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Impacts of DNA methylation on H2A.Z deposition and nucleosome stability

ABSTRACT: DNA methylation and the histone variant H2A.Z are maintained in mutually exclusive sections of the genome. How this antagonism is established, however, remains an open question. Here, we examined the impacts of DNA methylation on both the intrinsic stability of H2A.Z nucleosomes and chaperone-mediated H2A.Z deposition. Cryo-EM and endonuclease-based assays show that H2A.Z nucleosomes on methylated DNA substrates are more open and accessible compared to their unmethylated counterparts. In Xenopus, H2A.Z preferentially associates with unmethylated DNA of both sperm pronuclei in the transcriptionally silent egg extract as well as in somatic cells, though a substantial proportion of H2A.Z colocalizes with DNA methylation in sperm pronuclei. By monitoring nucleosome assembly on synthetic DNA constructs in egg extract, we find that the H2A.Z bias for unmethylated substrates is dependent on the SRCAP complex. Accordingly, DNA-binding of SRCAP is suppressed by DNA methylation. Altogether, we propose that the SRCAP complex is the major determinant for preferential H2A.Z enrichment on unmethylated DNA, and that DNA methylation destabilizes DNA wrapping in H2A.Z-containing nucleosomes.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE295057 | GEO | 2025/10/28

REPOSITORIES: GEO

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Project description:Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted high-throughput nucleosome reconstitution experiments on 572 KB of human DNA and 668 KB of mouse DNA that was unmethylated or methylated in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes. The DNA loci from both species contained the genes that encode the serum albumin family, the MYC protein, and the tumor suppressor p53. The results demonstrated that a small subset of nucleosomes positioned by nucleotide sequence was sensitive to methylation where the modification increased the affinity of these sequences for the histone octamer. The features that distinguished these nucleosomes from the bulk of the methylation-insensitive nucleosomes were an increase in the frequency of CpG dinucleotides and a unique rotational orientation of CpGs such that their minor grooves tended to face toward the histones in the nucleosome rather than away. We propose that these features serve to enhance the affinity of methylated DNA for the histone octamer and that this effect could be involved in gene regulatory mechanisms such as silencing. These methylation-sensitive nucleosomes were preferentially associated with exons as compared to introns while unmethylated CpG islands near transcription start sites became enriched in nucleosomes upon methylation. The results of this study suggest that the effects of DNA methylation on nucleosome stability in vitro can recapitulate what has been observed in the cell and provide a direct link between DNA methylation and the structure and function of chromatin. For the human data, there were 3 unmethylated nucleosome replicates, 2 methylated nucleosome replicates, an unmethylated MNase control, and an unmethylated sonicated control. For the mouse data, there were 2 unmethylated nucleosome replicates, 2 methylated nucleosome replicates, an unmethylated MNase control, a methylated MNase control, and an unmethylated sonicated control.

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Impacts of DNA methylation on H2A.Z deposition and nucleosome stability

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