Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications
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eLife assessment
This valuable simulation study proposes a new coarse-grained model to explain the effects of CpG methylation on nucleosome wrapping energy and nucleosome positioning. The evidence to support the claims in the paper looks solid, although the novelty of the findings should be discussed in connection with the previous works. This work will be of interest to the researchers working on gene regulation and mechanisms of DNA methylation.
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Abstract
The majority of vertebrate promoters have a distinct DNA composition, known as a CpG island. Cytosine methylation in promoter CpG islands is associated with a substantial reduction of transcription initiation. We hypothesise that both atypical sequence composition, and epigenetic base modifications may affect the mechanical properties of DNA in CpG islands, influencing the ability of proteins to bind and initiate transcription. In this work, we model two scalar measures of the sequence-dependent propensity of DNA to wrap into nucleosomes: the energy of DNA required to assume a particular nucleosomal configuration and a measure related to the probability of linear DNA spontaneously reaching the nucleosomal configuration. We find that CpG density and modification state can alter DNA mechanics by creating states more or less compatible with nucleosome formation.
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eLife assessment
This valuable simulation study proposes a new coarse-grained model to explain the effects of CpG methylation on nucleosome wrapping energy and nucleosome positioning. The evidence to support the claims in the paper looks solid, although the novelty of the findings should be discussed in connection with the previous works. This work will be of interest to the researchers working on gene regulation and mechanisms of DNA methylation.
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Reviewer #1 (Public Review):
Summary:
In this manuscript, the authors used a coarse-grained DNA model (cgNA+) to explore how DNA sequences and CpG methylation/hydroxymethylation influence nucleosome wrapping energy and the probability density of optimal nucleosomal configuration. Their findings indicate that both methylated and hydroxymethylated cytosines lead to increased nucleosome wrapping energy. Additionally, the study demonstrates that methylation of CpG islands increases the probability of nucleosome formation.
Strengths:
The major strength of this method is that the model explicitly includes elastic constraints on the positions of phosphate groups facing a histone octamer, as DNA-histone binding site constraints. The authors claim that their model enhances the accuracy and computational efficiency and allows comprehensive …
Reviewer #1 (Public Review):
Summary:
In this manuscript, the authors used a coarse-grained DNA model (cgNA+) to explore how DNA sequences and CpG methylation/hydroxymethylation influence nucleosome wrapping energy and the probability density of optimal nucleosomal configuration. Their findings indicate that both methylated and hydroxymethylated cytosines lead to increased nucleosome wrapping energy. Additionally, the study demonstrates that methylation of CpG islands increases the probability of nucleosome formation.
Strengths:
The major strength of this method is that the model explicitly includes elastic constraints on the positions of phosphate groups facing a histone octamer, as DNA-histone binding site constraints. The authors claim that their model enhances the accuracy and computational efficiency and allows comprehensive calculations of DNA mechanical properties and deformation energies.
Weaknesses:
A significant limitation of this study is that the parameter sets for the methylated and hydroxymethylated CpG steps in the cgNA+ model are derived from all-atom molecular dynamics (MD) simulations that suggest that both methylated and hydroxymethylated cytosines increase DNA stiffness and nucleosome wrapping energy (Pérez A, et al. Biophys J. 2012; Battistini, et al. PLOS Comput Biol. 2021). It could predispose the coarse-grained model to replicate these findings. Notably, conflicting results from other all-atom MD simulations, such as those by Ngo T in Nat. Commun. 2016, shows that hydroxymethylated cytosines increase DNA flexibility, contrary to methylated cytosines. If the cgNA+ model was trained on these later parameters or other all-atom force fields, different conclusions might be obtained regarding the effects of methylated and hydroxymethylation on nucleosome formation.
Despite the training parameters of the cgNA+ model, the results presented in the manuscript indicate that methylated cytosines increase both DNA stiffness and nucleosome wrapping energy. However, when comparing nucleosome occupancy scores with predicted nucleosome wrapping energies and optimal configurations, the authors find that methylated CGIs exhibit higher nucleosome occupancies than unmethylated ones, which seems to contradict their findings from the same paper which showed that increased stiffness should reduce nucleosome formation affinity. In the manuscript, the authors also admit that these conclusions "apparently runs counter to the (perhaps naive) intuition that high nucleosome forming affinity should arise for fragments with low wrapping energy". Previous all-atom MD simulations (Pérez A, et al. Biophys J. 2012; Battistini, et al. PLOS Comput Biol. 202; Ngo T, et al. Nat. Commun. 20161) show that the stiffer DNA upon CpG methylation reduces the affinity of DNA to assemble into nucleosomes or destabilizes nucleosomes. Given these findings, the authors need to address and reconcile these seemingly contradictory results, as the influence of epigenetic modifications on DNA mechanical properties and nucleosome formation are critical aspects of their study.
Understanding the influence of sequence-dependent and epigenetic modifications of DNA on mechanical properties and nucleosome formation is crucial for comprehending various cellular processes. The authors' study, focusing on these aspects, will definitely garner interest from the DNA methylation research community. -
Reviewer #2 (Public Review):
Summary:
This study uses a coarse-grained model for double-stranded DNA, cgNA+, to assess nucleosome sequence affinity. cgNA+ coarse-grains DNA on the level of bases and accounts also explicitly for the positions of the backbone phosphates. It has been proven to reproduce all-atom MD data very accurately. It is also ideally suited to be incorporated into a nucleosome model because it is known that DNA is bound to the protein core of the nucleosome via the phosphates.
It is still unclear whether this harmonic model parametrized for unbound DNA is accurate in describing DNA inside the nucleosome. Previous models by other authors, using more coarse-grained models of DNA, have been rather successful in predicting base pair sequence-dependent nucleosome behavior. This is at least the case as far as DNA shape is …
Reviewer #2 (Public Review):
Summary:
This study uses a coarse-grained model for double-stranded DNA, cgNA+, to assess nucleosome sequence affinity. cgNA+ coarse-grains DNA on the level of bases and accounts also explicitly for the positions of the backbone phosphates. It has been proven to reproduce all-atom MD data very accurately. It is also ideally suited to be incorporated into a nucleosome model because it is known that DNA is bound to the protein core of the nucleosome via the phosphates.
It is still unclear whether this harmonic model parametrized for unbound DNA is accurate in describing DNA inside the nucleosome. Previous models by other authors, using more coarse-grained models of DNA, have been rather successful in predicting base pair sequence-dependent nucleosome behavior. This is at least the case as far as DNA shape is concerned whereas assessing the role of DNA bendability (something this paper focuses on) has been consistently challenging in all nucleosome models, to my knowledge.
It is thus of major interest whether this more sophisticated model is also more successful in handling this issue. As far as I can tell the work is technically sound and properly accounts for not only the energy required in wrapping DNA but also entropic effects, namely the change in entropy that DNA experiences when going from the free state to the bound state. The authors make an approximation here which seems to me to be a reasonable first step.
Of interest is also that the authors have the parameters at hand to study the effect of methylation of CpG-steps. This is especially interesting as it allows us to study a scenario where changes in the physical properties of base pair steps via methylation might influence nucleosome positioning and stability in a cell-type-specific way.
Overall, this is an important contribution to the question of how the sequence affects nucleosome positioning and affinity. The findings suggest that cgNA+ has something new to offer. But the problem is complex, also on the experimental side, so many questions remain open.
Strengths:
The authors use their state-of-the-art coarse-grained DNA model which seems ideally suited to be applied to nucleosomes as it accounts explicitly for the backbone phosphates.
Weaknesses:
(1) According to the abstract the authors consider two "scalar measures of the sequence-dependent propensity of DNA to wrap into nucleosomes". One is the bending energy and the other, is the free energy. Specifically in the latter, the authors take the difference between the free energies of the wrapped and the free DNA. Whereas the entropy of the latter can be calculated exactly, they assume that the bound DNA always has the same entropy (independent of sequence) in its more confined state. The problem is the way in which this is written (e.g. below Eq. 6) which is hard to understand. The authors should mention that the negative of Eq. 6 is what physicists call free energy, namely especially the free energy difference between bound and free DNA.
(2) In Eq. 5 the authors introduce penalty coefficients c_i. They write that values are "set by numerical experiment to keep distances ... within the ranges observed in the PDB structure, while avoiding sterical clashes in DNA." This is rather vague, especially since it is unclear to me what type of sterical clashes might occur. Figure 1 shows then a comparison between crystal structures and simulated structures. They are reasonably similar but standard deviations in the fluctuations of the simulation are smaller than in the experiments. Why did the authors not choose smaller c_i-values to have a better fit? Do smaller values lead to unwanted large fluctuations that would lead to steric clashes between the two DNA turns? I also wonder what side views of the nucleosomes look like (experiments and simulations) and whether in this side view larger fluctuations of the phosphates can be observed in the simulation that would eventually lead to turn-turn clashes for smaller c_i-values.
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Reviewer #3 (Public Review):
Summary:
In this study, the authors utilize biophysical modeling to investigate differences in free energies and nucleosomal configuration probability density of CpG islands and nonmethylated regions in the genome. Toward this goal, they develop and apply the cgNA+ coarse-grained model, an extension of their prior molecular modeling framework.
Strengths:
The study utilizes biophysical modeling to gain mechanistic insight into nucleosomal occupancy differences in CpG and nonmethylated regions in the genome.
Weaknesses:
Although the overall study is interesting, the manuscripts need more clarity in places. Moreover, the rationale and conclusion for some of the analyses are not well described.
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