Histones and Their Role in Activating DNA Replication Origins

DNA replication is a tightly regulated process that ensures the precise duplication of the genome during cell proliferation. Replication is initiated in the genome at specific loci called origins. The human genome contains tens of thousands of origins; however, only about 10% of them are used in each cell cycle. In a study published yesterday in Nature, researchers showed that the histone variant H2A.Z facilitates the licensing and activation of early DNA replication origins.

In eukaryotes, DNA wraps around histone octamers to form chromatin in the nucleus. Certain features of chromatin, along with the DNA sequence, regulate the licensing and activation of replication origins. However, the chromatin-based regulatory mechanisms remain largely uncharacterized.

In this study, the scientists found that knocking down H2AFZ genes in HeLa cells results in cell growth defects. Through mass spectrometry, many subunits of the pre-replication complex were enriched on H2A.Z mono-nucleosomes, indicating that H2A.Z may be involved in the licensing of DNA replication origins.

To find the mechanism of interaction between H2A.Z and the pre-replication complex, the scientists then performed in vitro biochemical analysis and found that H2A.Z-containing nucleosomes bind directly to the histone lysine methyltransferase enzyme SUV420H1. This process promotes H4K20me2 deposition, which further recruits origins recognition complex 1 (ORC1) to help accomplish the licensing of DNA replication origins.

In addition, through genome-wide studies in HeLa cells, the scientists confirmed the role of H2A.Z in DNA replication. The results showed that signals from H4K20me2, ORC1, and nascent DNA strands (indicating active DNA replication origins) co-localize with H2A.Z and that the depletion of H2A.Z results in decreased H4K20me2, ORC1, and nascent-strand signals. H2A.Z-regulated replication origins have a higher firing efficiency and earlier replication timing compared with other origins.

Furthermore, the scientists generated CD4CreH2A.Zf/f mice to study the function of H2A.Z-regulated replication in a more physiological context. Using these mice, they conditionally knocked out (CKO) H2az1/H2az2 in T cells. They then found that in H2A.Z CKO mice, the activated T cells have defects in cell proliferation and DNA replication.

This study describes a novel epigenetic regulation mechanism for DNA replication origin selection and offers a new way of understanding DNA replication regulation in eukaryotes. Importantly, this regulatory pathway can potentially serve as a target for cancer treatment and regulation of T cell function during immunotherapy.

Image: Origin selection: H2A.Z nucleosomes bind Suv420H1 directly to establish H4K20me2 on chromatin, which then recruits ORC1 to bind to replication origins; Origin firing: H2A.Z-Suv420H1-H4K20me2-ORC1 axis selectively license and activate early replication origins. Image courtesy of Dr. Li Guohong's lab.