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Cackett G, Sýkora M, Portugal R, Dulson C, Dixon L, Werner F. Transcription termination and readthrough in African swine fever virus. Front Immunol 2024; 15:1350267. [PMID: 38545109 PMCID: PMC10965686 DOI: 10.3389/fimmu.2024.1350267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/30/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction African swine fever virus (ASFV) is a nucleocytoplasmic large DNA virus (NCLDV) that encodes its own host-like RNA polymerase (RNAP) and factors required to produce mature mRNA. The formation of accurate mRNA 3' ends by ASFV RNAP depends on transcription termination, likely enabled by a combination of sequence motifs and transcription factors, although these are poorly understood. The termination of any RNAP is rarely 100% efficient, and the transcriptional "readthrough" at terminators can generate long mRNAs which may interfere with the expression of downstream genes. ASFV transcriptome analyses reveal a landscape of heterogeneous mRNA 3' termini, likely a combination of bona fide termination sites and the result of mRNA degradation and processing. While short-read sequencing (SRS) like 3' RNA-seq indicates an accumulation of mRNA 3' ends at specific sites, it cannot inform about which promoters and transcription start sites (TSSs) directed their synthesis, i.e., information about the complete and unprocessed mRNAs at nucleotide resolution. Methods Here, we report a rigorous analysis of full-length ASFV transcripts using long-read sequencing (LRS). We systematically compared transcription termination sites predicted from SRS 3' RNA-seq with 3' ends mapped by LRS during early and late infection. Results Using in-vitro transcription assays, we show that recombinant ASFV RNAP terminates transcription at polyT stretches in the non-template strand, similar to the archaeal RNAP or eukaryotic RNAPIII, unaided by secondary RNA structures or predicted viral termination factors. Our results cement this T-rich motif (U-rich in the RNA) as a universal transcription termination signal in ASFV. Many genes share the usage of the same terminators, while genes can also use a range of terminators to generate transcript isoforms varying enormously in length. A key factor in the latter phenomenon is the highly abundant terminator readthrough we observed, which is more prevalent during late compared with early infection. Discussion This indicates that ASFV mRNAs under the control of late gene promoters utilize different termination mechanisms and factors to early promoters and/or that cellular factors influence the viral transcriptome landscape differently during the late stages of infection.
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Affiliation(s)
- Gwenny Cackett
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Michal Sýkora
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | | | - Christopher Dulson
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Linda Dixon
- Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
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2
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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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Draft Genome Sequence of an Isolate of Genotype VII Newcastle Disease Virus Isolated from an Outbreak in Fighting Cock in Peru. Microbiol Resour Announc 2023; 12:e0129322. [PMID: 36719208 PMCID: PMC9933683 DOI: 10.1128/mra.01293-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
This study presents a draft genome sequence of a Newcastle disease virus (NDV) strain (VFAR-136) isolated from a fighting cock (Gallus gallus) in the south of Peru. Strain VFAR-136 is a new report of NDV genotype VII circulating in Peru.
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Li D, Shao L, Xu T, Wang X, Zhang R, Zhang K, Xia Y, Zhang J. Hybrid RNA Sequencing Strategy for the Dynamic Transcriptomes of Winter Dormancy in an Evergreen Herbaceous Perennial, Iris japonica. Front Genet 2022; 13:841957. [PMID: 35368689 PMCID: PMC8965894 DOI: 10.3389/fgene.2022.841957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/11/2022] [Indexed: 11/30/2022] Open
Abstract
Japanese iris (Iris japonica) is a popular perennial ornamental that originated in China; it has a long display period and remains green outdoors throughout the year. winter dormancy characteristics contribute greatly to the evergreenness of herbaceous perennials. Thus, it is crucial to explore the mechanism of winter dormancy in this evergreen herbaceous perennial. Here, we used the hybrid RNA-seq strategy including single-molecule real-time (SMRT) and next-generation sequencing (NGS) technologies to generate large-scale Full-length transcripts to examine the shoot apical meristems of Japanese iris. A total of 10.57 Gb clean data for SMRT and over 142 Gb clean data for NGS were generated. Using hybrid error correction, 58,654 full-length transcripts were acquired and comprehensively analysed, and their expression levels were validated by real-time qPCR. This is the first full-length RNA-seq study in the Iris genus; our results provide a valuable resource and improve understanding of RNA processing in this genus, for which little genomic information is available as yet. In addition, our data will facilitate in-depth analyses of winter dormancy mechanisms in herbaceous perennials, especially evergreen monocotyledons.
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Affiliation(s)
| | | | | | | | | | | | - Yiping Xia
- *Correspondence: Jiaping Zhang, ; Yiping Xia,
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African Swine Fever Virus and host response - transcriptome profiling of the Georgia 2007/1 strain and porcine macrophages. J Virol 2022; 96:e0193921. [PMID: 35019713 PMCID: PMC8906413 DOI: 10.1128/jvi.01939-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
African swine fever virus (ASFV) has a major global economic impact. With a case fatality in domestic pigs approaching 100%, it currently presents the largest threat to animal farming. Although genomic differences between attenuated and highly virulent ASFV strains have been identified, the molecular determinants for virulence at the level of gene expression have remained opaque. Here, we characterize the transcriptome of ASFV genotype II Georgia 2007/1 (GRG) during infection of the physiologically relevant host cells, porcine macrophages. In this study, we applied cap analysis gene expression sequencing (CAGE-seq) to map th0e 5′ ends of viral mRNAs at 5 and 16 h postinfection. A bioinformatics analysis of the sequence context surrounding the transcription start sites (TSSs) enabled us to characterize the global early and late promoter landscape of GRG. We compared transcriptome maps of the GRG isolate and the lab-attenuated BA71V strain that highlighted GRG virulence-specific transcripts belonging to multigene families, including two predicted MGF 100 genes, I7L and I8L. In parallel, we monitored transcriptome changes in the infected host macrophage cells. Of the 9,384 macrophage genes studied, transcripts for 652 host genes were differentially regulated between 5 and 16 h postinfection compared with only 25 between uninfected cells and 5 h postinfection. NF-κB activated genes and lysosome components such as S100 were upregulated, and chemokines such as CCL24, CXCL2, CXCL5, and CXCL8 were downregulated. IMPORTANCE African swine fever virus (ASFV) causes hemorrhagic fever in domestic pigs, with case fatality rates approaching 100% and no approved vaccines or antivirals. The highly virulent ASFV Georgia 2007/1 strain (GRG) was the first isolated when ASFV spread from Africa to the Caucasus region in 2007, then spreading through Eastern Europe and, more recently, across Asia. We used an RNA-based next-generation sequencing technique called CAGE-seq to map the starts of viral genes across the GRG DNA genome. This has allowed us to investigate which viral genes are expressed during early or late stages of infection and how this is controlled, comparing their expression to the nonvirulent ASFV-BA71V strain to identify key genes that play a role in virulence. In parallel, we investigated how host cells respond to infection, which revealed how the ASFV suppresses components of the host immune response to ultimately win the arms race against its porcine host.
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Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay. Pathogens 2021; 10:pathogens10080919. [PMID: 34451383 PMCID: PMC8398953 DOI: 10.3390/pathogens10080919] [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: 05/24/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
Viral transcriptomes that are determined using first- and second-generation sequencing techniques are incomplete. Due to the short read length, these methods are inefficient or fail to distinguish between transcript isoforms, polycistronic RNAs, and transcriptional overlaps and readthroughs. Additionally, these approaches are insensitive for the identification of splice and transcriptional start sites (TSSs) and, in most cases, transcriptional end sites (TESs), especially in transcript isoforms with varying transcript ends, and in multi-spliced transcripts. Long-read sequencing is able to read full-length nucleic acids and can therefore be used to assemble complete transcriptome atlases. Although vaccinia virus (VACV) does not produce spliced RNAs, its transcriptome has a high diversity of TSSs and TESs, and a high degree of polycistronism that leads to enormous complexity. We applied single-molecule, real-time, and nanopore-based sequencing methods to investigate the time-lapse transcriptome patterns of VACV gene expression.
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Maróti Z, Tombácz D, Prazsák I, Moldován N, Csabai Z, Torma G, Balázs Z, Kalmár T, Dénes B, Snyder M, Boldogkői Z. Time-course transcriptome analysis of host cell response to poxvirus infection using a dual long-read sequencing approach. BMC Res Notes 2021; 14:239. [PMID: 34167576 PMCID: PMC8223271 DOI: 10.1186/s13104-021-05657-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/15/2021] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE In this study, we applied two long-read sequencing (LRS) approaches, including single-molecule real-time and nanopore-based sequencing methods to investigate the time-lapse transcriptome patterns of host gene expression as a response to Vaccinia virus infection. Transcriptomes determined using short-read sequencing approaches are incomplete because these platforms are inefficient or fail to distinguish between polycistronic RNAs, transcript isoforms, transcriptional start sites, as well as transcriptional readthroughs and overlaps. Long-read sequencing is able to read full-length nucleic acids and can therefore be used to assemble complete transcriptome atlases. RESULTS In this work, we identified a number of novel transcripts and transcript isoforms of Chlorocebus sabaeus. Additionally, analysis of the most abundant 768 host transcripts revealed a significant overrepresentation of the class of genes in the "regulation of signaling receptor activity" Gene Ontology annotation as a result of viral infection.
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Affiliation(s)
- Zoltán Maróti
- Department of Pediatrics, 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
| | - István Prazsák
- 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
| | - Zsolt Csabai
- 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
| | - Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Tibor Kalmár
- Department of Pediatrics, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Béla Dénes
- Veterinary Diagnostic Directorate of the National Food Chain Safety Office, Budapest, 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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Transcriptome view of a killer: African swine fever virus. Biochem Soc Trans 2021; 48:1569-1581. [PMID: 32725217 PMCID: PMC7458399 DOI: 10.1042/bst20191108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023]
Abstract
African swine fever virus (ASFV) represents a severe threat to global agriculture with the world's domestic pig population reduced by a quarter following recent outbreaks in Europe and Asia. Like other nucleocytoplasmic large DNA viruses, ASFV encodes a transcription apparatus including a eukaryote-like RNA polymerase along with a combination of virus-specific, and host-related transcription factors homologous to the TATA-binding protein (TBP) and TFIIB. Despite its high impact, the molecular basis and temporal regulation of ASFV transcription is not well understood. Our lab recently applied deep sequencing approaches to characterise the viral transcriptome and gene expression during early and late ASFV infection. We have characterised the viral promoter elements and termination signatures, by mapping the RNA-5' and RNA-3' termini at single nucleotide resolution. In this review, we discuss the emerging field of ASFV transcripts, transcription, and transcriptomics.
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Torma G, Tombácz D, Csabai Z, Moldován N, Mészáros I, Zádori Z, Boldogkői Z. Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus. Viruses 2021; 13:v13040579. [PMID: 33808073 PMCID: PMC8103240 DOI: 10.3390/v13040579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/17/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022] Open
Abstract
African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Short-read sequencing (SRS) can produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for comprehensively annotating transcriptomes. Long-read sequencing (LRS) can overcome some of SRS's limitations, but it also has drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the ASFV transcriptomic atlas. This work identified many novel transcripts and transcript isoforms and annotated the precise termini of previously described RNAs. This study identified a novel species of ASFV transcripts, the replication origin-associated RNAs. Additionally, we discovered several nested genes embedded into larger canonical genes. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism. A multifaceted meshwork of transcriptional overlaps was also discovered.
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Affiliation(s)
- Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - István Mészáros
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143 Budapest, Hungary; (I.M.); (Z.Z.)
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143 Budapest, Hungary; (I.M.); (Z.Z.)
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
- Correspondence:
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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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