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Rottenberg JT, Taslim TH, Soto-Ugaldi LF, Martinez-Cuesta L, Martinez-Calejman C, Fuxman Bass JI. Viral cis-regulatory elements as sensors of cellular states and environmental cues. Trends Genet 2024:S0168-9525(24)00108-2. [PMID: 38821843 DOI: 10.1016/j.tig.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
To withstand a hostile cellular environment and replicate, viruses must sense, interpret, and respond to many internal and external cues. Retroviruses and DNA viruses can intercept these cues impinging on host transcription factors via cis-regulatory elements (CREs) in viral genomes, allowing them to sense and coordinate context-specific responses to varied signals. Here, we explore the characteristics of viral CREs, the classes of signals and host transcription factors that regulate them, and how this informs outcomes of viral replication, immune evasion, and latency. We propose that viral CREs constitute central hubs for signal integration from multiple pathways and that sequence variation between viral isolates can rapidly rewire sensing mechanisms, contributing to the variability observed in patient outcomes.
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Affiliation(s)
| | - Tommy H Taslim
- Department of Biology, Boston University, Boston, MA, USA; Molecular and Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Lucia Martinez-Cuesta
- Department of Biology, Boston University, Boston, MA, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA; Molecular and Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA.
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2
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Iturbe P, Martín AS, Hamamoto H, Marcet-Houben M, Galbaldón T, Solano C, Lasa I. Noncontiguous operon atlas for the Staphylococcus aureus genome. MICROLIFE 2024; 5:uqae007. [PMID: 38651166 PMCID: PMC11034616 DOI: 10.1093/femsml/uqae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Bacteria synchronize the expression of genes with related functions by organizing genes into operons so that they are cotranscribed together in a single polycistronic messenger RNA. However, some cellular processes may benefit if the simultaneous production of the operon proteins coincides with the inhibition of the expression of an antagonist gene. To coordinate such situations, bacteria have evolved noncontiguous operons (NcOs), a subtype of operons that contain one or more genes that are transcribed in the opposite direction to the other operon genes. This structure results in overlapping transcripts whose expression is mutually repressed. The presence of NcOs cannot be predicted computationally and their identification requires a detailed knowledge of the bacterial transcriptome. In this study, we used direct RNA sequencing methodology to determine the NcOs map in the Staphylococcus aureus genome. We detected the presence of 18 NcOs in the genome of S. aureus and four in the genome of the lysogenic prophage 80α. The identified NcOs comprise genes involved in energy metabolism, metal acquisition and transport, toxin-antitoxin systems, and control of the phage life cycle. Using the menaquinone operon as a proof of concept, we show that disarrangement of the NcO architecture results in a reduction of bacterial fitness due to an increase in menaquinone levels and a decrease in the rate of oxygen consumption. Our study demonstrates the significance of NcO structures in bacterial physiology and emphasizes the importance of combining operon maps with transcriptomic data to uncover previously unnoticed functional relationships between neighbouring genes.
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Affiliation(s)
- Pablo Iturbe
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Hospital Universitario de Navarra (HUN), IdiSNA, Irunlarrea 3, Pamplona, 31008 Navarra, Spain
| | - Alvaro San Martín
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Hospital Universitario de Navarra (HUN), IdiSNA, Irunlarrea 3, Pamplona, 31008 Navarra, Spain
| | - Hiroshi Hamamoto
- Faculty of Medicine, Department of Infectious diseases, Yamagata University, 2-2-2 Lida-Nishi, 990-9585 Yamagata, Japan
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Galbaldón
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Solano
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Hospital Universitario de Navarra (HUN), IdiSNA, Irunlarrea 3, Pamplona, 31008 Navarra, Spain
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Hospital Universitario de Navarra (HUN), IdiSNA, Irunlarrea 3, Pamplona, 31008 Navarra, Spain
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3
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Prazsák I, Tombácz D, Fülöp Á, Torma G, Gulyás G, Dörmő Á, Kakuk B, McKenzie Spires L, Toth Z, Boldogkői Z. KSHV 3.0: a state-of-the-art annotation of the Kaposi's sarcoma-associated herpesvirus transcriptome using cross-platform sequencing. mSystems 2024; 9:e0100723. [PMID: 38206015 PMCID: PMC10878076 DOI: 10.1128/msystems.01007-23] [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: 09/19/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches to map the transcription start and end sites, the splice junctions, and the translation initiation sites. Despite these efforts, the comprehensive annotation of the viral transcriptome remains incomplete. In the present study, we generated a long-read sequencing data set of the lytic and latent KSHV transcriptome using native RNA and direct cDNA-sequencing methods. This was supplemented with Cap Analysis of Gene Expression sequencing based on a short-read platform. We also utilized data sets from previous publications for our analysis. As a result of this combined approach, we have identified a number of novel viral transcripts and RNA isoforms and have either corroborated or improved the annotation of previously identified viral RNA molecules, thereby notably enhancing our comprehension of the transcriptomic architecture of the KSHV genome. We also evaluated the coding capability of transcripts previously thought to be non-coding by integrating our data on the viral transcripts with translatomic information from other publications.IMPORTANCEDeciphering the viral transcriptome of Kaposi's sarcoma-associated herpesvirus is of great importance because we can gain insight into the molecular mechanism of viral replication and pathogenesis, which can help develop potential targets for antiviral interventions. Specifically, the identification of substantial transcriptional overlaps by this work suggests the existence of a genome-wide interference between transcriptional machineries. This finding indicates the presence of a novel regulatory layer, potentially controlling the expression of viral genes.
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Affiliation(s)
- István Prazsák
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Lauren McKenzie Spires
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
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4
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Torma G, Tombácz D, Csabai Z, Almsarrhad IAA, Nagy GÁ, Kakuk B, Gulyás G, Spires LM, Gupta I, Fülöp Á, Dörmő Á, Prazsák I, Mizik M, Dani VÉ, Csányi V, Harangozó Á, Zádori Z, Toth Z, Boldogkői Z. Identification of herpesvirus transcripts from genomic regions around the replication origins. Sci Rep 2023; 13:16395. [PMID: 37773348 PMCID: PMC10541914 DOI: 10.1038/s41598-023-43344-y] [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: 05/16/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023] Open
Abstract
Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a 'super regulatory center' in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries.
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Affiliation(s)
- Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Islam A A Almsarrhad
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gergely Ármin Nagy
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Lauren McKenzie Spires
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India
| | - Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - István Prazsák
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Máté Mizik
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Virág Éva Dani
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Viktor Csányi
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Harangozó
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Zoltán Zádori
- HUN-REN Veterinary Medical Research Institute HU, Budapest, Hungary
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary.
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary.
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5
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Afrasiabi A, Ahlenstiel C, Swaminathan S, Parnell GP. The interaction between Epstein-Barr virus and multiple sclerosis genetic risk loci: insights into disease pathogenesis and therapeutic opportunities. Clin Transl Immunology 2023; 12:e1454. [PMID: 37337612 PMCID: PMC10276892 DOI: 10.1002/cti2.1454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic neurodegenerative autoimmune disease, characterised by the demyelination of neurons in the central nervous system. Whilst it is unclear what precisely leads to MS, it is believed that genetic predisposition combined with environmental factors plays a pivotal role. It is estimated that close to half the disease risk is determined by genetic factors. However, the risk of developing MS cannot be attributed to genetic factors alone, and environmental factors are likely to play a significant role by themselves or in concert with host genetics. Epstein-Barr virus (EBV) infection is the strongest known environmental risk factor for MS. There has been increasing evidence that leaves little doubt that EBV is necessary, but not sufficient, for developing MS. One plausible explanation is EBV may alter the host immune response in the presence of MS risk alleles and this contributes to the pathogenesis of MS. In this review, we discuss recent findings regarding how EBV infection may contribute to MS pathogenesis via interactions with genetic risk loci and discuss possible therapeutic interventions.
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Affiliation(s)
- Ali Afrasiabi
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- The Graduate School of Biomedical EngineeringUniversity of New South WalesSydneyNSWAustralia
| | - Chantelle Ahlenstiel
- Kirby InstituteUniversity of New South WalesSydneyNSWAustralia
- RNA InstituteUniversity of New South WalesSydneyNSWAustralia
| | - Sanjay Swaminathan
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- Department of MedicineWestern Sydney UniversitySydneyNSWAustralia
| | - Grant P Parnell
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- Biomedical Informatics and Digital Health, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
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6
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Kakuk B, Dörmő Á, Csabai Z, Kemenesi G, Holoubek J, Růžek D, Prazsák I, Dani VÉ, Dénes B, Torma G, Jakab F, Tóth GE, Földes FV, Zana B, Lanszki Z, Harangozó Á, Fülöp Á, Gulyás G, Mizik M, Kiss AA, Tombácz D, Boldogkői Z. In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing. Sci Data 2023; 10:262. [PMID: 37160911 PMCID: PMC10170163 DOI: 10.1038/s41597-023-02149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023] Open
Abstract
The recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level.
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Affiliation(s)
- Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Jiří Holoubek
- Veterinary Research Institute, Hudcova 70, CZ-62100, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005, Ceske Budejovice, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice, 753/5, Brno, CZ-62500, Czech Republic
| | - Daniel Růžek
- Veterinary Research Institute, Hudcova 70, CZ-62100, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005, Ceske Budejovice, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice, 753/5, Brno, CZ-62500, Czech Republic
| | - István Prazsák
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Virág Éva Dani
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Béla Dénes
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143, Budapest, Hungária krt. 23-25, Hungary
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Gábor E Tóth
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Fanni V Földes
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Zsófia Lanszki
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ákos Harangozó
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Máté Mizik
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - András Attila Kiss
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary.
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7
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Reactivation of Epstein-Barr Virus from Latency Involves Increased RNA Polymerase Activity at CTCF Binding Sites on the Viral Genome. J Virol 2023; 97:e0189422. [PMID: 36744959 PMCID: PMC9972995 DOI: 10.1128/jvi.01894-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The ability of Epstein-Barr virus (EBV) to switch between latent and lytic infection is key to its long-term persistence, yet the molecular mechanisms behind this switch remain unclear. To investigate transcriptional events during the latent-to-lytic switch, we utilized Precision nuclear Run On followed by deep Sequencing (PRO-Seq) to map cellular RNA polymerase (Pol) activity to single-nucleotide resolution on the host and EBV genome in three different models of EBV latency and reactivation. In latently infected Mutu-I Burkitt lymphoma (BL) cells, Pol activity was enriched at the Qp promoter, the EBER region, and the BHLF1/LF3 transcripts. Upon reactivation with phorbol ester and sodium butyrate, early-phase Pol activity occurred bidirectionally at CTCF sites within the LMP-2A, EBER-1, and RPMS1 loci. PRO-Seq analysis of Akata cells reactivated from latency with anti-IgG and a lymphoblastoid cell line (LCL) reactivated with small molecule C60 showed a similar pattern of early bidirectional transcription initiating around CTCF binding sites, although the specific CTCF sites and viral genes were different for each latency model. The functional importance of CTCF binding, transcription, and reactivation was confirmed using an EBV mutant lacking the LMP-2A CTCF binding site. This virus was unable to reactivate and had disrupted Pol activity at multiple CTCF binding sites relative to the wild-type (WT) virus. Overall, these data suggest that CTCF regulates the viral early transcripts during reactivation from latency. These activities likely help maintain the accessibility of the viral genome to initiate productive replication. IMPORTANCE The ability of EBV to switch between latent and lytic infection is key to its long-term persistence in memory B cells, and its ability to persist in proliferating cells is strongly linked to oncogenesis. During latency, most viral genes are epigenetically silenced, and the virus must overcome this repression to reactivate lytic replication. Reactivation occurs once the immediate early (IE) EBV lytic genes are expressed. However, the molecular mechanisms behind the switch from the latent transcriptional program to begin transcription of the IE genes remain unknown. In this study, we mapped RNA Pol positioning and activity during latency and reactivation. Unexpectedly, Pol activity accumulated at distinct regions characteristic of transcription initiation on the EBV genome previously shown to be associated with CTCF. We propose that CTCF binding at these regions retains Pol to maintain a stable latent chromosome conformation and a rapid response to various reactivation signals.
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8
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Tombácz D, Kakuk B, Torma G, Csabai Z, Gulyás G, Tamás V, Zádori Z, Jefferson VA, Meyer F, Boldogkői Z. In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing. Viruses 2022; 14:v14061289. [PMID: 35746760 PMCID: PMC9229804 DOI: 10.3390/v14061289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
In this work, a long-read sequencing (LRS) technique based on the Oxford Nanopore Technology MinION platform was used for quantifying and kinetic characterization of the poly(A) fraction of bovine alphaherpesvirus type 1 (BoHV-1) lytic transcriptome across a 12-h infection period. Amplification-based LRS techniques frequently generate artefactual transcription reads and are biased towards the production of shorter amplicons. To avoid these undesired effects, we applied direct cDNA sequencing, an amplification-free technique. Here, we show that a single promoter can produce multiple transcription start sites whose distribution patterns differ among the viral genes but are similar in the same gene at different timepoints. Our investigations revealed that the circ gene is expressed with immediate–early (IE) kinetics by utilizing a special mechanism based on the use of the promoter of another IE gene (bicp4) for the transcriptional control. Furthermore, we detected an overlap between the initiation of DNA replication and the transcription from the bicp22 gene, which suggests an interaction between the two molecular machineries. This study developed a generally applicable LRS-based method for the time-course characterization of transcriptomes of any organism.
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Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Vivien Tamás
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, 1143 Budapest, Hungary; (V.T.); (Z.Z.)
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, 1143 Budapest, Hungary; (V.T.); (Z.Z.)
| | - Victoria A. Jefferson
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 408 Dorman P.O. Box 9655, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (F.M.)
| | - Florencia Meyer
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 408 Dorman P.O. Box 9655, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (F.M.)
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
- Correspondence:
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