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

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. Overall design: CUT&Tag-bisulfite sequencing (Li et al. 2021; https://doi.org/10.1016/j.crmeth.2021.100118) on H3 and H2A.Z in Xenopus laevis sperm pronuclei incubated in interphase-cycled Xenopus egg extract as well as XTC-2 cells (a Xenopus laevis fibroblast cell line).