Biology subjects

Dremel, S. E.

Publications and source records attributed to Dremel, S. E..

5 recordsLinked to original sources

bioRxiv2025

Interferon Dependent Immune Memory during HSV-1 Neuronal Latency Results in Increased H3K9me3 and Restriction of Reactivation by ATRX

Herpes simplex virus-1 (HSV-1) establishes a lifelong latent infection in neurons and reactivation from this latent state is the cause of recurrent oral and ocular infections, herpes simplex keratitis, and encephalitis. Neuronal conditions during initial HSV-1 infection have a long-term impact on latency, modulating how responsive latent genomes are to reactivation and, therefore, their ability to cause disease. Type I interferon (IFN) exposure during initial infection results in promyelocytic leukemia nuclear-body (PML-NB) formation and a more restrictive form of HSV-1 latency. Here we demonstrate that IFN induced PML-NBs recruit histone chaperones to the viral genome and promote the deposition of the repressive heterochromatin mark, histone H3 lysine 9 tri-methylation (H3K9me3), and its reader, ATRX (alpha-thalassemia/mental retardation, X-linked). This work reveals the mechanism by which immune signaling during initial infection induces an epigenetic memory on HSV-1 genomes that is maintained during latency and inhibits reactivation. ATRX is highly abundant in neurons and is essential for maintaining cellular heterochromatin during neuronal stress. Here we find that ATRX prevents transcription, and subsequent reactivation, from H3K9me3-bound latent genomes by remaining associated with viral chromatin following stress-induced phosphorylation of histone H3. This indicates that H3K9me3-associated viral genomes are refractory to reactivation when read by ATRX. This work demonstrates that ATRX acts as a neuronal restriction factor against HSV-1 reactivation, elucidating a new potential target for inhibiting HSV-1 reactivation and subsequent human disease.

microbiology↗

bioRxiv2023

Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection

A first line of defense during infection is expression of interferon (IFN)-stimulated gene products which suppress viral lytic infection. To combat this, herpesviruses express endoribonucleases to deplete host RNAs. Here we demonstrate that IFN-induced circular RNAs (circRNAs) can escape viral-mediated degradation. We performed comparative circRNA expression profiling for representative alpha- (Herpes simplex virus-1, HSV-1), beta- (human cytomegalovirus, HCMV), and gamma-herpesviruses (Kaposi sarcoma herpesvirus, KSHV; murine gamma-herpesvirus 68, MHV68). Strikingly, we found that circRNAs are, as a population, resistant to host shutoff. This observation was confirmed by ectopic expression assays of human and murine herpesvirus endoribonucleases. During primary lytic infection, ten circRNAs were commonly regulated across all subfamilies of human herpesviruses, suggesting a common mechanism of regulation. We tested one such mechanism, namely how interferon-stimulation influences circRNA expression. 67 circRNAs were upregulated by either IFN-{beta} or -{gamma} treatment, with half of these also upregulated during lytic infection. Using gain and loss of function studies we found an interferon-stimulated circRNA, circRELL1, inhibited lytic HSV-1 infection. We have previously reported circRELL1 inhibits lytic KSHV infection, suggesting a pan-herpesvirus antiviral activity. We propose a two-pronged model in which interferon-stimulated genes may encode both mRNA and circRNA with antiviral activity. This is critical in cases of host shutoff, such as alpha- and gamma-herpesvirus infection, where the mRNA products are degraded but circRNAs escape.

microbiology↗

bioRxiv2022

Alternative splicing and circRNA biogenesis driven by alpha and gamma herpesviruses

Herpesviruses rely on the host transcriptional machinery for expression of their >100 different transcripts. To prioritize viral transcripts, herpesviruses affect significant changes in all stages of gene expression. Herein, we examined how herpesviruses alter circular RNA (circRNA) synthesis resulting in distinct characteristics for those expressed from the host or viral genome. CircRNA were identified with our Circrnas in Host And viRuses anaLysis pIpEline (CHARLIE) capable of de novo annotation using aggregated calls from five distinct tools. Comparative profiling for Herpes Simplex Virus-1, Kaposi sarcoma-associated herpesvirus, and murine gammaherpesvirus 68 identified thousands of back splicing variants, including circRNA species commonly expressed in all phases of infection. CircRNA expression was highest during lytic infection, with a transcriptional density 500-fold greater than the host. We characterized cis- and trans-elements controlling back splicing and found viral circRNAs are generally resistant to spliceosome inhibition or depletion, with >90% lacking canonical splice donor-acceptor sites. Using eCLIP and 4sU-Sequencing, we determined that the viral RNA binding protein, ORF57, enhanced synthesis for a subset of viral and host circRNAs. Our work elucidates a unique splicing mechanism driven by late lytic replication and identifies a class of transcripts with potential to function in replication, persistence, or tumorigenesis.

microbiology↗

bioRxiv2021

Manipulation of RNA Polymerase III by Herpes Simplex Virus-1

RNA Polymerase III (Pol III) transcribes noncoding RNA, including transfer RNA (tRNA), and acts as a pathogen sensor during the innate immune response. To promote enhanced proliferation, the Pol III machinery is commonly targeted during cancer and viral infection. Herein we employ DM-RNA-Seq, 4SU-Seq, ChIP-Seq, and ATAC-Seq to characterize how Herpes Simplex Virus-1 (HSV-1) perturbs the Pol III landscape. We find that HSV-1 stimulates tRNA expression 10-fold, with mature tRNAs exhibiting a 2-fold increase within 12 hours of infection. Perturbation of host tRNA synthesis requires nuclear viral entry, but not synthesis of specific viral transcripts, nascent viral genomes, or viral progeny. Host tRNA with a specific codon bias were not targeted--rather increased transcription was observed from euchromatic, actively transcribed loci. tRNA upregulation is linked to unique crosstalk between the Pol II and III transcriptional machinery. While viral infection is known to mediate host transcriptional shut off and lead to a depletion of Pol II on host mRNA promoters, we find that Pol II binding to tRNA loci increases. Finally, we report Pol III and associated factors bind the HSV genome, which suggests a previously unrecognized role in HSV-1 gene expression. These data provide insight into novel mechanisms by which HSV-1 alters the host nuclear environment, shifting key processes in favor of the pathogen.

molecular biology↗

bioRxiv2019

Herpes Simplex nucleoprotein creates a competitive environment facilitating robust viral transcription and host shut off

Herpes simplex virus-1 (HSV-1) replicates within the nucleus coopting the hosts RNA Polymerase II (Pol II) machinery for production of viral mRNAs culminating in host transcriptional shut off. The mechanism behind this rapid reprogramming of the host transcriptional environment is largely unknown. We identified ICP4 as responsible for preferential recruitment of the Pol II machinery to the viral genome. ICP4 is a viral nucleoprotein which binds double stranded DNA. We determined ICP4 discriminately binds the viral genome due to the absence of cellular nucleosomes and high density of cognate binding sites. We posit that ICP4s ability to recruit not just Pol II, but also more limiting essential components, such as TBP and Mediator create a competitive transcriptional environment. These distinguishing characteristics ultimately result in a rapid and efficient reprogramming of the hosts transcriptional machinery, which does not occur in the absence of ICP4.\n\nHighlightsO_LIHSV-1 ICP4 coats the viral genome promoting robust recruitment of Pol II transcription machinery.\nC_LIO_LIICP4 prefers the viral genome due to the absence of nucleosomes and density of binding motifs.\nC_LIO_LIAt high concentrations ICP4 promiscuously binds DNA including euchromatic host promoters.\nC_LIO_LIICP4 is required for host transcriptional shut off, independent of genome replication.\nC_LI

genomics↗