Loss of Ezh2 function remodels the DNA replication initiation landscape

• Published in: Cell reports (Cambridge) 2023-04, Vol.42 (4), p.112280-112280, Article 112280
• Main Authors: Prorok, Paulina, Forouzanfar, Faezeh, Murugarren, Nerea, Peiffer, Isabelle, Charton, Romain, Akerman, Ildem, Méchali, Marcel
• Format: Article
• Language: English
• Subjects: bivalent promoters; chromatin; CP: Molecular biology; DNA replication initiation; DNA replication origins; EZH2 knockout; H3K27me3; polycomb; PRC2; SNS-seq
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2023.112280

In metazoan cells, DNA replication initiates from thousands of genomic loci scattered throughout the genome called DNA replication origins. Origins are strongly associated with euchromatin, particularly open genomic regions such as promoters and enhancers. However, over a third of transcriptionally silent genes are associated with DNA replication initiation. Most of these genes are bound and repressed by the Polycomb repressive complex-2 (PRC2) through the repressive H3K27me3 mark. This is the strongest overlap observed for a chromatin regulator with replication origin activity. Here, we asked whether Polycomb-mediated gene repression is functionally involved in recruiting DNA replication origins to transcriptionally silent genes. We show that the absence of EZH2, the catalytic subunit of PRC2, results in increased DNA replication initiation, specifically in the vicinity of EZH2 binding sites. The increase in DNA replication initiation does not correlate with transcriptional de-repression or the acquisition of activating histone marks but does correlate with loss of H3K27me3 from bivalent promoters. [Display omitted] •Polycomb-repressed promoters are hotspots for DNA replication initiation•EZH2−/− cells display a substantial increase in replication initiation at repressed promoters•Increased replication initiation does not correlate with de novo H3K27ac or transcription•Instead, replication initiates at sites of H3K27me3 loss and increased open chromatin Most promoters repressed by the Polycomb group of proteins also harbor DNA replication initiation in pluripotent stem cells. Prorok et al. find that EZH2 loss of function leads to marked increase in DNA replication initiation at these repressed promoters with loss of H3K27me3, irrespective of the activating histone H3K27ac mark or transcription.