4C-seq genomic methodology used to examine HHV-6A integration sites

Chromatin interactions help silence transcription of HHV-6A genes following integration.

The process by which HHV-6A integrates into the telomere of a host cell, and thereby achieves latency, was investigated by Mariani et al of the University of Vermont. The team first examined the expression pattern of HHV-6A genes over time as the virus integrated into the host genome. In the first several days following infection, there were high expression levels of all HHV-6A RNA transcripts, slowing considerably by 5 days post infection and becoming essentially undetectable by 7 days post infection. It was not possible to determine if the expression of viral genes occurred from extrachromosomal virus or from integrated virus, and if the process of integration somehow led to the suppression of viral gene expression.

To investigate the mechanisms for achieving the suppression of these viral genes, the team used the technique of 4C-seq to determine the points of contact between regions of interest in the viral genome and specific structures in both the virus and the host genome, including chromatin structures. They found that many regions of the viral genome became associated with repressive host chromatin structures, possibly explaining the progressive silencing of viral genes.

The 4C-seq technique also identified a variety of virus-virus interactions, demonstrating that the viral genome may exist in a highly folded state.

Finally, the 4C-seq technique was able to serve as a high-resolution, highly accurate method for identifying HHV-6A integration sites in the human genome.

Read the full article: Mariani 2021