Supra-epigenomic impact of the human JC polyomavirus

Human and animal viruses possess remarkable capabilities in hijacking host processes to facilitate viral infection. Viruses use various strategies to target antiviral response mechanisms while promoting cellular phenotypic states that benefit viral replication. Viruses that replicate and assemble in the nucleus, including human pathogenic DNA viruses, need to balance maximal use of the host DNA replication machinery while at the same time avoid damage to the nucleus before generating a large number of viruses that will support the spread of infection. We have identified a novel mechanism of virus interference with the cell nucleus that involves virus-mediated modulation of nuclear mechanical properties. One of the most widespread human viruses, the JC polyomavirus, interferes with nuclear architecture to form virus-occupied space and substantially reduces the rigidity of the infected human cell nucleus. The JC virus's impact on nuclear rigidity is mediated by the viral nonstructural protein, Agnoprotein (Agno). The Agno interference with nuclear mechanics is governed by structurally diverse mimics of host proteins that support chromatin interaction with the key chromatin regulator, heterochromatin protein 1 alpha (HP1α), and is critical for JC virus infection in vitro. The ability to control chromatin organization and thus nuclear mechanics reveals a previously unknown virus strategy of hijacking the mechanism controlling nuclear physical properties to maximize virus production within the nucleus. In vitro cultured primary human astrocytes (Creative Biolabs; NCC20-9PZ01; Lot NR34) at passage number 3 cultured in 6-wells were infected with JC virus (NHA_JCV-WT) or Agno-deficient JC virus (NHA_JCV-deltaAgno) by incubation with the virus for 12h or were left uninfected (NHA_uninfected). 10 days after infection, cells were collected and directly used for single cell RNA-Seq library generation followed by paired-end sequencing on the Illumina NovaSeq 6000 platform. After alignment and quality control of the data, the sequencing data were used to address the degree of virus infection and for differential gene expression analysis to address the impact of JC virus infection of primary human astrocyres on host gene expression by comparing the gene expression data from JCV infected cells with the gene expression data from uninfected cells. The contribution of Agnoprotein to the virus induced gene expression changes were addressed by comparing the gene expression data from JCV infected cells with the gene expression data from Agno-deficient JCV infected cells. One biological replicate per condition was used for the analysis.