect of methylation on nucleosome structure, the modulation of dsDNA bendability by methylation has been extensively studied. [18][19][20][21][22][23][24][25] The increment of the looping time of methylation-mediated dsDNA, i.e., the increase in the stiffness of dsDNA, was observed by DNA cyclization kinetic measurements. 18,19 In line with these results, an increase in the persistence length of dsDNA was observed by atomic force microscopy (AFM).…”

“…However, the functions of methylation in the stability of nucleosomes and chromatin remodeling are still unclear. 17 Recently, due to the importance of the effect of methylation on nucleosome structure, the modulation of dsDNA bendability by methylation has been extensively studied [18][19][20][21][22][23][24][25] . The increment of the looping time of methylation-mediated dsDNA, i.e., the increase in the stiffness of dsDNA, was observed by DNA cyclization kinetic measurements.…”

N,N,N’,N’-Tetramethylethylenediamine-Enabled Photoredox-Catalyzed C–H Methylation of N-Heteroarenes

“…Methylation is a fundamentally important transformation in both biological systems and medicinal chemistry . In biology, the modification by introducing a methyl group plays a vital role in impacting gene expression and mammalian embryo development . Pharmaceutical sciences leverage this “magic methyl effect” to improve solubility, bioavailability, and metabolism of drug molecules .…”