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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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2
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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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3
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Jefferson VA, Bostick H, Oldenburg D, Meyer F. Evidence of a Protein-Coding Gene Antisense to the U L5 Gene in Bovine Herpesvirus I. Viruses 2023; 15:1977. [PMID: 37896756 PMCID: PMC10610667 DOI: 10.3390/v15101977] [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] [Received: 07/05/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Bovine herpesvirus type 1 (BoHV-1) is an important agricultural pathogen that infects cattle and other ruminants worldwide. Though it was first sequenced and annotated over twenty years ago, the Cooper strain, used in this study, was sequenced as recently as 2012 and is currently said to encode 72 unique proteins. However, tandem mass spectrometry has identified several peptides produced during active infection that align with the BoHV-1 genome in unannotated regions. One of these abundant peptides, "ORF M", aligned antisense to the DNA helicase/primase protein UL5. This study characterizes the novel transcript and its protein product and provides evidence to support the existence of homolog protein-coding genes in other Herpesviruses.
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Affiliation(s)
- Victoria A. Jefferson
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (H.B.)
| | - Hannah Bostick
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (H.B.)
| | - Darby Oldenburg
- Gundersen Medical Foundation, 1900 South Ave., La Crosse, WI 54601, USA;
| | - Florencia Meyer
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (H.B.)
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Prazsák I, Tombácz D, Fülöp Á, Torma G, Gulyás G, Dörmő Á, Kakuk B, Spires LM, 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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558842. [PMID: 37790386 PMCID: PMC10542539 DOI: 10.1101/2023.09.21.558842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
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 dataset of the lytic and latent KSHV transcriptome using native RNA and direct cDNA sequencing methods. This was supplemented with CAGE sequencing based on a short-read platform. We also utilized datasets 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.
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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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Tombácz D, Torma G, Gulyás G, Fülöp Á, Dörmő Á, Prazsák I, Csabai Z, Mizik M, Hornyák Á, Zádori Z, Kakuk B, Boldogkői Z. Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1. Heliyon 2023; 9:e17716. [PMID: 37449092 PMCID: PMC10336594 DOI: 10.1016/j.heliyon.2023.e17716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/05/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
This study employed both short-read sequencing (SRS, Illumina) and long-read sequencing (LRS Oxford Nanopore Technologies) platforms to conduct a comprehensive analysis of the equid alphaherpesvirus 1 (EHV-1) transcriptome. The study involved the annotation of canonical mRNAs and their transcript variants, encompassing transcription start site (TSS) and transcription end site (TES) isoforms, in addition to alternative splicing forms. Furthermore, the study revealed the presence of numerous non-coding RNA (ncRNA) molecules, including intergenic and antisense transcripts, produced by EHV-1. An intriguing finding was the abundant production of chimeric transcripts, some of which potentially encode fusion polypeptides. Moreover, EHV-1 exhibited a greater incidence of transcriptional overlaps and splicing compared to related viruses. It is noteworthy that many genes have their unique TESs along with the co-terminal transcription ends, a characteristic scarcely seen in other alphaherpesviruses. The study also identified transcripts that overlap the replication origins of the virus. Moreover, a novel ncRNA, referred to as NOIR, was found to intersect with the 5'-ends of longer transcript isoform specified by the major transactivator genes ORF64 and ORF65, surrounding the OriL. These findings together imply the existence of a key regulatory mechanism that governs both transcription and replication through, among others, a process that involves interference between the DNA and RNA synthesis machineries.
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Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ádám Fülöp
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - István Prazsák
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Máté Mizik
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ákos Hornyák
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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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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7
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Fülöp Á, Torma G, Moldován N, Szenthe K, Bánáti F, Almsarrhad IAA, Csabai Z, Tombácz D, Minárovits J, Boldogkői Z. Integrative profiling of Epstein-Barr virus transcriptome using a multiplatform approach. Virol J 2022; 19:7. [PMID: 34991630 PMCID: PMC8740505 DOI: 10.1186/s12985-021-01734-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV) is an important human pathogenic gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been analyzed using both Illumina-based short read-sequencing and Pacific Biosciences RS II-based long-read sequencing technologies. Since the various sequencing methods have distinct strengths and limitations, the use of multiplatform approaches have proven to be valuable. The aim of this study is to provide a more complete picture on the transcriptomic architecture of EBV. METHODS In this work, we apply the Oxford Nanopore Technologies MinION (long-read sequencing) platform for the generation of novel transcriptomic data, and integrate these with other's data generated by another LRS approach, Pacific BioSciences RSII sequencing and Illumina CAGE-Seq and Poly(A)-Seq approaches. Both amplified and non-amplified cDNA sequencings were applied for the generation of sequencing reads, including both oligo-d(T) and random oligonucleotide-primed reverse transcription. EBV transcripts are identified and annotated using the LoRTIA software suite developed in our laboratory. RESULTS This study detected novel genes embedded into longer host genes containing 5'-truncated in-frame open reading frames, which potentially encode N-terminally truncated proteins. We also detected a number of novel non-coding RNAs and transcript length isoforms encoded by the same genes but differing in their start and/or end sites. This study also reports the discovery of novel splice isoforms, many of which may represent altered coding potential, and of novel replication-origin-associated transcripts. Additionally, novel mono- and multigenic transcripts were identified. An intricate meshwork of transcriptional overlaps was revealed. CONCLUSIONS An integrative approach applying multi-technique sequencing technologies is suitable for reliable identification of complex transcriptomes because each techniques has different advantages and limitations, and the they can be used for the validation of the results obtained by a particular approach.
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Affiliation(s)
- Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Norbert Moldován
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Kálmán Szenthe
- Carlsbad Research Organization Ltd., Szabadság u. 2., Újrónafő, 9244 Hungary
| | - Ferenc Bánáti
- RT-Europe Research Center, Vár tér 2., Mosonmagyaróvár, 9200 Hungary
| | - Islam A. A. Almsarrhad
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - János Minárovits
- Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza Lajos krt. 64, Szeged, 6720 Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
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8
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Maróti Z, Tombácz D, Moldován N, Torma G, Jefferson VA, Csabai Z, Gulyás G, Dörmő Á, Boldogkői M, Kalmár T, Meyer F, Boldogkői Z. Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing. Sci Rep 2021; 11:14219. [PMID: 34244540 PMCID: PMC8270970 DOI: 10.1038/s41598-021-93142-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/14/2021] [Indexed: 11/09/2022] Open
Abstract
Third-generation sequencing is able to read full-length transcripts and thus to efficiently identify RNA molecules and transcript isoforms, including transcript length and splice isoforms. In this study, we report the time-course profiling of the effect of bovine alphaherpesvirus type 1 on the gene expression of bovine epithelial cells using direct cDNA sequencing carried out on MinION device of Oxford Nanopore Technologies. These investigations revealed a substantial up- and down-regulatory effect of the virus on several gene networks of the host cells, including those that are associated with antiviral response, as well as with viral transcription and translation. Additionally, we report a large number of novel bovine transcript isoforms identified by nanopore and synthetic long-read sequencing. This study demonstrates that viral infection causes differential expression of host transcript isoforms. We could not detect an increased rate of transcriptional readthroughs as described in another alphaherpesvirus. According to our knowledge, this is the first report on the use of LoopSeq for the analysis of eukaryotic transcriptomes. This is also the first report on the application of nanopore sequencing for the kinetic characterization of cellular transcriptomes. This study also demonstrates the utility of nanopore sequencing for the characterization of dynamic transcriptomes in any organisms.
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Affiliation(s)
- Zoltán Maróti
- Department of Pediatrics, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary.,MTA-SZTE Momentum GeMiNI Research Group, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Victoria A Jefferson
- Department of Biochemistry and Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 408 Dorman Hall, 32 Creelman St., Box 9655, Starkville, MS, 39762, USA
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Miklós Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Tibor Kalmár
- Department of Pediatrics, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Florencia Meyer
- Department of Biochemistry and Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 408 Dorman Hall, 32 Creelman St., Box 9655, Starkville, MS, 39762, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary.
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Torma G, Tombácz D, Csabai Z, Göbhardter D, Deim Z, Snyder M, Boldogkői Z. An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome. Pathogens 2021; 10:pathogens10020242. [PMID: 33672563 PMCID: PMC7924054 DOI: 10.3390/pathogens10020242] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/06/2023] Open
Abstract
In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencing with our earlier data generated by other LRS and short-read sequencing techniques. As a result, we identified a number of novel genes, transcripts, and transcript isoforms, including splice and length variants, and also confirmed earlier annotated RNA molecules. One of the major findings of this study is the discovery of a large number of 5′-truncations of larger putative mRNAs being 3′-co-terminal with canonical mRNAs of PRV. A large fraction of these putative RNAs contain in-frame ATGs, which might initiate translation of N-terminally truncated polypeptides. Our analyses indicate that CTO-S, a replication origin-associated RNA molecule is expressed at an extremely high level. This study demonstrates that the PRV transcriptome is much more complex than previously appreciated.
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Affiliation(s)
- Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (D.G.)
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (D.G.)
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94304, USA;
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (D.G.)
| | - Dániel Göbhardter
- Department of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (D.G.)
| | - Zoltán Deim
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary;
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94304, USA;
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (D.G.)
- Correspondence:
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