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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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Lau B, Kerr K, Camiolo S, Nightingale K, Gu Q, Antrobus R, Suárez NM, Loney C, Stanton RJ, Weekes MP, Davison AJ. Human Cytomegalovirus RNA2.7 Is Required for Upregulating Multiple Cellular Genes To Promote Cell Motility and Viral Spread Late in Lytic Infection. J Virol 2021; 95:e0069821. [PMID: 34346763 PMCID: PMC8475523 DOI: 10.1128/jvi.00698-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/22/2021] [Indexed: 11/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are frequently associated with broad modulation of gene expression and thus provide the cell with the ability to synchronize entire metabolic processes. We used transcriptomic approaches to investigate whether the most abundant human cytomegalovirus-encoded lncRNA, RNA2.7, has this characteristic. By comparing cells infected with wild-type virus (WT) to cells infected with RNA2.7 deletion mutants, RNA2.7 was implicated in regulating a large number of cellular genes late in lytic infection. Pathway analysis indicated that >100 of these genes are associated with promoting cell movement, and the 10 most highly regulated of these were validated in further experiments. Morphological analysis and live cell tracking of WT- and RNA2.7 mutant-infected cells indicated that RNA2.7 is involved in promoting the movement and detachment of infected cells late in infection, and plaque assays using sparse cell monolayers indicated that RNA2.7 is also involved in promoting cell-to-cell spread of virus. Consistent with the observation that upregulated mRNAs are relatively A+U-rich, which is a trait associated with transcript instability, and that they are also enriched in motifs associated with mRNA instability, transcriptional inhibition experiments on WT- and RNA2.7 mutant-infected cells showed that four upregulated transcripts lived longer in the presence of RNA2.7. These findings demonstrate that RNA2.7 is required for promoting cell movement and viral spread late in infection and suggest that this may be due to general stabilization of A+U-rich transcripts. IMPORTANCE In addition to messenger RNAs (mRNAs), the human genome encodes a large number of long noncoding RNAs (lncRNAs). Many lncRNAs that have been studied in detail are associated with broad modulation of gene expression and have important biological roles. Human cytomegalovirus, which is a large, clinically important DNA virus, specifies four lncRNAs, one of which (RNA2.7) is expressed at remarkably high levels during lytic infection. Our studies show that RNA2.7 is required for upregulating a large number of human genes, about 100 of which are associated with cell movement, and for promoting the movement of infected cells and the spread of virus from one cell to another. Further bioinformatic and experimental analyses indicated that RNA2.7 may exert these effects by stabilizing mRNAs that are relatively rich in A and U nucleotides. These findings increase our knowledge of how human cytomegalovirus regulates the infected cell to promote its own success.
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Affiliation(s)
- Betty Lau
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Karen Kerr
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Salvatore Camiolo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Katie Nightingale
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Nicolás M. Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard J. Stanton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Andrew J. Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Kakuk B, Tombácz D, Balázs Z, Moldován N, Csabai Z, Torma G, Megyeri K, Snyder M, Boldogkői Z. Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome. Sci Rep 2021; 11:14487. [PMID: 34262076 PMCID: PMC8280142 DOI: 10.1038/s41598-021-93593-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/28/2021] [Indexed: 02/08/2023] Open
Abstract
Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice variants. In this work, we profile the human cytomegalovirus transcriptome using two third-generation LRS platforms: the Sequel from Pacific BioSciences, and MinION from Oxford Nanopore Technologies. We carried out both cDNA and direct RNA sequencing, and applied the LoRTIA software, developed in our laboratory, for the transcript annotations. This study identified a large number of novel transcript variants, including splice isoforms and transcript start and end site isoforms, as well as putative mRNAs with truncated in-frame ORFs (located within the larger ORFs of the canonical mRNAs), which potentially encode N-terminally truncated polypeptides. Our work also disclosed a highly complex meshwork of transcriptional read-throughs and overlaps.
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Affiliation(s)
- Balázs Kakuk
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
- MTA-SZTE Momentum GeMiNI Research Group, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr, Stanford, CA, USA
| | - Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Klára Megyeri
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr, Stanford, CA, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, 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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Adamson CS, Nevels MM. Bright and Early: Inhibiting Human Cytomegalovirus by Targeting Major Immediate-Early Gene Expression or Protein Function. Viruses 2020; 12:v12010110. [PMID: 31963209 PMCID: PMC7019229 DOI: 10.3390/v12010110] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
The human cytomegalovirus (HCMV), one of eight human herpesviruses, establishes lifelong latent infections in most people worldwide. Primary or reactivated HCMV infections cause severe disease in immunosuppressed patients and congenital defects in children. There is no vaccine for HCMV, and the currently approved antivirals come with major limitations. Most approved HCMV antivirals target late molecular processes in the viral replication cycle including DNA replication and packaging. “Bright and early” events in HCMV infection have not been exploited for systemic prevention or treatment of disease. Initiation of HCMV replication depends on transcription from the viral major immediate-early (IE) gene. Alternative transcripts produced from this gene give rise to the IE1 and IE2 families of viral proteins, which localize to the host cell nucleus. The IE1 and IE2 proteins are believed to control all subsequent early and late events in HCMV replication, including reactivation from latency, in part by antagonizing intrinsic and innate immune responses. Here we provide an update on the regulation of major IE gene expression and the functions of IE1 and IE2 proteins. We will relate this insight to experimental approaches that target IE gene expression or protein function via molecular gene silencing and editing or small chemical inhibitors.
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Finkel Y, Schmiedel D, Tai-Schmiedel J, Nachshon A, Winkler R, Dobesova M, Schwartz M, Mandelboim O, Stern-Ginossar N. Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features. eLife 2020; 9:e50960. [PMID: 31944176 PMCID: PMC6964970 DOI: 10.7554/elife.50960] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
Human herpesvirus-6 (HHV-6) A and B are ubiquitous betaherpesviruses, infecting the majority of the human population. They encompass large genomes and our understanding of their protein coding potential is far from complete. Here, we employ ribosome-profiling and systematic transcript-analysis to experimentally define HHV-6 translation products. We identify hundreds of new open reading frames (ORFs), including upstream ORFs (uORFs) and internal ORFs (iORFs), generating a complete unbiased atlas of HHV-6 proteome. By integrating systematic data from the prototypic betaherpesvirus, human cytomegalovirus, we uncover numerous uORFs and iORFs conserved across betaherpesviruses and we show uORFs are enriched in late viral genes. We identified three highly abundant HHV-6 encoded long non-coding RNAs, one of which generates a non-polyadenylated stable intron appearing to be a conserved feature of betaherpesviruses. Overall, our work reveals the complexity of HHV-6 genomes and highlights novel features conserved between betaherpesviruses, providing a rich resource for future functional studies.
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Affiliation(s)
- Yaara Finkel
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Dominik Schmiedel
- The Lautenberg Center for General and Tumor ImmunologyInstitute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical SchoolJerusalemIsrael
| | | | - Aharon Nachshon
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Roni Winkler
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Martina Dobesova
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Michal Schwartz
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Ofer Mandelboim
- The Lautenberg Center for General and Tumor ImmunologyInstitute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical SchoolJerusalemIsrael
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Balázs Z, Tombácz D, Csabai Z, Moldován N, Snyder M, Boldogkői Z. Template-switching artifacts resemble alternative polyadenylation. BMC Genomics 2019; 20:824. [PMID: 31703623 PMCID: PMC6839120 DOI: 10.1186/s12864-019-6199-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/17/2019] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming. RESULTS Here, we analyzed both long-read cDNA sequencing and direct RNA sequencing data of two organisms, generated by different sequencing platforms. We developed a filtering algorithm which takes into consideration that template-switching can be a source of artifactual polyadenylation when filtering out spurious polyadenylation sites. The algorithm outperformed the conventional internal priming filters based on comparison to direct RNA sequencing data. We also showed that the polyadenylation artifacts arise in cDNA sequencing at consecutive stretches of as few as three adenines. There was no substantial difference between the lengths of poly(A) tails at the artifactual and the true transcriptional end sites even though it is expected that internal priming artifacts have shorter poly(A) tails than genuine polyadenylated reads. CONCLUSIONS Our findings suggest that template switching plays an important role in the generation of spurious polyadenylation and support the need for more rigorous filtering of artifactual polyadenylation sites in cDNA data, or that alternative polyadenylation should be annotated using native RNA sequencing.
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Affiliation(s)
- Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary.
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Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Getting the Entire Message: Progress in Isoform Sequencing. Front Genet 2019; 10:709. [PMID: 31475029 PMCID: PMC6706457 DOI: 10.3389/fgene.2019.00709] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/04/2019] [Indexed: 01/31/2023] Open
Abstract
The advent of second-generation sequencing and its application to RNA sequencing have revolutionized the field of genomics by allowing quantification of gene expression, as well as the definition of transcription start/end sites, exons, splice sites and RNA editing sites. However, due to the sequencing of fragments of cDNAs, these methods have not given a reliable picture of complete RNA isoforms. Third-generation sequencing has filled this gap and allows end-to-end sequencing of entire RNA/cDNA molecules. This approach to transcriptomics has been a "niche" technology for a couple of years but now is becoming mainstream with many different applications. Here, we review the background and progress made to date in this rapidly growing field. We start by reviewing the progressive realization that alternative splicing is omnipresent. We then focus on long-noncoding RNA isoforms and the distinct combination patterns of exons in noncoding and coding genes. We consider the implications of the recent technologies of direct RNA sequencing and single-cell isoform RNA sequencing. Finally, we discuss the parameters that define the success of long-read RNA sequencing experiments and strategies commonly used to make the most of such data.
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Affiliation(s)
- Simon A. Hardwick
- Brain and Mind Research Institute, Weill Cornell Medicine, NY, United States
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Anoushka Joglekar
- Brain and Mind Research Institute, Weill Cornell Medicine, NY, United States
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Hagen U. Tilgner
- Brain and Mind Research Institute, Weill Cornell Medicine, NY, United States
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Martí-Carreras J, Maes P. Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges. Virus Genes 2019; 55:138-164. [PMID: 30604286 PMCID: PMC6458973 DOI: 10.1007/s11262-018-1627-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
The human cytomegalovirus (HCMV) genome was sequenced by hierarchical shotgun almost 30 years ago. Over these years, low and high passaged strains have been sequenced, improving, albeit still far from complete, the understanding of the coding potential, expression dynamics and diversity of wild-type HCMV strains. Next-generation sequencing (NGS) platforms have enabled a huge advancement, facilitating the comparison of differentially passaged strains, challenging diagnostics and research based on a single or reduced gene set genotyping. In addition, it allowed to link genetic features to different viral phenotypes as for example, correlating large genomic re-arrangements to viral attenuation or different mutations to antiviral resistance and cell tropism. NGS platforms provided the first high-resolution experiments to HCMV dynamics, allowing the study of intra-host viral population structures and the description of rare transcriptional events. Long-read sequencing has recently become available, helping to identify new genomic re-arrangements, partially accounting for the genetic variability displayed in clinical isolates, as well as, in changing the understanding of the HCMV transcriptome. Better knowledge of the transcriptome resulted in a vast number of new splicing events and alternative transcripts, although most of them still need additional validation. This review summarizes the sequencing efforts reached so far, discussing its approaches and providing a revision and new nuances on HCMV sequence variability in the sequencing field.
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Affiliation(s)
- Joan Martí-Carreras
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium.
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Tombácz D, Prazsák I, Szucs A, Dénes B, Snyder M, Boldogkoi Z. Dynamic transcriptome profiling dataset of vaccinia virus obtained from long-read sequencing techniques. Gigascience 2018; 7:5202462. [PMID: 30476066 PMCID: PMC6290886 DOI: 10.1093/gigascience/giy139] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/12/2018] [Indexed: 12/21/2022] Open
Abstract
Background Poxviruses are large DNA viruses that infect humans and animals. Vaccinia virus (VACV) has been applied as a live vaccine for immunization against smallpox, which was eradicated by 1980 as a result of worldwide vaccination. VACV is the prototype of poxviruses in the investigation of the molecular pathogenesis of the virus. Short-read sequencing methods have revolutionized transcriptomics; however, they are not efficient in distinguishing between the RNA isoforms and transcript overlaps. Long-read sequencing (LRS) is much better suited to solve these problems and also allow direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome to date. Findings For the deep characterization of the VACV RNA profile, various LRS platforms and library preparation approaches were applied. The raw reads were mapped to the VACV reference genome and also to the host (Chlorocebus sabaeus) genome. In this study, we applied the Pacific Biosciences RSII and Sequel platforms, which altogether resulted in 937,531 mapped reads of inserts (1.42 Gb), while we obtained 2,160,348 aligned reads (1.75 Gb) from the different library preparation methods using the MinION device from Oxford Nanopore Technologies. Conclusions By applying cutting-edge technologies, we were able to generate a large dataset that can serve as a valuable resource for the investigation of the dynamic VACV transcriptome, the virus-host interactions, and RNA base modifications. These data can provide useful information for novel gene annotations in the VACV genome. Our dataset can also be used to analyze the currently available LRS platforms, library preparation methods, and bioinformatics pipelines.
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Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary
| | - István Prazsák
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary
| | - Attila Szucs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary
| | - Béla Dénes
- Veterinary Diagnostic Directorate of the National Food Chain Safety Office, Tábornok u. 2., 1143 Budapest, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr, Stanford, California, USA
| | - Zsolt Boldogkoi
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary
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