scholarly journals Nanopore Assay Reveals Cell-Type-Dependent Gene Expression of Vesicular Stomatitis Indiana Virus and Differential Host Cell Response

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1196
Author(s):  
Balázs Kakuk ◽  
András Attila Kiss ◽  
Gábor Torma ◽  
Zsolt Csabai ◽  
István Prazsák ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Patterns ◽  
Viral Gene Expression ◽  
Fibroblast Cell ◽  
Economic Loss ◽  
Viral Gene ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Vesicular Stomatitis

Vesicular stomatitis Indiana virus (VSIV) of genus Vesiculovirus, species IndianaVesiculovirus (formerly as Vesicular stomatitis virus, VSV) causes a disease in livestock that is very similar to the foot and mouth disease, thereby an outbreak may lead to significant economic loss. Long-read sequencing (LRS) -based approaches already reveal a hidden complexity of the transcriptomes in several viruses. This technique has been utilized for the sequencing of the VSIV genome, but our study is the first for the application of this technique for the profiling of the VSIV transcriptome. Since LRS is able to sequence full-length RNA molecules, it thereby provides more accurate annotation of the transcriptomes than the traditional short-read sequencing methods. The objectives of this study were to assemble the complete transcriptome of using nanopore sequencing, to ascertain cell-type specificity and dynamics of viral gene expression, and to evaluate host gene expression changes induced by the viral infection. We carried out a time-course analysis of VSIV gene expression in human glioblastoma and primate fibroblast cell lines using a nanopore-based LRS approach and applied both amplified and direct cDNA sequencing (as well as cap-selection) for a fraction of samples. Our investigations revealed that, although the VSIV genome is simple, it generates a relatively complex transcriptomic architecture. In this study, we also demonstrated that VSIV transcripts vary in structure and exhibit differential gene expression patterns in the two examined cell types.

scholarly journals Nanopore Assay Reveals Cell-type-dependent Gene Expression of Indiana Vesiculovirus and Differential Host Cell Response

2021 ◽  
Author(s):  
Balázs Kakuk ◽  
András Attila Kiss ◽  
Gábor Torma ◽  
Zsolt Csabai ◽  
István Prazsák ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Patterns ◽  
Viral Gene Expression ◽  
Fibroblast Cell ◽  
Economic Loss ◽  
Viral Gene ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Vesicular Stomatitis

Indiana Vesiculovirus (IVV; formerly as Vesicular stomatitis virus and Vesicular stomatitis Indiana virus) causes a disease in livestock that is very similar to the foot and mouth disease thereby an outbreak may lead to significant economic loss. Long-read sequencing (LRS) -based approaches revealed a hidden complexity of the transcriptomes in several viruses already. This technique was utilized already for the sequencing of the IVV genome, but our study is the first for the application of this technique for the profiling of IVV transcriptome. Since LRS is able to sequence full-length RNA molecules, and thereby providing more accurate annotation of the transcriptomes than the traditional short-read sequencing methods. The objectives of this study were to assemble the complete transcriptome of using nanopore sequencing, to ascertain cell-type specificity and dynamics of viral gene expression and to evaluate host gene expression changes induced by the viral infection. We carried out a time-course analysis of IVV gene expression in human glioblastoma and primate fibroblast cell lines using a nanopore-based LRS approach and applied both amplified and direct cDNA sequencing, as well as cap-selection for a fraction of samples. Our investigations revealed that, although the IVV genome is simple, it generates a relative complex transcriptomic architecture. In this study, we also demonstrated that IVV transcripts vary in structure and exhibit differential gene expression patterns in the two examined cell types.

scholarly journals The Presence of p53 Influences the Expression of Multiple Human Cytomegalovirus Genes at Early Times Postinfection

2009 ◽  
Vol 83 (9) ◽  
pp. 4316-4325 ◽  
Author(s):  
Holger Hannemann ◽  
Kyle Rosenke ◽  
John M. O'Dowd ◽  
Elizabeth A. Fortunato
Keyword(s):  
Gene Expression ◽  
Human Cytomegalovirus ◽  
Time Course ◽  
Viral Gene Expression ◽  
Fibroblast Cell ◽  
Viral Gene ◽  
Group 3 ◽  
Group 2 ◽  
Microarray Analyses ◽  
Group 1

ABSTRACT Human cytomegalovirus (HCMV) is a common cause of morbidity and mortality in immunocompromised and immunosuppressed individuals. During infection, HCMV is known to employ host transcription factors to facilitate viral gene expression. To further understand the previously observed delay in viral replication and protein expression in p53 knockout cells, we conducted microarray analyses of p53+/+ and p53−/− immortalized fibroblast cell lines. At a multiplicity of infection (MOI) of 1 at 24 h postinfection (p.i.), the expression of 22 viral genes was affected by the absence of p53. Eleven of these 22 genes (group 1) were examined by real-time reverse transcriptase, or quantitative, PCR (q-PCR). Additionally, five genes previously determined to have p53 bound to their nearest p53-responsive elements (group 2) and three control genes without p53 binding sites in their upstream sequences (group 3) were also examined. At an MOI of 1, >3-fold regulation was found for five group 1 genes. The expression of group 2 and 3 genes was not changed. At an MOI of 5, all genes from group 1 and four of five genes from group 2 were found to be regulated. The expression of control genes from group 3 remained unchanged. A q-PCR time course of four genes revealed that p53 influences viral gene expression most at immediate-early and early times p.i., suggesting a mechanism for the reduced and delayed production of virions in p53−/− cells.

scholarly journals Temporal Transcription Program of Recombinant Autographa californica Multiple Nucleopolyhedrosis Virus

2006 ◽  
Vol 80 (18) ◽  
pp. 8989-8999 ◽  
Author(s):  
Shih Sheng Jiang ◽  
I-Shou Chang ◽  
Lin-Wei Huang ◽  
Po-Cheng Chen ◽  
Chi-Chung Wen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Patterns ◽  
Viral Gene Expression ◽  
Autographa Californica ◽  
Viral Gene ◽  
Lepidopteran Insects ◽  
Custom Made ◽  
Nucleopolyhedrosis Virus ◽  
Transcription Program

ABSTRACT Baculoviruses, a family of large, rod-shaped viruses that mainly infect lepidopteran insects, have been widely used to transduce various cells for exogenous gene expression. Nonetheless, how a virus controls its transcription program in cells is poorly understood. With a custom-made baculovirus DNA microarray, we investigated the recombinant Autographa californica multiple nucleopolyhedrosis virus (AcMNPV) gene expression program in lepidopteran Sf21 cells over the time course of infection. Our analysis of transcription kinetics in the cells uncovered sequential viral gene expression patterns possibly regulated by different mechanisms during different phases of infection. To gain further insight into the regulatory network, we investigated the transcription program of a mutant virus deficient in an early transactivator (pe38) and uncovered several pe38-dependent and pe38-independent genes. This study of baculovirus dynamic transcription programs in different virus genetic backgrounds provides new molecular insights into how gene expression in viruses is regulated.

scholarly journals Viral Gene Expression Patterns in Human Herpesvirus 6B-Infected T Cells

2002 ◽  
Vol 76 (15) ◽  
pp. 7578-7586 ◽  
Author(s):  
Bodil Øster ◽  
Per Höllsberg
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Protein Synthesis ◽  
De Novo ◽  
Expression Patterns ◽  
Human Herpesvirus ◽  
Viral Gene Expression ◽  
Polymerase Activity ◽  
Viral Gene ◽  
De Novo Protein Synthesis

ABSTRACT Herpesvirus gene expression is divided into immediate-early (IE) or α genes, early (E) or β genes, and late (L) or γ genes on the basis of temporal expression and dependency on other gene products. By using real-time PCR, we have investigated the expression of 35 human herpesvirus 6B (HHV-6B) genes in T cells infected by strain PL-1. Kinetic analysis and dependency on de novo protein synthesis and viral DNA polymerase activity suggest that the HHV-6B genes segregate into six separate kinetic groups. The genes expressed early (groups I and II) and late (groups V and VI) corresponded well with IE and L genes, whereas the intermediate groups III and IV contained E and L genes. Although HHV-6B has characteristics similar to those of other roseoloviruses in its overall gene regulation, we detected three B-variant-specific IE genes. Moreover, genes that were independent of de novo protein synthesis clustered in an area of the viral genome that has the lowest identity to the HHV-6A variant. The organization of IE genes in an area of the genome that differs from that of HHV-6A underscores the distinct differences between HHV-6B and HHV-6A and may provide a basis for further molecular and immunological analyses to elucidate their different biological behaviors.

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

2012 ◽  
Vol 93 (5) ◽  
pp. 1046-1058 ◽  
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.

scholarly journals Global Analysis of Baculovirus Autographa californica Multiple Nucleopolyhedrovirus Gene Expression in the Midgut of the Lepidopteran HostTrichoplusia ni

2018 ◽  
Vol 92 (23) ◽  
Author(s):  
Anita Shrestha ◽  
Kan Bao ◽  
Yun-Ru Chen ◽  
Wenbo Chen ◽  
Ping Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Trichoplusia Ni ◽  
Cultured Cells ◽  
Expression Profiles ◽  
Secondary Infection ◽  
Expression Patterns ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Viral Genes

ABSTRACTThe baculovirusAutographa californica multiple nucleopolyhedrovirus(AcMNPV) is a large double-stranded DNA (dsDNA) virus that encodes approximately 156 genes and is highly pathogenic to a variety of larval lepidopteran insects in nature. Oral infection of larval midgut cells is initiated by the occlusion-derived virus (ODV), while secondary infection of other tissues is mediated by the budded virus (BV). Global viral gene expression has been studied in detail in BV-infected cell cultures, but studies of ODV infection in the larval midgut are limited. In this study, we examined expression of the ∼156 AcMNPV genes inTrichoplusia nimidgut tissue using a transcriptomic approach. We analyzed expression profiles of viral genes in the midgut and compared them with profiles from aT. nicell line (Tnms42). Several viral genes (p6.9,orf76,orf75,pp31,Ac-bro,odv-e25, andodv-ec27) had high expression levels in the midgut throughout the infection. Also, the expression of genes associated with occlusion bodies (polhandp10) appeared to be delayed in the midgut in comparison with the cell line. Comparisons of viral gene expression profiles revealed remarkable similarities between the midgut and cell line for most genes, although substantial differences were observed for some viral genes. These included genes associated with high level BV production (fp-25k), acceleration of systemic infection (v-fgf), and enhancement of viral movement (arif-1/orf20). These differential expression patterns appear to represent specific adaptations for virus infection and transmission through the polarized cells of the lepidopteran midgut.IMPORTANCEBaculoviruses such as AcMNPV are pathogens that are natural regulators of certain insect populations. Baculovirus infections are biphasic, with a primary phase initiated by oral infection of midgut epithelial cells by occlusion-derived virus (ODV) virions and a secondary phase in which other tissues are infected by budded-virus (BV) virions. While AcMNPV infections in cultured cells have been studied extensively, comparatively little is known regarding primary infection in the midgut. In these studies, we identified gene expression patterns associated with ODV-mediated infection of the midgut inTrichoplusia niand compared those results with prior results from BV-infected cultured cells, which simulate secondary infection. These studies provide a detailed analysis of viral gene expression patterns in the midgut, which likely represent specific viral strategies to (i) overcome or avoid host defenses in the gut and (ii) rapidly move infection from the midgut, into the hemocoel to facilitate systemic infection.

scholarly journals Regulation of Gene Expression in Primate Polyomaviruses

2009 ◽  
Vol 83 (21) ◽  
pp. 10846-10856 ◽  
Author(s):  
Martyn K. White ◽  
Mahmut Safak ◽  
Kamel Khalili
Keyword(s):  
Gene Expression ◽  
Jc Virus ◽  
Regulation Of Gene Expression ◽  
T Antigen ◽  
Bk Virus ◽  
Viral Gene ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Karolinska Institute ◽  
Human Polyomaviruses

ABSTRACT Polyomaviruses are a growing family of small DNA viruses with a narrow tropism for both the host species and the cell type in which they productively replicate. Species host range may be constrained by requirements for precise molecular interactions between the viral T antigen, host replication proteins, including DNA polymerase, and the viral origin of replication, which are required for viral DNA replication. Cell type specificity involves, at least in part, transcription factors that are necessary for viral gene expression and restricted in their tissue distribution. In the case of the human polyomaviruses, BK virus (BKV) replication occurs in the tubular epithelial cells of the kidney, causing nephropathy in kidney allograft recipients, while JC virus (JCV) replication occurs in the glial cells of the central nervous system, where it causes progressive multifocal leukoencephalopathy. Three new human polyomaviruses have recently been discovered: MCV was found in Merkel cell carcinoma samples, while Karolinska Institute Virus and Washington University Virus were isolated from the respiratory tract. We discuss control mechanisms for gene expression in primate polyomaviruses, including simian vacuolating virus 40, BKV, and JCV. These mechanisms include not only modulation of promoter activities by transcription factor binding but also enhancer rearrangements, restriction of DNA methylation, alternate early mRNA splicing, cis-acting elements in the late mRNA leader sequence, and the production of viral microRNA.

scholarly journals 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

2002 ◽  
Vol 76 (19) ◽  
pp. 9744-9755 ◽  
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.

scholarly journals Prediction of a cell-type specific mouse mesoconnectome using gene expression data

2019 ◽  
Author(s):  
Nestor Timonidis ◽  
Rembrandt Bakker ◽  
Paul Tiesinga
Keyword(s):  
Gene Expression ◽  
Computational Models ◽  
Missing Values ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Brain Regions ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Major Step ◽  
Gene Modules

AbstractReconstructing brain connectivity at sufficient resolution for computational models designed to study the biophysical mechanisms underlying cognitive processes is extremely challenging. For such a purpose, a mesoconnectome that includes laminar and cell-type specificity would be a major step forward. We analysed the ability of gene expression patterns to predict cell-type and laminar specific projection patterns and analyzed the biological context of the most predictive groups of genes. To achieve our goal, we used publicly available volumetric gene expression and connectivity data and pre-processed it for prediction by averaging across brain regions, imputing missing values and rescaling. Afterwards, we predicted the strength of axonal projections and their binary form using expression patterns of individual genes and co-expression patterns of spatial gene modules.For predicting projection strength, we found that ridge (L2-regularized) regression had the highest cross-validated accuracy with a median r2 score of 0.54 which corresponded for binarized predictions to a median area under the ROC value of 0.89. Next, we identified 200 spatial gene modules using the dictionary learning and sparse coding approach. We found that these modules yielded predictions of comparable accuracy, with a median r2 score of 0.51. Finally, a gene ontology enrichment analysis of the most predictive gene groups resulted in significant annotations related to postsynaptic function.Taken together, we have demonstrated a prediction pipeline that can be used to perform multimodal data integration to improve the accuracy of the predicted mesoconnectome and support other neuroscience use cases.

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