IMPACTS OF DNA METHYLATION ON H2A.Z DEPOSITION AND NUCLEOSOME STABILITY

ABSTRACT In eukaryotes with DNA methylation, the histone variant H2A.Z and DNA methylation 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 accessibility analyses show that H2A.Z nucleosomes with methylated DNA are more open and accessible compared to their unmethylated counterparts. In Xenopus laevis, H2A.Z preferentially associates with unmethylated DNA in both the fibroblast cell line XTC-2 and sperm pronuclei formed in the transcriptionally silent egg extract. The proportion of H2A.Z that colocalizes with methylated DNA, however, is higher in sperm pronuclei than in XTC-2. By monitoring nucleosome assembly on synthetic DNA constructs in Xenopus egg extracts, we find that the H2A.Z bias for unmethylated substrates is dependent on the SRCAP complex, the major H2A.Z deposition chaperone. Consistently, recruitment of the SRCAP complex to DNA is suppressed by DNA methylation. Altogether, we propose that the SRCAP complex is the major determinant for preferential H2A.Z enrichment on unmethylated DNA, whereas DNA methylation destabilizes DNA wrapping in H2A.Z-containing nucleosomes.