Abstract
Human herpesvirus-6A (HHV-6A) and 6B (HHV-6B) are two closely related betaherpesviruses that are associated with various diseases including seizures and encephalitis. The HHV-6A/B genomes have been shown to be present in an integrated state in the telomeres of latently infected cells. In addition, integration of HHV-6A/B in germ cells has resulted in individuals harboring this inherited chromosomally integrated HHV-6A/B (iciHHV-6) in every cell of their body. Until now, the viral transcriptome and the epigenetic modifications that contribute to the silencing of the integrated virus genome remain elusive. In the current study, we used a patient-derived iciHHV-6A cell line to assess the global viral gene expression profile by RNA-seq, and the chromatin profiles by MNase-seq and ChIP-seq analyses. In addition, we investigated an in vitro generated cell line (293-HHV-6A) that expresses GFP upon the addition of agents commonly used to induce herpesvirus reactivation such as TPA. No viral gene expression including miRNAs was detected from the HHV-6A genomes, indicating that the integrated virus is transcriptionally silent. Intriguingly, upon stimulation of the 293-HHV-6A cell line with TPA, only foreign promoters in the virus genome were activated, while all HHV-6A promoters remained completely silenced. The transcriptional silencing of latent HHV-6A was further supported by MNase-seq results, which demonstrate that the latent viral genome resides in a highly condensed nucleosome-associated state. We further explored the enrichment profiles of histone modifications via ChIP-seq analysis. Our results indicated that the HHV-6 genome is modestly enriched with the repressive histone marks H3K9me3/H3K27me3 and does not possess the active histone modifications H3K27ac/H3K4me3. Overall, these results indicate that HHV-6 genomes reside in a condensed chromatin state, providing insight into the epigenetic mechanisms associated with the silencing of the integrated HHV-6A genome.
Highlights
The repressive marks H3K9me3 or H3K27me3 are enriched over nonspecific IgG or pan-histone H3 antibodies, albeit at lower levels than cellular regions (Figure 4C). These results suggest that the repressive histone modifications H3K9me3 and H3K27me3 are present on the latent virus genome and may be involved in chromatin-mediated repression of integrated Human herpesvirus-6A (HHV-6A) gene expression
This study provides an unbiased integrative genomics approach toward uncovering the chromatin profile in patient-derived iciHHV-6 and experimentally infected 293-HHV-6A cell lines
Our results demonstrate that chromosomally integrated HHV-6A is completely transcriptionally silent, resides in a heterochromatic state, and is associated with H3K9me3 and H3K27me3 repressive histone modifications
Summary
Human herpesvirus 6 (HHV-6) was first discovered in patients with lymphoproliferative disorders (Salahuddin et al, 1986) and has a seroprevalence of more than 90% (Zerr et al, 2005). Both viruses integrate their genome into the telomere region of host chromosomes (Arbuckle et al, 2010, 2013). This integration is facilitated by telomeric repeats (TTAGGG)n at the ends of the virus genome (Kaufer et al, 2011; Kaufer and Flamand, 2014; Wallaschek et al, 2016); the viral and/or cellular proteins that mediate integration remain elusive. A higher frequency and severity of both graft-versus-host disease (GvHD) and cytomegalovirus (CMV) viremia were observed in HSCT patients when either the recipient or donor were iciHHV-6 positive (Hill et al, 2017)
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