My laboratory studies the replication of two human herpesviruses, Kaposi's sarcoma associated herpesvirus (KSHV) and human cytomegalovirus (HCMV)
HCMV is a ubiquitous herpesvirus that infects 60-90% of the population and is usually subclinical however virus infection can cause severe disease and mortality in immune compromised patients. Disease manifestations include retinitis, pneumonia and hepatitis. HCMV latency is established after an initial infection and the primary site of latency is CD34 (+) cells and CD14 (+) monocytes. During latency no virus is produced and only a small subset of viral genes are expressed. The regulation and maintenance of latency is poorly understood and the reactivation of latent virus is a major cause of serious disease and death. Reactivation from latency is associated with the differentiation of CD34 (+) or CD14 (+) cells in culture by the use of various cytokines. Published data from our laboratory using RNA-Seq confirmed the presence of previously described latency-associated transcripts, UL138, LUNA and UL111A in both experimental and natural latency systems. RNA-Seq evaluation of experimental and natural HCMV latent infections in CD14 (+) monocytes and CD34 (+) hematopoietic progenitor cells (HPCs) revealed that several other latency associated transcripts were present in both cell types during latency. These common transcripts include two long non-coding RNAs (lncRNA), RNA2.7 and RNA4.9, and mRNA encoding UL84, UL44, UL95, UL87, UL79, UL50 and UL52. Subsequent ChIP-Seq analysis showed that UL44 and UL84 interacted with the viral genome during latency suggesting a significant role for these factors. The contribution of these factors toward establishment or maintenance of HCMV latent infection is not known. However, data shows that lncRNA4.9 interacts with polycomb group proteins and physically interacts with the viral genome. This interaction may repress expression of the viral transactivator IE2 protein. lncRNAs play an major role in regulation of gene expression and control of cellular processes, act through a variety of mechanisms and are implicated in a number of diseases. For HCMV we are interested in the mechanism involved in latency and the role of long non-coding RNAs in regulation of viral gene expression.
KSHV is the cause of Kaposi's sarcoma (KS) and is the most common associated malignancy in AIDS. KSHV is also implicated in primary effusion lymphoma (PEL), or body cavity lymphoma and multicentric Castleman's disease. Suppression of lytic infection with the use of anti-herpesvirus drugs such as Ganciclovir or Foscarnet can slow the progression of KS. One of the main mechanisms for KSHV survival is through immune evasion. Suppression of immune response by KSHV was shown to involve various virus-encoded proteins. The understanding of the mechanisms involved in the regulation of cellular and viral gene expression is of great significance. There is increasing and significant evidence that suggests that lncRNAs are major regulators of gene expression. One of the most abundant transcripts present in KSHV infected cells is a long non-coding RNA referred to as polyadenylated nuclear RNA (PAN RNA). We previously showed that PAN RNA interacts with cellular and viral encoded factors and mediates the regulation of immune response gene expression. Data from our laboratory and others indicated that PAN RNA is a major regulator of viral gene expression through a mechanism that involves a direct interaction with the viral chromosome. PAN RNA interacts with the demethylases UTX and JMJD3 to remove the suppressive H3K23me3 mark within the KSHV viral genome. PAN RNA also interacts with polycomb repression complex components and hence has the ability to activate or repress gene expression. Two reports, describing the transcriptome of KSHV infected cell lines show that PAN RNA was detected in the absence of lytic phase induction, suggesting that PAN RNA is expressed during chronic latent infection in cell culture. These observations suggest that PAN RNA has the potential to influence viral and cellular gene expression during all phases of the viral life cycle. RNA-Seq analysis of cells containing a recombinant BAC with the PAN RNA locus deleted show that the lack of PAN RNA leads to a complete abrogation of the initiation of the viral lytic phase transcription program. PAN RNA expression in a BJAB cell line showed that expression of PAN RNA primarily mediates changes in cellular gene expression pathways that regulate cell cycle, immune response and production of inflammatory cytokines. The combination of all these data suggests that PAN RNA is a major regulatory factor that globally controls viral and cellular gene expression. We are interested in the mechanisms involved in how PAN RNA regulates viral and cellular gene expression.