Faculty Bibliography

Toxic cytoplasmic aggregates containing the nuclear RNA-binding protein TDP-43 form in several neurodegenerative diseases; however, the molecular triggers driving aggregation remain unclear. Epidemiological evidence has linked latent and reactivating herpes simplex virus type-1 (HSV-1) infections to neurodegenerative disease onset, but it is unknown if HSV-1 infection impacts TDP-43 subcellular distribution. Here, we demonstrate that HSV-1 infection of epithelial cells and DRG-derived neurons results in nuclear TDP-43 redistribution and TDP-43 accumulation within distinct nuclear assemblies. Cytoplasmic TDP-43 was not detected under these conditions. Nuclear TDP-43 assembly occurred early in infection and was dependent upon expression of the critical ICP0 regulatory gene. Remarkably, ectopic ICP0 expression in uninfected cells was sufficient for nuclear TDP-43 assembly. Thus, expression of a single viral gene product encoded by a near ubiquitous human herpesvirus can alter TDP-43 nuclear localization. Moreover, our work identifies a potential mechanistic link between herpesvirus infection and neuronal disease factor mislocalization.

N6-methyladenosine (m⁶A) is a pervasive mRNA modification that regulates RNA fate through effects on RNA-protein interactions, stability and translation. We previously showed that replication of human betacoronaviruses, OC43 (hCoV-OC43) and SARS-CoV-2, is sensitive to depletion or pharmacological inhibition of the m⁶A RNA methyltransferase METTL3, resulting in reduced viral RNA and protein accumulation. In other viral systems, such antiviral effects have been attributed to enhanced interferon (IFN) signalling and interferon-stimulated gene (ISG) induction. Here, using hCoV-OC43 we show a requirement for METTL3 that is independent of canonical IFN responses. Pharmacological inhibition of METTL3 with STM2457 failed to potentiate type I IFN signalling, global ISG expression, or the non-canonical inflammatory transcriptional programme associated with OC43 infection. Furthermore, pathogen-associated RNA sensing by RIG-I or MDA5 is not required for the antiviral effect of the STM2457. ISGs reported to be most potently antiviral against OC43 are either not significantly induced by METTL3 inhibition during infection or are not required for the antiviral activity. Nevertheless, defects in viral gene expression and progression through the viral life cycle are detectable within 6 h of STM2457 treatment and host cell transcription is dispensable for STM2457 antiviral activity. Lastly, a METTL3-directed Proteolysis Targeting Chimera (PROTAC) phenocopied STM2457, producing IFN-independent antiviral activity and ruling out off-target inhibition of viral RNA methyltransferases as a plausible explanation. Together, these findings define a direct, proviral role for METTL3 in coronavirus infection consistent with a model in which METTL3-catalysed m6A modification of viral RNA is required for efficient viral life cycle progression.

All life-forms can be infected by viruses with double-stranded DNA genomes. Typically, permissive cells support a productive infection, where virus gene expression and DNA replication yield virion progeny resulting in cell death and/or immune clearance. Alternatively, certain viruses, including prokaryotic temperate bacteriophage and herpesviruses that infect multicellular eukaryotes, establish a persistent state in permissive cells (lysogeny in bacteria, latency in eukaryotes) where productive infection is repressed, permitting viral genome maintenance while deferring virus replication and particle assembly until conditions shift to favor productive infection. We compare examples drawn from temperate bacteriophage with more recent developments using the prototypical human α-herpesvirus herpes simplex virus 1 to illustrate mechanisms that control persistence or foster productive infection. Remarkably, despite vast evolutionary distance, similar physiological cues (genome integrity, nutrient status, cell communication signals) govern the switch between persistence and productive infection. Thus, monitoring basic homeostatic indicators determines lysogenic/latent or productive infection outcomes, representing a conserved virus persistence strategy.

Poly(A) tails are present on most cellular and viral mRNAs, providing a platform for poly(A)-binding proteins that stimulate translation and regulate the deadenylation and stability of transcripts in the cytoplasm. Here we leverage nanopore direct RNA sequencing to analyse the distribution of poly(A) tail lengths on cellular and viral mRNAs across Herpesviridae and other DNA and RNA virus infections. We find that herpesvirus mRNA poly(A) tails are consistently longer than those on cellular and other viral transcripts, presenting a previously unrecognized yet widespread mechanism to potentially advantage herpesviral gene expression. This contrasts with the templated poly(A) tails on coronavirus RNAs and those on cytoplasmically transcribed poxviral mRNAs, which are more similar in length to those on host mRNAs. Herpesviral noncoding RNAs display differential poly(A) tailing patterns while individual herpesviral mRNAs also show variation in the extent to which their poly(A) tail lengths change during the virus lifecycle, suggestive of additional uncharacterised layers of poly(A) tail length regulation. Importantly, while we detect non-adenosine nucleotides within herpesviral poly(A) tails, which are known to oppose deadenylase activity, this "mixed tailing" is not at sufficient frequency to explain the widespread extended tails of herpesvirus mRNAs.

Molecular processes are profoundly influenced by the biophysical properties of the cell interior. However, the mechanisms that control these physical properties and the processes they impact remain poorly understood, especially in the nucleus. We hypothesized that some viruses might change the biophysical properties of the nucleus to favor virus survival and replication and found that herpes simplex virus 1 (HSV-1) increases the mesoscale fluidity of the nucleus. The HSV-1 protein ICP4 (infected cell protein 4) caused fluidization and enabled the growth of synthetic nuclear condensates. Conversely, conditions that decreased nuclear fluidity inhibited the growth of viral replication compartment condensates and reduced infectious virus production. Together, our data suggest that ICP4 increases nuclear fluidity to promote the formation of condensates that drive the progression of the HSV-1 life cycle. We speculate that a key function of ICP4 is to overcome the crowding and elastic confinement within cell nuclei that are a fundamental barrier to virus replication.

TAR DNA-binding protein 43 (TDP-43) is a versatile nuclear RNA-binding protein that performs important functions in RNA localization, processing, and stability. In the neurodegenerative disease amyotrophic lateral sclerosis (ALS) TDP-43 forms toxic, insoluble cytoplasmic aggregates that ultimately lead to neuronal loss. Although TDP-43 is expressed in every cell type, its function and subcellular localization are particularly important for neuronal homeostasis. However, it is unknown if TDP-43 has a role during herpesvirus infection. Herpes simplex virus type-1 (HSV-1), a ubiquitous neurotropic pathogen, is considered a contributing factor to neurodegenerative disorders. In this study, we tested the requirement for TDP-43 during HSV-1 infection in neuronal and non-neuronal cells. HSV-1 infection of epithelial cells and primary fibroblasts did not change overall TDP-43 abundance, nor did TDP-43 depletion detectably alter HSV-1 productive replication in a multicycle growth experiment. By contrast, when TDP-43 was depleted in neuronally-derived, differentiated HD10.6 cells, HSV-1 infectious virus production was significantly reduced in both single- and multicycle growth experiments. Notably, TDP-43 depletion restricts viral lytic gene expression at the immediate-early phase. Through nanopore direct RNA-sequencing, we uncovered enhanced intron retention in two essential viral genes-ICP0 and UL15-upon TDP-43 depletion. Thus, while depletion of TDP-43 does not detectably affect HSV-1 reproduction in epithelial cells and fibroblasts, TDP-43 is required for efficient replication in HD10.6 cells through modifying the abundance and splicing of viral mRNAs.IMPORTANCEHerpes simplex virus type-1 is a widespread neurotropic pathogen that can cause life-threatening infections of the brain and is increasingly linked to neurodegenerative disease. However, due to the lack of scalable in vitro human neuronal models or small animal models that recapitulate disease, little is known about virus-host interactions in neurons specifically. Using human epithelial cells, primary fibroblasts and a human neuron-derived cell line, we uncovered a cell type specific TDP-43 requirement for efficient HSV-1 virus replication. TDP-43 is a critical neuronal disease factor gene, and we showed it promotes HSV-1 gene expression and splicing of viral mRNAs in neuron-derived cells. This raises the possibility that targeting of TDP-43 could reveal a new antiviral strategy for severe HSV-1 infections. This work further provides valuable insights into the possible etiology of neurodegenerative disease and highlights the importance of studying virus-host interactions in relevant cell types.

The factors that install and recognize N⁶-methyladenosine (m⁶A) on RNA to regulate gene expression are well characterized, but how their spatial organization responds to physiological stress, including infection, is unclear. Here, we show that human cytomegalovirus (HCMV) infection induces accumulation of m⁶A methyltransferase subunits, including WTAP, together with nuclear m⁶A reader YTHDC1, into distinctive, membraneless nuclear bodies (NBs) overlapping with incoming virus genomes and immediate-early (IE) RNA transcripts. De novo assembly and integrity of these DNA-associated, IE, virus-activated NBs requires RNAPII transcription, METTL3 m⁶A methyltransferase activity, and m⁶A recognition by YTHDC1, but not new protein synthesis. Depleting YTHDC1 or WTAP limits the accumulation of critical HCMV RNAs required for virus DNA replication, interfering with virus reproduction. This reveals a surprising strategy whereby a discrete sub-nuclear RNA biogenesis compartment replete with RNAPII and m⁶A modification components is swiftly consolidated in proximity to infecting HCMV genomes to initialize and sustain virus gene expression.

UNLABELLED:Nanopore direct RNA sequencing (DRS) enables the capture and full-length sequencing of native RNAs, without recoding or amplification bias. Resulting data sets may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails, on individual RNA molecules. The success of these analyses is highly dependent on the provision of high-resolution transcriptome annotations in combination with workflows that minimize misalignments and other analysis artifacts. Existing software solutions for generating high-resolution transcriptome annotations are poorly suited to small gene-dense genomes of viruses due to the challenge of identifying distinct transcript isoforms where alternative splicing and overlapping RNAs are prevalent. To resolve this, we identified key characteristics of DRS data sets that inform resulting read alignments and developed the nanopore guided annotation of transcriptome architectures (NAGATA) software package (https://github.com/DepledgeLab/NAGATA). We demonstrate, using a combination of synthetic and original DRS data sets derived from adenoviruses, herpesviruses, coronaviruses, and human cells, that NAGATA outperforms existing transcriptome annotation software and yields a consistently high level of precision and recall when reconstructing both gene sparse and gene-dense transcriptomes. Finally, we apply NAGATA to generate the first high-resolution transcriptome annotation of the neglected pathogen human adenovirus type F41 (HAdV-41) for which we identify 77 distinct transcripts encoding at least 23 different proteins. IMPORTANCE/OBJECTIVE:The transcriptome of an organism denotes the full repertoire of encoded RNAs that may be expressed. This is critical to understanding the biology of an organism and for accurate transcriptomic and epitranscriptomic-based analyses. Annotating transcriptomes remains a complex task, particularly in small gene-dense organisms such as viruses which maximize their coding capacity through overlapping RNAs. To resolve this, we have developed a new software nanopore guided annotation of transcriptome architectures (NAGATA) which utilizes nanopore direct RNA sequencing (DRS) datasets to rapidly produce high-resolution transcriptome annotations for diverse viruses and other organisms.