CpG islands shape the epigenome landscape.

Epigenetic modifications and nucleosome positioning play an important role in modulating gene expression. However, how the patterns of epigenetic modifications and nucleosome positioning are established around promoters is not well understood. Here, we have addressed these questions in a series of genome-wide experiments coupled to a novel bioinformatic analysis approach. Our data reveal a clear correlation between CpG density, promoter activity and accumulation of active or repressive histone marks. CGI boundaries define the chromatin promoter regions that will be epigenetically modified. CpG-rich promoters are targeted by histone modifications and histone variants, while CpG-poor promoters are regulated by DNA methylation. CGIs boundaries, but not transcriptional activity, are essential determinants of H2A.Z positioning in vicinity of the promoters, suggesting that the presence of H2A.Z is not related to transcriptional control. Accordingly, H2A.Z depletion has no impact on gene expression of arrested mouse embryonic fibroblasts. Therefore, the underlying DNA sequence, the promoter CpG density and, to a lesser extent, transcriptional activity, are key factors implicated in promoter chromatin architecture. We have generated genome-wide ChIP-seq and MeDIP-seq for the following main epigenetic marks: H2A.Z, H3.3, H3K4me1, 5mC and 5hmC in mouse embryonic fibroblasts (MEFs). We also measured the impact of H2A.Z depletion on gene transcription of arrested MEFs. We derived MEFs from our mouse cKO H2A.Z-1flox/flox : H2A.Z-2flox/flox lines and grew them until confluency to reach the G0 phase of the cell cycle. This allows to dissociate the role of H2A.Z from its implication in replication. H2A-Z.1flox/flox : H2A-Z.2flox/flox MEFs were infected with control adenovirus or adenovirus expressing Cre recombinase to generate control (WT) or double KO (dKO) cell lines.