Mechanisms & Consequences of Virus-Induced mRNA Destruction

The ability to regulate RNA stability has the potential to impact gene expression on a global scale, but is also critical for fine-tuning cellular responses to specific stimuli as well as eliminating flawed and potentially deleterious transcripts. Lytic gammaherpesvirus infection promotes widespread destruction of messenger RNAs (mRNAs), a phenotype driven primarily by the viral endonuclease SOX. By probing how SOX and other functionally related viral proteins drive messenger RNA degradation, we hope to reveal novel interplay between viruses and host gene regulatory pathways, as well as identify cellular factors with capacity to broadly influence message stability. We are also probing how cells sense and respond to broad changes in RNA levels. Gene expression is often considered as a linear series of events starting with mRNA synthesis in the nucleus and ending with mRNA degradation after translation in the cytoplasm. However, by manipulating mRNA abundance in the cytoplasm--something herpesviruses do very efficiently--we are finding surprising interconnectivity in the gene expression cascade.

Discovering Nuclease Escape Elements

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Although the vast majority of messages are degraded during lytic gamma-herpesvirus infection, we know that some transcripts escape degradation and accumulate robustly. An example of these is human interleukin 6 (IL-6), a B cell growth factor that has been demonstrated to play a role in the pathogenesis of several KSHV-associated neoplasms. We identified a specific element within IL-6 that renders it directly refractory to degradation by multiple viral endonucleases. Using the IL-6 escape element as a model, we are exploring how networks of RNA-protein interactions can impact endonuclease targeting. We are also searching for other escape elements to identify parallel features involved in directing RNA fate.

Novel Modes of Transcriptional Regulation During Infection

A universal feature of dsDNA viruses is that they all encode a class of genes whose expression is intimately linked to replication of the viral genome. These are termed ‘late genes’, and their transcription is robustly stimulated after the onset of DNA replication but otherwise restricted. Recent studies indicate that late gene transcriptional regulation in these viruses is unique, as it incorporates both molecular mimicry and selective recruitment of key host transcriptional machinery in a manner not previously observed in viral or host gene expression. In particular, one of the viral proteins required for late gene transcription directly binds both Pol II and promoter DNA, making this a unique viral transcriptional coordinator—and the first example of its kind in higher eukaryotes or eukaryotic viruses. We are currently working to understand how this hybrid virus-host preinitiation complex is assmembed and regulated. This viral model is anticipated to reveal new modes of transcriptional control, which may well have parallels in mammalian gene expression.

Viral activation and co-option of noncoding retrotransposons

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Nearly half of the mammalian genome is composed of transposable elements, which are silent—at least most of the time. However, a subset of these elements that do not encode for any proteins, termed short interspersed nuclear repeats, or SINEs, can get activated in response to viral infection. We hypothesize that these RNA polymerase III-transcribed SINE ncRNAs might have been co-opted by cells as an early warning system to alert the cell of a potential incoming virus. Indeed, SINE ncRNAs that are generated in response to infection with the mouse herpesvirus MHV68 activate the NF-kB pathway, an integral part of the cell’s antiviral defenses. While this may help guard the cell against certain types of viruses, it turns out to be a double-edged sword during gammaherpesvirus infection, as they have evolved to subvert and benefit from pathways activated by SINE RNAs. We are developing methods to analyze SINE activation profiles, and exploring the consequences of virus-induced SINE ncRNA production in regards to gene expression control and antiviral signaling.