Viral remodeling of the 4D nucleome

The dynamic spatial organization of genomes across time, referred to as the four-dimensional nucleome (4DN), is a key component of gene regulation and biological fate. Viral infections can lead to a reconfiguration of viral and host genomes, impacting gene expression, replication, latency, and oncogenic transformation. This review provides a summary of recent research employing three-dimensional genomic methods such as Hi-C, 4C, ChIA-PET, and HiChIP in virology. We review how viruses induce changes in gene loop formation between regulatory elements, modify chromatin accessibility, and trigger shifts between A and B compartments in the host genome. We highlight the central role of cellular chromatin organizing factors, such as CTCF and cohesin, that reshape the 3D structure of both viral and cellular genomes. We consider how viral episomes, viral proteins, and viral integration sites can alter the host epigenome and how host cell type and conditions determine viral epigenomes. This review consolidates current knowledge of the diverse host-viral interactions that impact the 4DN. This research examines how viruses can change the 3D structure of host DNA, focusing on the role of CTCF and cohesin proteins in altering both viral and cellular 3D DNA structures. The scientists used various techniques, including chromosome conformation capture and next-generation sequencing, to study the 3D structure of both viral and cellular genomes. They discovered that viral infections can cause changes in gene loop formation, chromatin accessibility, and shifts in genome compartments. These changes can affect gene activity and various biological processes, potentially leading to diseases like cancer. The research concludes that understanding the spatial and temporal aspects of viral infection is vital for a full understanding of virus biology and the cellular 4D nucleome. This could lead to new treatment opportunities to fight virus infection, persistence, and disease development. "This summary was initially drafted using artificial intelligence, then revised and fact-checked by the author".