scholarly journals Native RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

2018 ◽  
Author(s):  
Daniel P. Depledge ◽  
Kalanghad Puthankalam Srinivas ◽  
Tomohiko Sadaoka ◽  
Devin Bready ◽  
Yasuko Mori ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Rna Splicing ◽  
Transcription Initiation ◽  
Productive Infection ◽  
Rna Modifications ◽  
Viral Pathogen ◽  
Viral Genomes ◽  
Alternative Transcription ◽  
Nanopore Arrays ◽  
Simplex Virus

ABSTRACTViral genomes exhibit a higher gene density and more diversified transcriptome than the host cell. Coding potential is maximized through the use of multiple reading frames, placement of genes on opposing strands, inefficient or modified use of termination signals, and the deployment of complex alternative splicing patterns. As a consequence, detailed characterization of viral transcriptomes by conventional methods can be challenging. Full length native RNA sequencing (nRNA-seq) using nanopore arrays offers an exciting alternative. Individual transcripts are sequenced directly, without the biases inherent to the recoding or amplification steps included in other sequencing methodologies. nRNA-seq simplifies the detection of variation brought about by RNA splicing, use of alternative transcription initiation and termination sites, and other RNA modifications. Here we use nRNA-seq to profile the herpes simplex virus type 1 transcriptome during early and late stages of productive infection of primary cells. We demonstrate the effectiveness of the approach and identify a novel class of intergenic transcripts, including an mRNA that accumulates late in infection that codes for a novel fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L.

scholarly journals Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Daniel P. Depledge ◽  
Kalanghad Puthankalam Srinivas ◽  
Tomohiko Sadaoka ◽  
Devin Bready ◽  
Yasuko Mori ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Viral Pathogen ◽  
Nanopore Arrays

scholarly journals Characterization of Herpes Simplex Virus 2 Primary MicroRNA Transcript Regulation

2015 ◽  
Vol 89 (9) ◽  
pp. 4837-4848 ◽  
Author(s):  
Shuang Tang ◽  
Marta Bosch-Marce ◽  
Amita Patel ◽  
Todd P. Margolis ◽  
Philip R. Krause
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Transcription Initiation ◽  
Regulation Of Gene Expression ◽  
Bidirectional Promoter ◽  
Initiation Site ◽  
Lytic Cycle ◽  
Productive Infection ◽  
Simplex Virus ◽  
Herpes Simplex Virus 2

ABSTRACTIn order to understand factors that may influence latency-associated transcription and latency-associated transcript (LAT) phenotypes, we studied the expression of the herpes simplex virus 2 (HSV-2) LAT-associated microRNAs (miRNAs). We mapped the transcription initiation sites of all three primary miRNA transcripts and identified the ICP4-binding sequences at the transcription initiation sites of both HSV-2 LAT (pri-miRNA for miR-I and miR-II, which target ICP34.5, and miR-III, which targets ICP0) and L/ST (a pri-miRNA for miR-I and miR-II) but not at that of the primary miR-H6 (for which the target is unknown). We confirmed activity of the putative HSV-2 L/ST promoter and found that ICP4trans-activates the L/ST promoter when the ICP4-binding site at its transcription initiation site is mutated, suggesting that ICP4 may play a dual role in regulating transcription of L/ST and, consequently, of miR-I and miR-II. LAT exon 1 (containing LAT enhancer sequences), together with the LAT promoter region, comprises a bidirectional promoter required for the expression of both LAT-encoded miRNAs and miR-H6 in latently infected mouse ganglia. The ability of ICP4 to suppress ICP34.5-targeting miRNAs and to activate lytic viral genes suggests that ICP4 could play a key role in the switch between latency and reactivation.IMPORTANCEThe HSV-2 LAT and viral miRNAs expressed in the LAT region are the most abundant viral transcripts during HSV latency. The balance between the expression of LAT and LAT-associated miRNAs and the expression of lytic viral transcripts from the opposite strand appears to influence whether individual HSV-infected neurons will be latently or productively infected. The outcome of neuronal infection may thus depend on regulation of gene expression of the corresponding primary miRNAs. In the present study, we characterize promoter sequences responsible for miRNA expression, including identification of the primary miRNA 5′ ends and evaluation of ICP4 response. These findings provide further insight into the virus' strategy to tightly control expression of lytic cycle genes (especially the neurovirulence factor, ICP34.5) and suggest a mechanism (via ICP4) for the transition from latency to reactivated productive infection.

scholarly journals Regulation of Krüppel-Like Factor 15 Expression by Herpes Simplex Virus Type 1 or Bovine Herpesvirus 1 Productive Infection

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1148
Author(s):  
Fouad S. El-mayet ◽  
Kelly S. Harrison ◽  
Clinton Jones
Keyword(s):  
Steady State ◽  
Promoter Activity ◽  
Bovine Herpesvirus ◽  
Productive Infection ◽  
Bovine Herpesvirus 1 ◽  
Protein Levels ◽  
Herpesvirus 1 ◽  
Simplex Virus ◽  
Hsv 1

Expression of Krüppel-like factor 15 (KLF15), a stress-induced transcription factor, is induced during bovine herpesvirus 1 (BoHV-1) reactivation from latency, and KLF15 stimulates BoHV-1 replication. Transient transfection studies revealed that KLF15 and glucocorticoid receptor (GR) cooperatively transactivate the BoHV-1-immediate-early transcription unit 1 (IEtu1), herpes simplex virus type 1 (HSV-1) infected cell protein 0 (ICP0), and ICP4 promoters. The IEtu1 promoter drives expression of bICP0 and bICP4, two key BoHV-1 transcriptional regulatory proteins. Based on these studies, we hypothesized infection is a stressful stimulus that increases KLF15 expression and enhances productive infection. New studies demonstrated that silencing KLF15 impaired HSV-1 productive infection, and KLF15 steady-state protein levels were increased at late stages of productive infection. KLF15 was primarily localized to the nucleus following infection of cultured cells with HSV-1, but not BoHV-1. When cells were transfected with a KLF15 promoter construct and then infected with HSV-1, promoter activity was significantly increased. The ICP0 gene, and to a lesser extent, bICP0 transactivated the KLF15 promoter in the absence of other viral proteins. In contrast, BoHV-1 or HSV-1 encoded VP16 had no effect on KLF15 promoter activity. Collectively, these studies revealed that HSV-1 and BoHV-1 productive infection increased KLF15 steady-state protein levels, which correlated with increased virus production.

scholarly journals Optimized approach for Ion Proton RNA sequencing reveals details of RNA splicing and editing features of the transcriptome

PLoS ONE ◽  
2017 ◽  
Vol 12 (5) ◽  
pp. e0176675 ◽  
Author(s):  
Roger B. Brown ◽  
Nathaniel J. Madrid ◽  
Hideaki Suzuki ◽  
Scott A. Ness
Keyword(s):  
Rna Sequencing ◽  
Rna Splicing ◽  
Ion Proton

scholarly journals Patterns of accumulation of miRNAs encoded by herpes simplex virus during productive infection, latency, and on reactivation

2014 ◽  
Vol 112 (1) ◽  
pp. E49-E55 ◽  
Author(s):  
Te Du ◽  
Zhiyuan Han ◽  
Guoying Zhou ◽  
Bernard Roizman
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Cultured Cells ◽  
Viral Gene Expression ◽  
The Body ◽  
Productive Infection ◽  
Viral Gene ◽  
Infected Cells ◽  
Simplex Virus ◽  
Portal Of Entry

The key events in herpes simplex virus (HSV) infections are (i) replication at a portal of entry into the body modeled by infection of cultured cells; (ii) establishment of a latent state characterized by a sole latency-associated transcript and microRNAs (miRNAs) modeled in murine peripheral ganglia 30 d after inoculation; and (iii) reactivation from the latent state modeled by excision and incubation of ganglia in medium containing anti-NGF antibody for a timespan of a single viral replicative cycle. In this report, we examine the pattern of synthesis and accumulation of 18 HSV-1 miRNAs in the three models. We report the following: (i) H2-3P, H3-3P, H4-3P, H5-3P, H6-3P, and H7-5P accumulated in ganglia harboring latent virus. All but H4-3P were readily detected in productively infected cells, and most likely they originate from three transcriptional units. (ii) H8-5P, H15, H17, H18, H26, and H27 accumulated during reactivation. Of this group, only H26 and H27 could be detected in productively infected cells. (iii) Of the 18 we have examined, only 10 miRNAs were found to accumulate above background levels in productively infected cells. The disparity in the accumulation of miRNAs in cell culture and during reactivation may reflect differences in the patterns of regulation of viral gene expression during productive infection and during reactivation from the latent state.

scholarly journals Type I IFN suppresses Cxcr2 driven neutrophil recruitment into the sensory ganglia during viral infection

2014 ◽  
Vol 211 (5) ◽  
pp. 751-759 ◽  
Author(s):  
Angus T. Stock ◽  
Jeffrey M. Smith ◽  
Francis R. Carbone
Keyword(s):  
Selective Inhibition ◽  
Neutrophil Recruitment ◽  
Type I ◽  
Sensory Ganglia ◽  
Type I Ifn ◽  
Viral Pathogen ◽  
Inflammatory Chemokines ◽  
Chemokine Ligands ◽  
Simplex Virus ◽  
Bone Marrow Chimeras

Infection induces the expression of inflammatory chemokines that recruit immune cells to the site of inflammation. Whereas tissues such as the intestine and skin express unique chemokines during homeostasis, whether different tissues express distinct chemokine profiles during inflammation remains unclear. With this in mind, we performed a comprehensive screen of the chemokines expressed by two tissues (skin and sensory ganglia) infected with a common viral pathogen (herpes simplex virus type 1). After infection, the skin and ganglia showed marked differences in their expression of the family of Cxcr2 chemokine ligands. Specifically, Cxcl1/2/3, which in turn controlled neutrophil recruitment, was up-regulated in the skin but absent from the ganglia. Within the ganglia, Cxcl2 expression and subsequent neutrophil recruitment was inhibited by type I interferon (IFN). Using a combination of bone marrow chimeras and intracellular chemokine staining, we show that type I IFN acted by directly suppressing Cxcl2 expression by monocytes, abrogating their ability to recruit neutrophils to the ganglia. Overall, our findings describe a novel role for IFN in the direct, and selective, inhibition of Cxcr2 chemokine ligands, which results in the inhibition of neutrophil recruitment to neuronal tissue.

scholarly journals Herpes Simplex Virus ICP27 Is Required for Virus-Induced Stabilization of the ARE-Containing IEX-1 mRNA Encoded by the Human IER3 Gene

2006 ◽  
Vol 80 (19) ◽  
pp. 9720-9729 ◽  
Author(s):  
Jennifer A. Corcoran ◽  
Wei-Li Hsu ◽  
James R. Smiley
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Mapk Pathway ◽  
Immediate Early ◽  
Productive Infection ◽  
Mrna Stabilization ◽  
Early Protein ◽  
Host Shutoff ◽  
Simplex Virus ◽  
Hsv 1

ABSTRACT Herpes simplex virus (HSV) stifles cellular gene expression during productive infection of permissive cells, thereby diminishing host responses to infection. Host shutoff is achieved largely through the complementary actions of two viral proteins, ICP27 and virion host shutoff (vhs), that inhibit cellular mRNA biogenesis and trigger global mRNA decay, respectively. Although most cellular mRNAs are thus depleted, some instead increase in abundance after infection; perhaps surprisingly, some of these contain AU-rich instability elements (AREs) in their 3′-untranslated regions. ARE-containing mRNAs normally undergo rapid decay; however, their stability can increase in response to signals such as cytokines and virus infection that activate the p38/MK2 mitogen-activated protein kinase (MAPK) pathway. We and others have shown that HSV infection stabilizes the ARE mRNA encoding the stress-inducible IEX-1 mRNA, and a previous report from another laboratory has suggested vhs is responsible for this effect. However, we now report that ICP27 is essential for IEX-1 mRNA stabilization whereas vhs plays little if any role. A recent report has documented that ICP27 activates the p38 MAPK pathway, and we detected a strong correlation between this activity and stabilization of IEX-1 mRNA by using a panel of HSV type 1 (HSV-1) isolates bearing an array of previously characterized ICP27 mutations. Furthermore, IEX-1 mRNA stabilization was abrogated by the p38 inhibitor SB203580. Taken together, these data indicate that the HSV-1 immediate-early protein ICP27 alters turnover of the ARE-containing message IEX-1 by activating p38. As many ARE mRNAs encode proinflammatory cytokines or other immediate-early response proteins, some of which may limit viral replication, it will be of great interest to determine if ICP27 mediates stabilization of many or all ARE-containing mRNAs.

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