Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis

Abstract

The histone variant H2A.Z has been implicated in the regulation of gene expression, and in plants antagonizes DNA methylation. Here, we ask whether a similar relationship exists in mammals, using a mouse B-cell lymphoma model, where chromatin states can be monitored during tumorigenesis. Using native chromatin immunoprecipitation with microarray hybridization (ChIP-chip), we found a progressive depletion of H2A.Z around transcriptional start sites (TSSs) during MYC-induced transformation of pre-B cells and, subsequently, during lymphomagenesis. In addition, we found that H2A.Z and DNA methylation are generally anticorrelated around TSSs in both wild-type and MYC-transformed cells, as expected for the opposite effects of these chromatin features on promoter competence. Depletion of H2A.Z over TSSs both in cells that are induced to proliferate and in cells that are developing into a tumor suggests that progressive loss of H2A.Z during tumorigenesis results from the advancing disease state. These changes were accompanied by increases in chromatin salt solubility. Surprisingly,~30% of all genes showed a redistribution of H2A.Z from around TSSs to bodies of active genes during the transition from MYC-transformed to tumor cells, with DNA methylation lost from gene bodies where H2A.Z levels increased. No such redistributions were observed during MYC-induced transformation of wild-type pre-B cells. The documented role of H2A.Z in regulating transcription suggests that 30% of genes have the potential to be aberrantly expressed during tumorigenesis. Our results imply that antagonism between H2A.Z deposition and DNA methylation is a conserved feature of eukaryotic genes, and that transcription-coupled H2A.Z changes may play a role in cancer initiation and progression.

Histone variants in pluripotency and disease

“…A greater understanding of the role of macroH2A in cancer progression might provide a diagnostic tool for deciding therapeutic strategies. Work in Arabidopsis has demonstrated the mutual antagonism between DNA methylation and H2A.Z occupancy, with this pattern also being observed in normal mammalian cells and during tumorigenesis (Zilberman et al, 2008;Conerly et al, 2010). Although the mechanism behind this interdependence is unclear, loss of H2A.Z at tumor suppressor genes could lead to DNA methylation and heritable repression, consistent with the observation that deposition of H2A.Z is required for the full reactivation of silent genes following 5-AzaC treatment (Yang et al, 2012).…”

Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer

“…One of these examined genome-wide DNA methylation in the same genetically driven Eµ-Myc mouse model of Burkitt lymphoma used in our current study. 31 Robust promoter CpG island DNA hypermethylation of individual genes was not described, but rather only a trend toward increasing promoter CpG island DNA hypermethylation could be discerned when data for all genes were analyzed in aggregate. A separate study in Eµ-Myc mice demonstrated a modest increase in DNA methylation by transgenic expression of DNMT3B7, a truncated isoform of DNA methyltransferase 3B that has been found in human cancer cells.…”

Basic concepts of epigenetics

“…The unstable dimer is collapsible, highly acetylated and enables chromatin expansion and nucleosome ejection at areas of unmethylated DNA targeted for active expression. 89 Unstable histone variants such as H2A.Z most often coincide with transcription start sites 90,91 and are highly concentrated in euchromatin marked with acetylated H3K9, H3K18, H3K27 and H4 tails circumscribing open 5' promoter regions of genes. 92,93 While methylation of histone tails is primarily associated with silencing, triple methylation at H2AR at serine residues within the H3 tail by enzymes such as PRMT5 are also associated with H2A.Z core exchange, unit collapse, nucleosomal ejection and active gene expression.…”