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Steer B, Adler B, Adler H. Open reading frames M12/M13 jointly contribute to MHV-68 latency. J Gen Virol 2023; 104. [PMID: 37552062 DOI: 10.1099/jgv.0.001880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
Murine gammaherpesvirus 68 (MHV-68), a widely used small-animal model for the analysis of gammaherpesvirus pathogenesis, encodes the MHV-68-specific ORFs M12 and M13. The function of M12 and M13 has not been investigated so far. Therefore, we constructed and analysed recombinant MHV-68 with mutations in either M12, M13 or M12/M13. Both the M12 and M13 mutants did not display any phenotype in vitro or in vivo. However, although the M12/13 double mutant showed similar lytic growth in fibroblasts in vitro and in the lungs of infected mice as wild-type MHV-68, it was significantly attenuated in vivo during latency. This phenotype was completely restored in a revertant of the M12/13 double mutant. Thus, it appears that M12 and M13 might have redundant functions that are only revealed if both genes are lacking. The observation that M12/13 have a function during latency not only contributes to the further understanding of the pathogenesis of MHV-68 infection but might also be of interest considering that M12/13 are located at a genomic position similar to that of LMP2A and K15. The latter are important proteins of their respective human gammaherpesviruses EBV and KSHV that contribute to cellular survival, cell activation and proliferation, which was deduced from in vitro studies.
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Affiliation(s)
- Beatrix Steer
- Institute of Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Barbara Adler
- Max von Pettenkofer-Institute and Gene Center, Virology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Heiko Adler
- Institute of Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Member of the German Center of Lung Research (DZL), Munich, Germany
- Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-University Munich, Member of the German Center of Lung Research (DZL), Munich, Germany
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2
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Identification and characterization of a novel group of natural anti-sense transcripts from RNA1.2 gene locus of human cytomegalovirus. Chin Med J (Engl) 2019; 132:1591-1598. [PMID: 31205077 PMCID: PMC6616230 DOI: 10.1097/cm9.0000000000000299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background: Natural anti-sense transcripts (NATs), which are transcribed from the complementary DNA strand of annotated genes, exert regulatory function of gene expression. Increasing studies recognized anti-sense transcription widespread throughout human cytomegalovirus (HCMV) genome, whereas the anti-sense transcription of RNA1.2 gene locus has never been investigated. In this study, the transcription of the RNA1.2 anti-sense strand was investigated in clinically isolated HCMV strain. Methods: Strand-specific high-through RNA-sequencing (RNA-seq) was performed to find possible anti-sense transcripts (ASTs). For analyzing and visualization of RNA-seq data sets, Integrative Genomics Viewer software was applied. To confirm these possibilities, Northern blotting and rapid amplification of cDNA ends (RACE) were used. Results: Transcription of the opposite strand of RNA1.2 gene locus was detected by RNA-sequencing using RNAs extracted from human embryonic lung fibroblasts infected with HCMV clinical isolate HAN. At least three HCMV NATs, named RNA1.2 AST 1, RNA1.2 AST2, and RNA1.2 AST3, were characterized by Northern blotting and RACE analyses. These RNA1.2 ASTs orientated from the complementary strand of RNA1.2 locus during the late phase of HCMV infection. The 5′- and 3′-termini of these transcripts were located within the opposite sequence of the predicted RNA1.2 gene. Conclusion: A cluster of novel NATs was transcribed from the opposite sequence of the HCMV RNA1.2 gene region.
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O'Grady T, Feswick A, Hoffman BA, Wang Y, Medina EM, Kara M, van Dyk LF, Flemington EK, Tibbetts SA. Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68. Cell Rep 2019; 27:3988-4002.e5. [PMID: 31242428 PMCID: PMC7071827 DOI: 10.1016/j.celrep.2019.05.086] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 02/27/2019] [Accepted: 05/22/2019] [Indexed: 12/18/2022] Open
Abstract
The gammaherpesviruses, including Epstein-Barr virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68 (MHV68, MuHV-4, γHV68), are etiologic agents of a wide range of lymphomas and non-hematological malignancies. These viruses possess large and highly dense dsDNA genomes that feature >80 bidirectionally positioned open reading frames (ORFs). The abundance of overlapping transcripts and extensive splicing throughout these genomes have until now prohibited high throughput-based resolution of transcript structures. Here, we integrate the capabilities of long-read sequencing with the accuracy of short-read platforms to globally resolve MHV68 transcript structures using the transcript resolution through integration of multi-platform data (TRIMD) pipeline. This approach reveals highly complex features, including: (1) pervasive overlapping transcript structures; (2) transcripts containing intra-gene or trans-gene splices that yield chimeric ORFs; (3) antisense and intergenic transcripts containing ORFs; and (4) noncoding transcripts. This work sheds light on the underappreciated complexity of gammaherpesvirus transcription and provides an extensively revised annotation of the MHV68 transcriptome.
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Affiliation(s)
- Tina O'Grady
- Laboratory of Gene Expression and Cancer, GIGA-R (MBD), University of Liège, Liège, Belgium
| | - April Feswick
- Department of Molecular Genetics & Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Brett A Hoffman
- Department of Molecular Genetics & Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Yiping Wang
- Department of Molecular Genetics & Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Eva M Medina
- Department of Immunology and Microbiology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Mehmet Kara
- Department of Molecular Genetics & Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Linda F van Dyk
- Department of Immunology and Microbiology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Erik K Flemington
- Department of Pathology, Tulane Cancer Center, Tulane University, New Orleans, LA, USA.
| | - Scott A Tibbetts
- Department of Molecular Genetics & Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
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4
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Depledge DP, Srinivas KP, Sadaoka T, Bready D, Mori Y, Placantonakis DG, Mohr I, Wilson AC. Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen. Nat Commun 2019; 10:754. [PMID: 30765700 PMCID: PMC6376126 DOI: 10.1038/s41467-019-08734-9] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
Characterizing complex viral transcriptomes by conventional RNA sequencing approaches is complicated by high gene density, overlapping reading frames, and complex splicing patterns. Direct RNA sequencing (direct RNA-seq) using nanopore arrays offers an exciting alternative whereby individual polyadenylated RNAs are sequenced directly, without the recoding and amplification biases inherent to other sequencing methodologies. Here we use direct RNA-seq to profile the herpes simplex virus type 1 (HSV-1) transcriptome during productive infection of primary cells. We show how direct RNA-seq data can be used to define transcription initiation and RNA cleavage sites associated with all polyadenylated viral RNAs and demonstrate that low level read-through transcription produces a novel class of chimeric HSV-1 transcripts, including a functional mRNA encoding a fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L. Thus, direct RNA-seq offers a powerful method to characterize the changing transcriptional landscape of viruses with complex genomes.
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Affiliation(s)
- Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA.
| | | | - Tomohiko Sadaoka
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Devin Bready
- Department of Neurosurgery, New York University School of Medicine, New York, NY, 10016, USA
| | - Yasuko Mori
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Dimitris G Placantonakis
- Department of Neurosurgery, New York University School of Medicine, New York, NY, 10016, USA
- Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
- Brain Tumor Center, New York University School of Medicine, New York, NY, 10016, USA
- Neuroscience Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA.
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
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5
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Bidnenko V, Nicolas P, Grylak-Mielnicka A, Delumeau O, Auger S, Aucouturier A, Guerin C, Repoila F, Bardowski J, Aymerich S, Bidnenko E. Termination factor Rho: From the control of pervasive transcription to cell fate determination in Bacillus subtilis. PLoS Genet 2017; 13:e1006909. [PMID: 28723971 PMCID: PMC5540618 DOI: 10.1371/journal.pgen.1006909] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/02/2017] [Accepted: 07/06/2017] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis. Rho inactivation strongly affected gene expression in B. subtilis, as assessed by transcriptome and proteome analysis of a rho-null mutant during exponential growth in rich medium. Subsequent physiological analyses demonstrated that a considerable part of Rho-controlled transcription is connected to balanced regulation of three mutually exclusive differentiation programs: cell motility, biofilm formation, and sporulation. In the absence of Rho, several up-regulated sense and antisense transcripts affect key structural and regulatory elements of these differentiation programs, thereby suppressing motility and biofilm formation and stimulating sporulation. We dissected how Rho is involved in the activity of the cell fate decision-making network, centered on the master regulator Spo0A. We also revealed a novel regulatory mechanism of Spo0A activation through Rho-dependent intragenic transcription termination of the protein kinase kinB gene. Altogether, our findings indicate that distinct Rho-controlled transcripts are functional and constitute a previously unknown built-in module for the control of cell differentiation in B. subtilis. In a broader context, our results highlight the recruitment of the termination factor Rho, for which the conserved biological role is probably to repress pervasive transcription, in highly integrated, bacterium-specific, regulatory networks.
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Affiliation(s)
- Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pierre Nicolas
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Aleksandra Grylak-Mielnicka
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Olivier Delumeau
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sandrine Auger
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Anne Aucouturier
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cyprien Guerin
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Francis Repoila
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jacek Bardowski
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Stéphane Aymerich
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elena Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
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6
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Prediction of Poly(A) Sites by Poly(A) Read Mapping. PLoS One 2017; 12:e0170914. [PMID: 28135292 PMCID: PMC5279776 DOI: 10.1371/journal.pone.0170914] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/12/2017] [Indexed: 11/19/2022] Open
Abstract
RNA-seq reads containing part of the poly(A) tail of transcripts (denoted as poly(A) reads) provide the most direct evidence for the position of poly(A) sites in the genome. However, due to reduced coverage of poly(A) tails by reads, poly(A) reads are not routinely identified during RNA-seq mapping. Nevertheless, recent studies for several herpesviruses successfully employed mapping of poly(A) reads to identify herpesvirus poly(A) sites using different strategies and customized programs. To more easily allow such analyses without requiring additional programs, we integrated poly(A) read mapping and prediction of poly(A) sites into our RNA-seq mapping program ContextMap 2. The implemented approach essentially generalizes previously used poly(A) read mapping approaches and combines them with the context-based approach of ContextMap 2 to take into account information provided by other reads aligned to the same location. Poly(A) read mapping using ContextMap 2 was evaluated on real-life data from the ENCODE project and compared against a competing approach based on transcriptome assembly (KLEAT). This showed high positive predictive value for our approach, evidenced also by the presence of poly(A) signals, and considerably lower runtime than KLEAT. Although sensitivity is low for both methods, we show that this is in part due to a high extent of spurious results in the gold standard set derived from RNA-PET data. Sensitivity improves for poly(A) sites of known transcripts or determined with a more specific poly(A) sequencing protocol and increases with read coverage on transcript ends. Finally, we illustrate the usefulness of the approach in a high read coverage scenario by a re-analysis of published data for herpes simplex virus 1. Thus, with current trends towards increasing sequencing depth and read length, poly(A) read mapping will prove to be increasingly useful and can now be performed automatically during RNA-seq mapping with ContextMap 2.
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7
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Dreyfus DH. Gene sharing between Epstein–Barr virus and human immune response genes. Immunol Res 2016; 65:37-45. [DOI: 10.1007/s12026-016-8814-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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8
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Karijolich J, Abernathy E, Glaunsinger BA. Infection-Induced Retrotransposon-Derived Noncoding RNAs Enhance Herpesviral Gene Expression via the NF-κB Pathway. PLoS Pathog 2015; 11:e1005260. [PMID: 26584434 PMCID: PMC4652899 DOI: 10.1371/journal.ppat.1005260] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023] Open
Abstract
Short interspersed nuclear elements (SINEs) are highly abundant, RNA polymerase III-transcribed noncoding retrotransposons that are silenced in somatic cells but activated during certain stresses including viral infection. How these induced SINE RNAs impact the host-pathogen interaction is unknown. Here we reveal that during murine gammaherpesvirus 68 (MHV68) infection, rapidly induced SINE RNAs activate the antiviral NF-κB signaling pathway through both mitochondrial antiviral-signaling protein (MAVS)-dependent and independent mechanisms. However, SINE RNA-based signaling is hijacked by the virus to enhance viral gene expression and replication. B2 RNA expression stimulates IKKβ-dependent phosphorylation of the major viral lytic cycle transactivator protein RTA, thereby enhancing its activity and increasing progeny virion production. Collectively, these findings suggest that SINE RNAs participate in the innate pathogen response mechanism, but that herpesviruses have evolved to co-opt retrotransposon activation for viral benefit. Short interspersed nuclear elements (SINEs) are noncoding mobile genetic elements that are present at ~106 copies per mammalian genome, roughly comprising 10% of mammalian genomic real estate. SINEs are typically transcriptionally silenced, though in some cases viral infection can promote their expression, yet to an unknown functional outcome. Thus, SINE elements represent the largest class of infection-inducible noncoding RNAs that are functionally uncharacterized. Here, we reveal that SINE RNAs play a critical role in the host-pathogen interaction in that they are required for efficient murine gammaherpesvirus 68 (MHV68) replication and gene expression. We demonstrate that SINE RNAs, both exogenously expressed and infection-induced, are robust activators of the IKKβ kinase, a key signaling molecule in the innate immune response. Activation of the IKKβ kinase by SINE RNA is mediated through both MAVS-dependent and independent mechanisms. Moreover, we demonstrate the activation of the IKKβ via SINE RNA is required to drive the phosphorylation of MHV68 RTA, the main viral transcriptional activator, which enhances its transcriptional activating property. Collectively, we reveal the first example of a role for SINE RNAs in the host-pathogen interaction and identify them as a key immune signaling molecule early during infection. Though SINE RNAs activate the innate immune response, MHV68 has co-opted SINE-mediate innate immune activation to enhance the viral lifecycle.
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Affiliation(s)
- John Karijolich
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Emma Abernathy
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Britt A. Glaunsinger
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
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9
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Sun L, Miyoshi H, Origanti S, Nice TJ, Barger AC, Manieri NA, Fogel LA, French AR, Piwnica-Worms D, Piwnica-Worms H, Virgin HW, Lenschow DJ, Stappenbeck TS. Type I interferons link viral infection to enhanced epithelial turnover and repair. Cell Host Microbe 2015; 17:85-97. [PMID: 25482432 PMCID: PMC4297260 DOI: 10.1016/j.chom.2014.11.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/30/2014] [Accepted: 11/05/2014] [Indexed: 02/06/2023]
Abstract
The host immune system functions constantly to maintain chronic commensal and pathogenic organisms in check. The consequences of these immune responses on host physiology are as yet unexplored, and may have long-term implications in health and disease. We show that chronic viral infection increases epithelial turnover in multiple tissues, and the antiviral cytokines type I interferons (IFNs) mediate this response. Using a murine model with persistently elevated type I IFNs in the absence of exogenous viral infection, the Irgm1(-/-) mouse, we demonstrate that type I IFNs act through nonepithelial cells, including macrophages, to promote increased epithelial turnover and wound repair. Downstream of type I IFN signaling, the highly related IFN-stimulated genes Apolipoprotein L9a and b activate epithelial proliferation through ERK activation. Our findings demonstrate that the host immune response to chronic viral infection has systemic effects on epithelial turnover through a myeloid-epithelial circuit.
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Affiliation(s)
- Lulu Sun
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hiroyuki Miyoshi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sofia Origanti
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy J Nice
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexandra C Barger
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas A Manieri
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Leslie A Fogel
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anthony R French
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Piwnica-Worms
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Helen Piwnica-Worms
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Deborah J Lenschow
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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10
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Creecy JP, Conway T. Quantitative bacterial transcriptomics with RNA-seq. Curr Opin Microbiol 2014; 23:133-40. [PMID: 25483350 DOI: 10.1016/j.mib.2014.11.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 02/06/2023]
Abstract
RNA sequencing has emerged as the premier approach to study bacterial transcriptomes. While the earliest published studies analyzed the data qualitatively, the data are readily digitized and lend themselves to quantitative analysis. High-resolution RNA sequence (RNA-seq) data allows transcriptional features (promoters, terminators, operons, among others) to be pinpointed on any bacterial transcriptome. Once the transcriptome is mapped, the activity of transcriptional features can be quantified. Here we highlight how quantitative transcriptome analysis can reveal biological insights and briefly discuss some of the challenges to be faced by the field of bacterial transcriptomics in the near future.
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Affiliation(s)
- James P Creecy
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States; Department of Biology, University of Central Oklahoma, Edmond, OK 73034, United States
| | - Tyrrell Conway
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States.
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11
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Moorman NJ, Murphy EA. Roseomics: a blank slate. Curr Opin Virol 2014; 9:188-93. [PMID: 25437230 PMCID: PMC4268339 DOI: 10.1016/j.coviro.2014.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/23/2014] [Accepted: 09/26/2014] [Indexed: 11/24/2022]
Abstract
Recent technological advances have led to an explosion in the system-wide profiling of biological processes in the study of herpesvirus biology, herein referred to as '-omics'. In many cases these approaches have revealed novel virus-induced changes to host cell biology that can be targeted with new antiviral therapeutics. Despite these successes, -omics approaches are not widely applied in the study of roseoloviruses. Here we describe examples of how -omics studies have shaped our understanding of herpesvirus biology, and discuss how these approaches might be used to identify host and viral factors that mediate roseolovirus pathogenesis.
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Affiliation(s)
- Nathaniel J Moorman
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eain A Murphy
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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12
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Abstract
Kaposi’s sarcoma (KS), caused by KS-associated herpesvirus (KSHV), is the most common cancer among HIV-infected patients in Malawi and in the United States today. In Malawi, KSHV is endemic. We conducted a cross-sectional study of patients with HIV infection and KS with no history of chemo- or antiretroviral therapy (ART). Seventy patients were enrolled. Eighty-one percent had T1 (advanced) KS. Median CD4 and HIV RNA levels were 181 cells/mm3 and 138,641 copies/ml, respectively. We had complete information and suitable plasma and biopsy samples for 66 patients. For 59/66 (89%) patients, a detectable KSHV load was found in plasma (median, 2,291 copies/ml; interquartile range [IQR], 741 to 5,623). We utilized a novel KSHV real-time quantitative PCR (qPCR) array with multiple primers per open reading frame to examine KSHV transcription. Seventeen samples exhibited only minimal levels of KSHV mRNAs, presumably due to the limited number of infected cells. For all other biopsy samples, the viral latency locus (LANA, vCyc, vFLIP, kaposin, and microRNAs [miRNAs]) was transcribed abundantly, as was K15 mRNA. We could identify two subtypes of treatment-naive KS: lesions that transcribed viral RNAs across the length of the viral genome and lesions that displayed only limited transcription restricted to the latency locus. This finding demonstrates for the first time the existence of multiple subtypes of KS lesions in HIV- and KS-treatment naive patients. KS is the leading cancer in people infected with HIV worldwide and is causally linked to KSHV infection. Using viral transcription profiling, we have demonstrated the existence of multiple subtypes of KS lesions for the first time in HIV- and KS-treatment-naive patients. A substantial number of lesions transcribe mRNAs which encode the viral kinases and hence could be targeted by the antiviral drugs ganciclovir or AZT in addition to chemotherapy.
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