scholarly journals Cytomegalovirus late transcription factor target sequence diversity orchestrates viral early to late transcription

2021 ◽  
Vol 17 (8) ◽  
pp. e1009796
Author(s):  
Ming Li ◽  
Qiaolin Hu ◽  
Geoffrey Collins ◽  
Mrutyunjaya Parida ◽  
Christopher B. Ball ◽  
...  
Keyword(s):  
Dna Replication ◽  
Rna Polymerase Ii ◽  
Core Promoter ◽  
Target Sequence ◽  
Viral Dna ◽  
Viral Dna Replication ◽  
Pol Ii ◽  
Viral Promoters ◽  
Late Transcription ◽  
Target Sequences

Beta- and gammaherpesviruses late transcription factors (LTFs) target viral promoters containing a TATT sequence to drive transcription after viral DNA replication has begun. Human cytomegalovirus (HCMV), a betaherpesvirus, uses the UL87 LTF to bind both TATT and host RNA polymerase II (Pol II), whereas the UL79 LTF has been suggested to drive productive elongation. Here we apply integrated functional genomics (dTag system, PRO-Seq, ChIP-Seq, and promoter function assays) to uncover the contribution of diversity in LTF target sequences in determining degree and scope to which LTFs drive viral transcription. We characterize the DNA sequence patterns in LTF-responsive and -unresponsive promoter populations, determine where and when Pol II initiates transcription, identify sites of LTF binding genome-wide, and quantify change in nascent transcripts from individual promoters in relation to core promoter sequences, LTF loss, stage of infection, and viral DNA replication. We find that HCMV UL79 and UL87 LTFs function concordantly to initiate transcription from over half of all active viral promoters in late infection, while not appreciably affecting host transcription. Both LTFs act on and bind to viral early-late and late kinetic-class promoters. Over one-third of these core promoters lack the TATT and instead have a TATAT, TGTT, or YRYT. The TATT and non-TATT motifs are part of a sequence block with a sequence code that correlates with promoter transcription level. LTF occupancy of a TATATA palindrome shared by back-to-back promoters is linked to bidirectional transcription. We conclude that diversity in LTF target sequences shapes the LTF-transformative program that drives the viral early-to-late transcription switch.

scholarly journals Human cytomegalovirus RNA2.7 regulates host cell cycle and facilitates viral DNA replication by inhibiting RNA polymerase II phosphorylation

2018 ◽  
Author(s):  
Yujing Huang ◽  
Jing Zhang ◽  
Xin Guo ◽  
Qing Wang ◽  
Zhongyang Liu ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Human Cytomegalovirus ◽  
Cell Cycle Control ◽  
S Phase ◽  
Viral Dna ◽  
Viral Dna Replication ◽  
Pol Ii

AbstractHuman cytomegalovirus (HCMV) is a ubiquitous pathogen belongs to the beta herpesvirus family. RNA2.7 is a viral long non-coding RNA accounting for more than 20% of total viral transcripts at early time of infection. By construction of RNA2.7 deleted mutant and genome transcriptomic analysis, RNA2.7 is demonstrated to repress host cellular RNA polymerase II (Pol II)-dependent transcription through inhibiting the phosphorylation of RNA polymerase II (Pol II). Co-immunoprecipitation, RNA immunoprecipitation and RNA electrophoretic mobility shift assay are followed to investigate its mechnism. A 145nt-in-length fragment in RNA2.7 is identified to bind to Pol II and block the interaction between Pol II and phosphorylated cyckin-dependent kinase 9 (phospho-CDK9). By inhibiting Pol II phosphorylation, RNA2.7 decreases the transcription and expression levels of chromatin licensing and DNA replication factor 1 (Cdt1) and cell division cycle gene 6 (Cdc6). Through above way, RNA2.7 prevents the entry of cells into S phase and facilitates viral DNA replication. Our results discover the functions of HCMV RNA2.7 in regulation of Pol II phosphorylation and cell cycle control during infection.Author summaryHuman cytomegalovirus (HCMV) RNA2.7 is a viral lncRNA that is most abundant during infection. Here we show that a 145nt-in-length fragment in RNA2.7 binds to RNA polymerase II (Pol II) and blocks the interaction between Pol II and phosphorylated cyckin-dependent kinase 9 (phospho-CDK9). By inhibiting Pol II phosphorylation, RNA2.7 decreases the transcription and expression levels of chromatin licensing and DNA replication factor 1 (Cdt1) and cell division cycle gene 6 (Cdc6), and blocks host cells entering into S phase. RNA2.7 is confirmed to facilitate viral DNA replication through decreasing Cdt1 and Cdc6. Therefore, our results discover the functions of HCMV RNA2.7 in regulation of Pol II phosphorylation and cell cycle control during infection.

scholarly journals Analysis of an Autographa californica Multicapsid Nucleopolyhedrovirus lef-6-Null Virus: LEF-6 Is Not Essential for Viral Replication but Appears To Accelerate Late Gene Transcription

2002 ◽  
Vol 76 (11) ◽  
pp. 5503-5514 ◽  
Author(s):  
Guangyun Lin ◽  
Gary W. Blissard
Keyword(s):  
Dna Replication ◽  
Viral Replication ◽  
Gene Transcription ◽  
Cellular Localization ◽  
Autographa Californica ◽  
Late Gene ◽  
Infection Cycle ◽  
Viral Dna ◽  
Viral Dna Replication ◽  
Late Transcription

ABSTRACT The Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) lef-6 gene was previously shown to be necessary for optimal transcription from an AcMNPV late promoter in transient late expression assays. In the present study, we examined the expression and cellular localization of lef-6 during the AcMNPV infection cycle and generated a lef-6-null virus for studies of the role of lef-6 in the infection cycle. Transcription of lef-6 was detected from 4 to 48 h postinfection, and the LEF-6 protein was identified in dense regions of infected cell nuclei, a finding consistent with its potential role as a late transcription factor. To examine lef-6 in the context of the AcMNPV infection cycle, we deleted the lef-6 gene from an AcMNPV genome propagated as an infectious BACmid in Escherichia coli. Unexpectedly, the resulting AcMNPV lef-6-null BACmid (vAclef6KO) was able to propagate in cell culture, although virus yields were substantially reduced. Thus, the lef-6 gene is not essential for viral replication in Sf9 cells. Two “repair” AcMNPV BACmids (vAclef6KO-REP-P and vAclef6KO-REP-ie1P) were generated by transposition of the lef-6 gene into the polyhedrin locus of the vAclef6KO BACmid. Virus yields from the two repair viruses were similar to those from wild-type AcMNPV or a control (BACmid-derived) virus. The lef-6-null BACmid (vAclef6KO) was further examined to determine whether the deletion of lef-6 affected DNA replication or late gene transcription in the context of an infection. The lef-6 deletion did not appear to affect viral DNA replication. Using Northern blot analysis, we found that although early transcription was apparently unaffected, both late and very late transcription were delayed in cells infected with the lef-6-null BACmid. This phenotype was rescued in viruses containing the lef-6 gene reinserted into the polyhedrin locus. Thus, the lef-6 gene was not essential for either viral DNA replication or late gene transcription, but the absence of lef-6 resulted in a substantial delay in the onset of late transcription. Therefore, lef-6 appears to accelerate the infection cycle of AcMNPV.

scholarly journals Analysis of an Autographa californica Nucleopolyhedrovirus lef-11 Knockout: LEF-11 Is Essential for Viral DNA Replication

2002 ◽  
Vol 76 (6) ◽  
pp. 2770-2779 ◽  
Author(s):  
Guangyun Lin ◽  
Gary W. Blissard
Keyword(s):  
Dna Replication ◽  
Viral Replication ◽  
Autographa Californica ◽  
Sf9 Cells ◽  
Infection Cycle ◽  
Wild Type ◽  
Viral Dna ◽  
Viral Dna Replication ◽  
Late Transcription ◽  
Late Expression

ABSTRACT The Autographa californica nucleopolyhedrovirus (AcMNPV) lef-11 gene was previously identified by transient late expression assays as a gene important for viral late gene expression. The lef-11 gene was not previously identified as necessary for DNA replication in transient origin-dependent plasmid DNA replication assays. To examine the role of lef-11 in the context of the infection cycle, we generated a deletion of the lef-11 gene by recombination in an AcMNPV genome propagated as a BACmid in Escherichia coli. The resulting AcMNPV lef-11-null BACmid (vAclef11KO) was unable to propagate in cell culture, although a “repair” AcMNPV BACmid (vAclef11KO-REP), which was generated by transposition of the lef-11 gene into the polyhedrin locus of the vAclef11KO BACmid, was able to replicate in a manner similar to wild-type or control AcMNPV viruses. Thus, the lef-11 gene is essential for viral replication in Sf9 cells. The vAclef11KO BACmid was examined to determine if the defect in viral replication resulted from a defect in DNA replication or from a defect in late transcription. The lef-11-null BACmid and control BACmids were transfected into Sf9 cells, and viral DNA replication was monitored. The viral DNA genome of the lef-11-null BACmid (vAclef11KO) was not amplified, whereas replication and amplification of the genomes of the repair BACmid (vAclef11KO-REP), wild-type AcMNPV, and a nonpropagating gp64-null control BACmid (vAcGUSgp64KO) were readily detected. Northern blot analysis of transcripts from selected early, late, and very late genes showed that late and very late transcription was absent in cells transfected with the lef-11-null BACmid. Thus, in contrast to prior studies using transient replication and late expression assays, studies of a lef-11-null BACmid indicate that LEF-11 is required for viral DNA replication during the infection cycle.

scholarly journals Antiviral Properties of the LSD1 Inhibitor SP-2509

2020 ◽  
Vol 94 (19) ◽  
Author(s):  
Mitchell R. Harancher ◽  
Jessica E. Packard ◽  
Shane P. Cowan ◽  
Neal A. DeLuca ◽  
Jill A. Dembowski
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Dna Replication ◽  
Viral Replication ◽  
Virus Production ◽  
Coupled Processes ◽  
Viral Dna ◽  
Viral Dna Replication ◽  
Pol Ii ◽  
Hsv 1

ABSTRACT Lysine-specific demethylase 1 (LSD1) targets cellular proteins, including histone H3, p53, E2F, and Dnmt1, and is involved in the regulation of gene expression, DNA replication, the cell cycle, and the DNA damage response. LSD1 catalyzes demethylation of histone H3K9 associated with herpes simplex virus 1 (HSV-1) immediate early (IE) promoters and is necessary for IE gene expression, viral DNA replication, and reactivation from latency. We previously found that LSD1 associates with HSV-1 replication forks and replicating viral DNA, suggesting that it may play a direct role in viral replication or coupled processes. We investigated the effects of the LSD1 inhibitor SP-2509 on the HSV-1 life cycle. Unlike previously investigated LSD1 inhibitors tranylcypromine (TCP) and OG-L002, which covalently attach to the LSD1 cofactor flavin adenine dinucleotide (FAD) to inhibit demethylase activity, SP-2509 has previously been shown to inhibit LSD1 protein-protein interactions. We found that SP-2509 does not inhibit HSV-1 IE gene expression or transcription factor and RNA polymerase II (Pol II) association with viral DNA prior to the onset of replication. However, SP-2509 does inhibit viral DNA replication, late gene expression, and virus production. We used EdC labeling of nascent viral DNA to image aberrant viral replication compartments that form in the presence of SP-2509. Treatment resulted in the formation of small replication foci that colocalize with replication proteins but are defective for Pol II recruitment. Taken together, these data highlight a potential new role for LSD1 in the regulation of HSV-1 DNA replication and gene expression after the onset of DNA replication. IMPORTANCE Treatment of HSV-1-infected cells with SP-2509 blocked viral DNA replication, gene expression after the onset of DNA replication, and virus production. These data support a potential new role for LSD1 in the regulation of viral DNA replication and successive steps in the virus life cycle, and further highlight the promising potential to utilize LSD1 inhibition as an antiviral approach.

The infection and viral DNA replication ofBocavirusminute virus of canine in permissive cells and non-permissive cells

2010 ◽  
Vol 34 (8) ◽  
pp. S60-S60
Author(s):  
Yuning Sun ◽  
Fang Li ◽  
Jianming Qiu ◽  
Xiaohong Lu
Keyword(s):  
Dna Replication ◽  
Viral Dna ◽  
Viral Dna Replication

scholarly journals Persistent Human Papillomavirus Infection

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 321
Author(s):  
Ashley N. Della Fera ◽  
Alix Warburton ◽  
Tami L. Coursey ◽  
Simran Khurana ◽  
Alison A. McBride
Keyword(s):  
Human Papillomavirus ◽  
Dna Replication ◽  
Cellular Proliferation ◽  
Basal Cells ◽  
Viral Dna ◽  
Viral Dna Replication ◽  
Viral Genomes ◽  
Cellular Environment ◽  
E6 And E7 ◽  
Cellular Replication

Persistent infection with oncogenic human papillomavirus (HPV) types is responsible for ~5% of human cancers. The HPV infectious cycle can sustain long-term infection in stratified epithelia because viral DNA is maintained as low copy number extrachromosomal plasmids in the dividing basal cells of a lesion, while progeny viral genomes are amplified to large numbers in differentiated superficial cells. The viral E1 and E2 proteins initiate viral DNA replication and maintain and partition viral genomes, in concert with the cellular replication machinery. Additionally, the E5, E6, and E7 proteins are required to evade host immune responses and to produce a cellular environment that supports viral DNA replication. An unfortunate consequence of the manipulation of cellular proliferation and differentiation is that cells become at high risk for carcinogenesis.

Mediator dynamics during heat shock in budding yeast

2021 ◽  
pp. gr.275750.121
Author(s):  
Debasish Sarkar ◽  
Z. Iris Zhu ◽  
Elisabeth R. Knoll ◽  
Emily Paul ◽  
David Landsman ◽  
...  
Keyword(s):  
Heat Shock ◽  
Rna Polymerase Ii ◽  
Budding Yeast ◽  
Core Promoter ◽  
Growth Conditions ◽  
Promoter Regions ◽  
Pol Ii ◽  
A Genome ◽  
Wide Scale ◽  
Stable Association

The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates pre-initiation complex (PIC) assembly, only transiently prior to Pol II escape. Interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes this association. However, Mediator occupancy and dynamics have not been examined on a genome-wide scale in yeast grown in nonstandard conditions. Here we investigate Mediator occupancy following heat shock or CdCl2 exposure, with and without depletion of Kin28. We find that Pol II occupancy exhibits similar dependence on Mediator under normal and heat shock conditions. However, while Mediator association increases at many genes upon Kin28 depletion under standard growth conditions, little or no increase is observed at most genes upon heat shock, indicating a more stable association of Mediator after heat shock. Mediator remains associated upstream of the core promoter at genes repressed by heat shock or CdCl2 exposure whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. This persistent association is strongest at promoters that bind the HMGB family member Hmo1, and is reduced but not eliminated in hmo1∆ yeast. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting altered dynamics or stronger engagement with activators under these conditions.

scholarly journals Computational identification and experimental characterization of preferred downstream positions in human core promoters

2021 ◽  
Author(s):  
René Dreos ◽  
Nati Malachi ◽  
Anna Sloutskin ◽  
Philipp Bucher ◽  
Tamar Juven-Gershon
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Motif Discovery ◽  
Core Promoter ◽  
Sequence Motifs ◽  
Promoter Element ◽  
Pol Ii ◽  
Core Promoters ◽  
The Core

AbstractMetazoan core promoters, which direct the initiation of transcription by RNA polymerase II (Pol II), may contain short sequence motifs termed core promoter elements/motifs (e.g. the TATA box, initiator (Inr) and downstream core promoter element (DPE)), which recruit Pol II via the general transcription machinery. The DPE was discovered and extensively characterized in Drosophila, where it is strictly dependent on both the presence of an Inr and the precise spacing from it. Since the Drosophila DPE is recognized by the human transcription machinery, it is most likely that some human promoters contain a downstream element that is similar, though not necessarily identical, to the Drosophila DPE. However, only a couple of human promoters were shown to contain a functional DPE, and attempts to computationally detect human DPE-containing promoters have mostly been unsuccessful. Using a newly-designed motif discovery strategy based on Expectation-Maximization probabilistic partitioning algorithms, we discovered preferred downstream positions (PDP) in human promoters that resemble the Drosophila DPE. Available chromatin accessibility footprints revealed that Drosophila and human Inr+DPE promoter classes are not only highly structured, but also similar to each other, particularly in the proximal downstream region. Clustering of the corresponding sequence motifs using a neighbor-joining algorithm strongly suggests that canonical Inr+DPE promoters could be common to metazoan species. Using reporter assays we demonstrate the contribution of the identified downstream positions to the function of multiple human promoters. Furthermore, we show that alteration of the spacing between the Inr and PDP by two nucleotides results in reduced promoter activity, suggesting a strict spacing dependency of the newly discovered human PDP on the Inr. Taken together, our strategy identified novel functional downstream positions within human core promoters, supporting the existence of DPE-like motifs in human promoters.Author summaryTranscription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properties to it. Interestingly, core promoter motifs can be located both upstream and downstream of the transcription start site. Variable compositions of core promoter elements have been identified. The initiator (Inr) motif and the downstream core promoter element (DPE) is a combination of elements that has been identified and extensively characterized in fruit flies. Although a few Inr+DPE - containing human promoters have been identified, the presence of transcriptionally important downstream core promoter positions within human promoters has been a matter of controversy in the literature. Here, using a newly-designed motif discovery strategy, we discovered preferred downstream positions in human promoters that resemble fruit fly DPE. Clustering of the corresponding sequence motifs in eight additional species indicated that such promoters could be common to multicellular non-plant organisms. Importantly, functional characterization of the newly discovered preferred downstream positions supports the existence of Inr+DPE-containing promoters in human genes.

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