DNA methylation cues in nucleosome geometry, stability, and unwrapping

Abstract

Cytosine methylation at the 5-carbon position is an essential DNA epigenetic mark in many eukaryotic organisms. Although countless structural and functional studies of cytosine methylation have been reported in both prokaryotes and eukaryotes, our understanding of how it influences the nucleosome assembly, structure, and dynamics remains obscure. Here we investigated the effects of cytosine methylation at CpG sites on nucleosome dynamics and stability. By applying long molecular dynamics simulations (five microsecond long trajectories, 60 microseconds in total), we generated extensive atomic level conformational full nucleosome ensembles. Our results revealed that methylation induces pronounced changes in geometry for both linker and nucleosomal DNA, leading to a more curved, under-twisted DNA, shifting the population equilibrium of sugar-phosphate backbone geometry. These conformational changes are associated with a considerable enhancement of interactions between methylated DNA and the histone octamer, doubling the number of contacts at some key arginines. H2A and H3 tails play important roles in these interactions, especially for DNA methylated nucleosomes. This, in turn, prevents a spontaneous DNA unwrapping of 3-4 helical turns for the methylated nucleosome with truncated histone tails, otherwise observed in the unmethylated system on several microsecond time scale.

Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility

“…First, as shown in Figures 1d and 1f, in both canonical and variant systems one DNA end unwraps, while another end stays more bound to a histone octamer. Indeed, previous single-molecule FRET experiments and MD simulations have demonstrated that the DNA unwrapping occurred asymmetrically and DNA unwrapping at one side stabilized the DNA end on the other side (29)(30)(31). Moreover, we observe the difference in terms of the degree of unwrapping for both DNA ends that can be related to the asymmetry of our nucleosomal DNA sequence with respect to the dyad position.…”

“…In the first section, we showed that DNA ends of H2A.Z-containing nucleosomes are more mobile and are easier to unwrap from the histone octamer when compared to nucleosomes containing canonical H2A. It has been reported earlier that H3 N-terminal and H2A C-terminal tails mediated the unwrapping of DNA ends in nucleosomes (30,31,37-41). Consistent with these findings, we show that the degree of DNA unwrapping is anti-correlated with the number of contacts between the H2A.Z C-terminal tail and the outer DNA region (Figure 2a, see Supplementary Figure S5 for definitions of DNA regions).…”

“…Second, we find that the overall DNA unwrapping from both ends is significantly enhanced in H2A.Z (up to 40 bps unwrapped in total from both ends) compared to canonical H2A nucleosomes (up to 18 bps from both ends) (Figure 1b). Previous microsecond long simulations and quantitative modeling showed that canonical nucleosomes exhibited spontaneous DNA unwrapping only for systems without histone tails (30-32). The roles of histone tails in DNA unwrapping will be discussed in the next sections.…”

Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility

“…1b, c, in both canonical and variant systems one DNA end unwraps, while another end stays bound to a histone octamer. Previous single-molecule FRET experiments and MD simulations demonstrated that DNA unwrapping indeed occurred asymmetrically and DNA unwrapping at one side stabilized the DNA end on the other side [31][32][33] . Moreover, we observe the difference in terms of the degree of unwrapping for both DNA ends that can be related to the asymmetry of our nucleosomal DNA sequence with respect to the dyad position.…”

Phase Separation and Correlated Motions in Motorized Genome

“…For example, acetylation could neutralize the positive charges on histone tails to weaken their binding with DNA, [34][35][36][37] while methylation may lead to under-twisted DNA that strengthens its interactions with histones. 38,39 It's conceivable that nucleosomes with similar histone marks share more favorable interactions, driving their separation from other differentially modified ones. On the other hand, chromatin regulators associated with specific histone marks often contain intrinsically disordered regions that exhibit multivalent interactions to undergo liquid-liquid phase separation themselves.…”