920 The non-coding control region of Trichodysplasia spinulosa polyomavirus is responsible for cell-type specific viral gene expression in vivo

AbstractMethylation at theN6position of adenosine (m6A) is a highly prevalent and reversible modification within eukaryotic mRNAs that has been linked to many stages of RNA processing and fate. Recent studies suggest that m6A deposition and proteins involved in the m6A pathway play a diverse set of roles in either restricting or modulating the lifecycles of select viruses. Here, we report that m6A levels are significantly increased in cells infected with the oncogenic human DNA virus Kaposi’s sarcoma-associated herpesvirus (KSHV). Transcriptome-wide m6A-sequencing of the KSHV-positive renal carcinoma cell line iSLK.219 during lytic reactivation revealed the presence of m6A across multiple kinetic classes of viral transcripts, and a concomitant decrease in m6A levels across much of the host transcriptome. However, we found that depletion of the m6A machinery had differential pro- and anti-viral impacts on viral gene expression depending on the cell-type analyzed. In iSLK.219 and iSLK.BAC16 cells the pathway functioned in a pro-viral manner, as depletion of the m6A writer METTL3 and the reader YTHDF2 significantly impaired virion production. In iSLK.219 cells the defect was linked to their roles in the post-transcriptional accumulation of the major viral lytic transactivator ORF50, which is m6A modified. In contrast, although the ORF50 mRNA was also m6A modified in KSHV infected B cells, ORF50 protein expression was instead increased upon depletion of METTL3, or, to a lesser extent, YTHDF2. These results highlight that the m6A pathway is centrally involved in regulating KSHV gene expression, and underscore how the outcome of this dynamically regulated modification can vary significantly between cell types.Author SummaryIn addition to its roles in regulating cellular RNA fate, methylation at theN6position of adenosine (m6A) of mRNA has recently emerged as a mechanism for regulating viral infection. While it has been known for over 40 years that the mRNA of nuclear replicating DNA viruses contain m6A, only recently have studies began to examine the distribution of this modification across viral transcripts, as well as characterize its functional impact upon viral lifecycles. Here, we apply m6A-sequencing to map the location of m6A modifications throughout the transcriptome of the oncogenic human DNA virus Kaposi’s sarcoma-associated herpesvirus (KSHV). We show that the m6A machinery functions in a cell type specific manner to either promote or inhibit KSHV gene expression. Thus, the KSHV lifecycle is impacted by the m6A pathway, but the functional outcome may depend on cell lineage specific differences in m6A-based regulation.

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Human cytomegalovirus transcriptome activity differs during replication in human fibroblast, epithelial and astrocyte cell lines

Journal of General Virology ◽

10.1099/vir.0.038083-0 ◽

2012 ◽

Vol 93 (5) ◽

pp. 1046-1058 ◽

Cited By ~ 11

Author(s):

James C. Towler ◽

Bahram Ebrahimi ◽

Brian Lane ◽

Andrew J. Davison ◽

Derrick J. Dargan

Keyword(s):

Gene Expression ◽

Human Cytomegalovirus ◽

Growth Kinetics ◽

Viral Gene Expression ◽

Cell Types ◽

Viral Gene ◽

Genome Replication ◽

Cell Type ◽

Low Passage ◽

Temporal Expression Pattern

Broad cell tropism contributes to the pathogenesis of human cytomegalovirus (HCMV), but the extent to which cell type influences HCMV gene expression is unclear. A bespoke HCMV DNA microarray was used to monitor the transcriptome activity of the low passage Merlin strain of HCMV at 12, 24, 48 and 72 h post-infection, during a single round of replication in human fetal foreskin fibroblast cells (HFFF-2s), human retinal pigmented epithelial cells (RPE-1s) and human astrocytoma cells (U373MGs). In order to correlate transcriptome activity with concurrent biological responses, viral cytopathic effect, growth kinetics and genomic loads were examined in the three cell types. The temporal expression pattern of viral genes was broadly similar in HFFF-2s and RPE-1s, but dramatically different in U373MGs. Of the 165 known HCMV protein-coding genes, 41 and 48 were differentially regulated in RPE-1s and U373MGs, respectively, compared with HFFF-2s, and 22 of these were differentially regulated in both RPE-1s and U373MGs. In RPE-1s, all differentially regulated genes were downregulated, but, in U373MGs, some were down- and others upregulated. Differentially regulated genes were identified among the immediate-early, early, early late and true-late viral gene classes. Grouping of downregulated genes according to function at landmark stages of the replication cycle led to the identification of potential bottleneck stages (genome replication, virion assembly, and virion maturation and release) that may account for cell type-dependent viral growth kinetics. The possibility that cell type-specific differences in expressed cellular factors are responsible for modulation of viral gene expression is discussed.

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B-Catenin Signaling Regulates the In Vivo Distribution of Hepatitis B Virus Biosynthesis across the Liver Lobule

Journal of Virology ◽

10.1128/jvi.00780-21 ◽

2021 ◽

Author(s):

Grant Tarnow ◽

Alan McLachlan

Keyword(s):

Gene Expression ◽

Transgenic Mice ◽

Viral Replication ◽

Viral Gene Expression ◽

Viral Gene ◽

Central Vein ◽

Liver Lobule ◽

Liver Gene ◽

Mice Liver

β-catenin (Ctnnb1) supports high levels of liver gene expression in hepatocytes in proximity to the central vein functionally defining zone 3 of the liver lobule. This region of the liver lobule supports the highest levels of viral biosynthesis in wildtype HBV transgenic mice. Liver-specific β-catenin-null HBV transgenic mice exhibit a stark loss of high levels of pericentral viral biosynthesis. Additionally, viral replication that does not depend directly on β-catenin activity appears to expand to include hepatocytes of zone 1 of the liver lobule in proximity to the portal vein, a region of the liver that typically lacks significant HBV biosynthesis in wildtype HBV transgenic mice. While the average amount of viral RNA transcripts does not change, viral DNA replication is reduced approximately three-fold. Together, these observations demonstrate that β-catenin signaling represents a major determinant of HBV biosynthesis governing the magnitude and distribution of viral replication across the liver lobule in vivo. Additionally, these findings reveal a novel mechanism for the regulation of HBV biosynthesis that is potentially relevant to the expression of additional liver-specific genes. IMPORTANCE Viral biosynthesis is highest around the central vein in the HBV transgenic mouse model of chronic infection. The associated HBV biosynthetic gradient across the liver lobule is primarily dependent upon β-catenin. In the absence of β-catenin, the gradient of viral gene expression spanning the liver lobule is absent and HBV replication is reduced. Therefore, therapeutically manipulating β-catenin activity in the liver of chronic HBV carriers may reduce circulating infectious virions without greatly modulating viral protein production. Together, these change in viral biosynthesis might limit infection of additional hepatocytes while permitting immunological clearance of previously infected cells, potentially limiting disease persistence.

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Cell-Type Specific Oxytocin Gene Expression from AAV Delivered Promoter Deletion Constructs into the Rat Supraoptic Nucleus in vivo

PLoS ONE ◽

10.1371/journal.pone.0032085 ◽

2012 ◽

Vol 7 (2) ◽

pp. e32085 ◽

Cited By ~ 17

Author(s):

Raymond L. Fields ◽

Todd A. Ponzio ◽

Makoto Kawasaki ◽

Harold Gainer

Keyword(s):

Gene Expression ◽

Supraoptic Nucleus ◽

Cell Type ◽

Promoter Deletion ◽

Cell Type Specific

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50. Inhibition of Hepatitis B Viral Gene Expression In Vitro and In Vivo by RNAi

Molecular Therapy ◽

10.1016/s1525-0016(16)40492-2 ◽

2003 ◽

Vol 7 (5) ◽

pp. S19-S20

Keyword(s):

Gene Expression ◽

Hepatitis B ◽

Viral Gene Expression ◽

Viral Gene

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An Early Regulatory Function Required in a Cell Type-Dependent Manner Is Expressed by the Genomic but Not the cDNA Copy of the Herpes Simplex Virus 1 Gene Encoding Infected Cell Protein 0

Journal of Virology ◽

10.1128/jvi.76.19.9744-9755.2002 ◽

2002 ◽

Vol 76 (19) ◽

pp. 9744-9755 ◽

Cited By ~ 18

Author(s):

Alice P. W. Poon ◽

Saul J. Silverstein ◽

Bernard Roizman

Keyword(s):

Gene Expression ◽

Viral Gene Expression ◽

Viral Gene ◽

Multiplicity Of Infection ◽

Cell Type ◽

Rabbit Skin ◽

Cdna Copy ◽

Intron 1 ◽

A Cell ◽

Hsv 1

ABSTRACT The α0 genes of herpes simplex virus 1 (HSV-1) contain three exons. Earlier studies have shown that the substitution of genomic sequences with a cDNA copy does not alter the capacity of the virus to replicate or establish latent infection. Other studies have demonstrated that HSV-1 may express alternatively spliced forms of α0 transcripts. The studies reported here centered on a mutant HSV-1(vCPc0) strain in which the genomic copies of the α0 gene were replaced with cDNA copies. From our research, we report the following observations. (i) In contrast to events transpiring in cells infected with wild-type virus, the expression of HSV-1(vCPc0) genes was delayed or restricted to α genes for many hours in rabbit skin cells and to a lesser extent in HEp-2 cells but not in Vero cells. This delay in the expression of HSV-1(vCPc0) β or γ genes was also multiplicity of infection dependent. (ii) Exposure to MG132, a proteasomal inhibitor, before infection with wild-type virus had no significant effect on the accumulation of viral proteins in Vero cells and caused an only slight delay in viral gene expression in rabbit skin cells in a multiplicity of infection-dependent fashion. The drug had no effect when it was added to the medium 3 h after infection. (iii) Rabbit skin or HEp-2 cells exposed to MG132 3 h after infection with the HSV-1(vCPc0) mutant accumulated only α proteins. This restriction was cell type dependent but not multiplicity of infection dependent. (iv) Both the delay in the expression of β and γ genes and the effect of MG132 added to the medium 3 h after infection were rescued by restoration of the intron 1 sequences in the HSV-1(vCPc0) mutant. However, cells transduced by baculoviruses expressing intron 1 RNA did not complement the HSV-1(vCPc0) mutant, suggesting that the function of intron 1 is in cis rather than in trans. We came to the following conclusions as a result. (i) Post-α gene expression requires the involvement of the proteasomal pathway in a cell type-dependent manner. Consistent with this requirement, the proapoptotic functions of MG132 are blocked in cells infected before exposure to the drug but not after exposure. (ii) A function encoded by the α0 gene that is absent from the cDNA copy is required for viral gene expression in a cell type- and multiplicity of infection-dependent fashion. The absence of this master function delays but does not ultimately block viral gene expression in the cell lines tested here.

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394 IN VIVO ORAL DOSING OF THE TLR7 AGONIST GS-9620 INDUCES AN ANTI-VIRAL GENE EXPRESSION SIGNATURE IN MURINE LIVER CONCURRENT WITH UNDETECTABLE SERUM LEVELS OF IFN-a

Journal of Hepatology ◽

10.1016/s0168-8278(13)60396-7 ◽

2013 ◽

Vol 58 ◽

pp. S162

Author(s):

S. Pflanz ◽

A. Fosdick ◽

T. Cihlar ◽

M. Subramanian

Keyword(s):

Gene Expression ◽

Gene Expression Signature ◽

Viral Gene Expression ◽

Serum Levels ◽

Viral Gene ◽

Oral Dosing ◽

Tlr7 Agonist ◽

Undetectable Serum ◽

Murine Liver

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Mechanisms of pathogenesis of emerging adenoviruses

F1000Research ◽

10.12688/f1000research.10152.1 ◽

2017 ◽

Vol 6 ◽

pp. 90 ◽

Cited By ~ 10

Author(s):

James Cook ◽

Jay Radke

Keyword(s):

Gene Expression ◽

Human Population ◽

Viral Gene Expression ◽

Critical Threshold ◽

Severe Illness ◽

Viral Gene ◽

Altered Expression ◽

Biological Studies ◽

Viral Genes

Periodic outbreaks of human adenovirus infections can cause severe illness in people with no known predisposing conditions. The reasons for this increased viral pathogenicity are uncertain. Adenoviruses are constantly undergoing mutation during circulation in the human population, but related phenotypic changes of the viruses are rarely detected because of the infrequency of such outbreaks and the limited biological studies of the emergent strains. Mutations and genetic recombinations have been identified in these new strains. However, the linkage between these genetic changes and increased pathogenicity is poorly understood. It has been observed recently that differences in virus-induced immunopathogenesis can be associated with altered expression of non-mutant viral genes associated with changes in viral modulation of the host innate immune response. Initial small animal studies indicate that these changes in viral gene expression can be associated with enhanced immunopathogenesisin vivo. Available evidence suggests the hypothesis that there is a critical threshold of expression of certain viral genes that determines both the sustainability of viral transmission in the human population and the enhancement of immunopathogenesis. Studies of this possibility will require extension of the analysis of outbreak viral strains from a sequencing-based focus to biological studies of relationships between viral gene expression and pathogenic responses. Advances in this area will require increased coordination among public health organizations, diagnostic microbiology laboratories, and research laboratories to identify, catalog, and systematically study differences between prototype and emergent viral strains that explain the increased pathogenicity that can occur during clinical outbreaks.

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