Abstract:
:We have developed a high-throughput sequencing (HTS) workflow for investigating paramyxovirus transcription and replication. We show that sequencing of oligo(dT)-selected polyadenylated mRNAs, without considering the orientation of the RNAs from which they had been generated, cannot accurately be used to analyze the abundance of viral mRNAs because genomic RNA copurifies with the viral mRNAs. The best method is directional sequencing of infected cell RNA that has physically been depleted of ribosomal and mitochondrial RNA followed by bioinformatic steps to differentiate data originating from genomes from viral mRNAs and antigenomes. This approach has the advantage that the abundance of viral mRNA (and antigenomes) and genomes can be analyzed and quantified from the same data. We investigated the kinetics of viral transcription and replication during infection of A549 cells with parainfluenza virus type 2 (PIV2), PIV3, PIV5, or mumps virus and determined the abundances of individual viral mRNAs and readthrough mRNAs. We found that the mRNA abundance gradients differed significantly between all four viruses but that for each virus the pattern remained relatively stable throughout infection. We suggest that rapid degradation of non-poly(A) mRNAs may be primarily responsible for the shape of the mRNA abundance gradient in parainfluenza virus 3, whereas a combination of this factor and disengagement of RNA polymerase at intergenic sequences, particularly those at the NP:P and P:M gene boundaries, may be responsible in the other viruses.IMPORTANCE High-throughput sequencing (HTS) of virus-infected cells can be used to study in great detail the patterns of virus transcription and replication. For paramyxoviruses, and by analogy for all other negative-strand RNA viruses, we show that directional sequencing must be used to distinguish between genomic RNA and mRNA/antigenomic RNA because significant amounts of genomic RNA copurify with poly(A)-selected mRNA. We found that the best method is directional sequencing of total cell RNA, after the physical removal of rRNA (and mitochondrial RNA), because quantitative information on the abundance of both genomic RNA and mRNA/antigenomes can be simultaneously derived. Using this approach, we revealed new details of the kinetics of virus transcription and replication for parainfluenza virus (PIV) type 2, PIV3, PIV5, and mumps virus, as well as on the relative abundance of the individual viral mRNAs.
journal_name
J Viroljournal_title
Journal of virologyauthors
Wignall-Fleming EB,Hughes DJ,Vattipally S,Modha S,Goodbourn S,Davison AJ,Randall REdoi
10.1128/JVI.00571-19subject
Has Abstractpub_date
2019-08-13 00:00:00issue
17eissn
0022-538Xissn
1098-5514pii
JVI.00571-19journal_volume
93pub_type
杂志文章abstract:UNLABELLED:During HIV-1 assembly, the Gag viral proteins are targeted and assemble at the inner leaflet of the cell plasma membrane. This process could modulate the cortical actin cytoskeleton, located underneath the plasma membrane, since actin dynamics are able to promote localized membrane reorganization. In additio...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00469-15
更新日期:2015-08-01 00:00:00
abstract::Expression of the human ADA cDNA encoded by the Moloney murine leukemia virus spliced RNA form is enhanced by intron-contained sequences. The presence of sequences corresponding to the viral gag gene in a Moloney murine leukemia virus-based vector results in the generation of 10- to 40-fold higher titers of virus. ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.61.5.1647-1650.1987
更新日期:1987-05-01 00:00:00
abstract::Adenovirus deletion mutants were studied to examine the influence of the 5' untranslated sequence on the translation of early region 1A mRNAs. Alterations of the 5' untranslated sequence, including complete deletion of the wild-type 5' untranslated sequence, did not significantly affect the rate of translation. ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.51.3.884-888.1984
更新日期:1984-09-01 00:00:00
abstract::Rat (3Y1) and hamster embryo brain cells were transformed by wild-type adenovirus type 12 or the DNA-minus temperature-sensitive mutant ts401. The ts401-transformed 3Y1 cells, but not the wild-type transformants, displayed a temperature-sensitive response with respect to the following characteristics of the transforme...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.29.1.250-260.1979
更新日期:1979-01-01 00:00:00
abstract::The cloned transcription factor hepatocyte nuclear factor 1 (HNF1) transactivates transcription from the hepatitis B virus (HBV) large surface antigen promoter but does not influence the transcriptional activities of the other three HBV promoters. This indicates that this transcription factor can differentially influe...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.65.11.5774-5781.1991
更新日期:1991-11-01 00:00:00
abstract::Bicistronic RNAs containing the 373-nucleotide-long 5' nontranslated region (NTR) of the classical swine fever virus (CSFV) genome as intercistronic spacer were used to show the presence of an internal ribosome entry site (IRES) in the 5' end of the CSFV genome. By coexpression of the poliovirus 2A protease it was dem...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.71.1.451-457.1997
更新日期:1997-01-01 00:00:00
abstract::Recently, significant numbers of individuals with primary human immunodeficiency virus (HIV) infection have been found to harbor viral strains with reduced susceptibility to antiretroviral drugs. In one study, HIV from 16% of such antiretroviral-naive individuals was shown to have a susceptibility to nonnucleoside rev...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.74.22.10269-10273.2000
更新日期:2000-11-01 00:00:00
abstract::Mechanisms by which the plus-sense RNA genomes of picornaviruses are replicated remain poorly defined, but existing models do not suggest a role for sequences encoding the capsid proteins. However, candidate RNA replicons (delta P1 beta gal and delta P1Luc), representing the sequence of human rhinovirus 14 virus (HRV-...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.70.3.1941-1952.1996
更新日期:1996-03-01 00:00:00
abstract::In contrast to humans, adult but not infant small animals are resistant to rotavirus diarrhea. The pathophysiological mechanism behind this age-restricted diarrhea is currently unresolved, and this question was investigated by studying the secretory state of the small intestines of adult mice infected with rotavirus. ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00152-06
更新日期:2006-11-01 00:00:00
abstract::Immature retroviral particles are assembled by self-association of the structural polyprotein precursor Gag. During maturation the Gag polyprotein is proteolytically cleaved, yielding mature structural proteins, matrix (MA), capsid (CA), and nucleocapsid (NC), that reassemble into a mature viral particle. Proteolytic ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.05564-11
更新日期:2012-02-01 00:00:00
abstract::As a subunit of both the P-L polymerase complex and the P-N assembly complex, the vesicular stomatitis virus (VSV) P protein plays a pivotal role in transcription and replication of the viral genome. Constitutive phosphorylation of this protein is currently thought to be essential for formation of the P-L complex. We ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.70.7.4538-4548.1996
更新日期:1996-07-01 00:00:00
abstract::Rubella virus contains three structural proteins, capsid, E2, and E1. E2 and E1 are type I membrane glycoproteins that form a heterodimer in the endoplasmic reticulum (ER) before they are transported to and retained in the Golgi complex, where virus assembly occurs. The bulk of unassembled E2 and E1 subunits are not t...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.71.10.7670-7680.1997
更新日期:1997-10-01 00:00:00
abstract::The Sindbis virus minimal subgenomic mRNA promoter (spanning positions -19 to +5 relative to the subgenomic mRNA start site) is approximately three- to sixfold less active than the fully active -98 to +14 promoter region. We identified two elements flanking the -19 to +5 region which increase its transcription to leve...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.75.8.3509-3519.2001
更新日期:2001-04-01 00:00:00
abstract::Three polyadenylated RNAs, 9, 7.3, and 3.5 kilobases long, of a human endogenous retrovirus, ERV3, are abundant in human placental chorion, representing about 0.03 to 0.05% of the total mRNA. We characterized the structure of these mRNAs by Northern blot and S1 nuclease mapping analyses. We found that all three RNAs w...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.61.7.2182-2191.1987
更新日期:1987-07-01 00:00:00
abstract::Linear hepadnavirus DNA in primary hepatocyte cultures efficiently participates in intra- and intermolecular nonhomologous recombination at its ends. The products of this recombination are (i) monomeric covalently closed circular DNAs (cccDNAs) with deletions and insertions around the site of joining and (ii) oligomer...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.69.7.4029-4036.1995
更新日期:1995-07-01 00:00:00
abstract::Presumably due to the capability of the hepatitis C virus (HCV) to evade the antiviral effects of alpha interferon, treatment is ineffective in more than half of chronically genotype HCV type 1 (HCV-1)-infected patients. Previous approaches to correlate the number of amino acid mutations within regions of HCV nonstruc...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.76.21.11079-11090.2002
更新日期:2002-11-01 00:00:00
abstract::The major structural glycoprotein E2 of classical swine fever virus (CSFV) is responsible for eliciting neutralizing antibodies and conferring protective immunity. The current structural model of this protein predicts its surface-exposed region at the N terminus with a short stretch of the C-terminal residues spanning...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.74.24.11619-11625.2000
更新日期:2000-12-01 00:00:00
abstract::Activation of IκB kinase subunit γ (IKKγ), a key regulator of the classical NF-κB pathway, by the vFLIP protein of Kaposi's sarcoma-associated herpesvirus (KSHV) and the Tax protein of human T cell lymphotropic virus type 1 (HTLV1) is essential for virus-associated cancer. We show that vFLIP and Tax activate this path...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.02337-10
更新日期:2011-07-01 00:00:00
abstract::Dengue virus (DENV) is a mosquito-borne virus that infects upward of 300 million people annually and has the potential to cause fatal hemorrhagic fever and shock. While the parameters contributing to dengue immunopathogenesis remain unclear, the collapse of redox homeostasis and the damage induced by oxidative stress ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01551-20
更新日期:2020-11-23 00:00:00
abstract:UNLABELLED:Many viruses have the capacity to prevent a cell from being infected by a second virus, often termed superinfection exclusion. Alphaherpesviruses, including the human pathogen herpes simplex virus 1 (HSV-1) and the animal herpesvirus pseudorabies virus (PRV), encode a membrane-bound glycoprotein, gD, that ca...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00089-16
更新日期:2016-03-28 00:00:00
abstract::Porcine epidemic diarrhea virus (PEDV) causes severe diarrhea and high mortality rates in newborn piglets, leading to massive losses to the swine industry worldwide during recent epidemics. Intense research efforts are now focusing on defining viral characteristics that confer a growth advantage, pathogenicity, or cel...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01660-16
更新日期:2017-01-03 00:00:00
abstract::Preferential integration into transcriptionally active regions of genomes has been observed for retroviral vectors based on gamma-retroviruses and lentiviruses. However, differences in the integration site preferences were detected, which might be explained by differences in viral components of the preintegration comp...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00373-06
更新日期:2006-08-01 00:00:00
abstract::The herpes simplex virus type 1 latency-associated transcript (LAT) inhibits apoptosis. We demonstrate here that LAT influences the accumulation of the Bcl-x(L) transcript versus the Bcl-x(S) transcript in Neuro-2A cells. Bcl-x(L) encodes an antiapoptotic protein, whereas Bcl-x(S) encodes a proapoptotic protein. Promo...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.77.19.10714-10718.2003
更新日期:2003-10-01 00:00:00
abstract::In this work we show evidence of mother-to-offspring transmission in a transgenic mouse line expressing bovine PrP (boTg) experimentally infected by intracerebral administration of bovine spongiform encephalopathy (BSE) prions. PrP(res) was detected in brains of newborns from infected mothers only when mating was allo...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.79.13.8665-8668.2005
更新日期:2005-07-01 00:00:00
abstract::Two of 25 healthy pet sooty mangabey (SM) monkeys (Cercocebus atys) living in West Africa were seropositive by immunoblot when surveyed for antibody to simian immunodeficiency virus of macaques (SIVmac). SIVsmLIB1 was isolated from one of the pet sooty mangabeys. Nucleotide sequence data showed that this isolate is a ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.65.8.4480-4485.1991
更新日期:1991-08-01 00:00:00
abstract::The latency-related (LR) gene of bovine herpesvirus 1 (BHV-1) is abundantly expressed during latency. A mutant BHV-1 strain that contains three stop codons at the 5' terminus of the LR gene (LR mutant) does not reactivate from latency. This study demonstrates that the LR mutant does not express open reading frame 2 or...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.78.6.3184-3189.2004
更新日期:2004-03-01 00:00:00
abstract::Canine distemper virus (CDV) uses signaling lymphocyte activation molecule (SLAM), expressed on immune cells, as a receptor. However, epithelial and neural cells are also affected by CDV in vivo. Wild-type CDV strains showed efficient replication with syncytia in Vero cells expressing dog nectin4, and the infection wa...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00824-12
更新日期:2012-09-01 00:00:00
abstract::The coding capacity of human cytomegalovirus (HCMV) for glycoproteins by far exceeds that of other herpesviruses. Few of these proteins have been characterized so far. We have investigated the gene product of reading frame UL132. The putative protein product of UL132 is a glycoprotein with a theoretical mass of 29.8 k...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.79.18.11837-11847.2005
更新日期:2005-09-01 00:00:00
abstract::Published work (D. J. McGeoch, Nucleic Acids Res. 18:4105-4110, 1990; J. E. McGeehan, N. W. Depledge, and D. J. McGeoch, Curr. Protein Peptide Sci. 2:325-333, 2001) has indicated that evolution of dUTPase in the class of herpesviruses that infect mammals and birds involved capture of a host gene followed by a duplicat...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.79.20.12880-12892.2005
更新日期:2005-10-01 00:00:00
abstract::The enzymatic activity of recombinant influenza virus RNA polymerase is strictly dependent on the addition of a template RNA containing 5' and 3' viral sequences. Here we report the analysis of the binding specificity and physical characterization of the complex by using gel shift, modification interference, and densi...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.68.8.5108-5116.1994
更新日期:1994-08-01 00:00:00