Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay
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. Additio...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-07-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/10/8/919 |
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| author | Dóra Tombácz István Prazsák Gábor Torma Zsolt Csabai Zsolt Balázs Norbert Moldován Béla Dénes Michael Snyder Zsolt Boldogkői |
| author_facet | Dóra Tombácz István Prazsák Gábor Torma Zsolt Csabai Zsolt Balázs Norbert Moldován Béla Dénes Michael Snyder Zsolt Boldogkői |
| author_sort | Dóra Tombácz |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T08:30:44Z |
| format | Article |
| id | doaj.art-ebef9ffc65f14ef6a9e3665412633909 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-10T08:30:44Z |
| publishDate | 2021-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-ebef9ffc65f14ef6a9e36654126339092023-11-22T09:07:58ZengMDPI AGPathogens2076-08172021-07-0110891910.3390/pathogens10080919Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length AssayDóra Tombácz0István Prazsák1Gábor Torma2Zsolt Csabai3Zsolt Balázs4Norbert Moldován5Béla Dénes6Michael Snyder7Zsolt Boldogkői8Department of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, HungaryVeterinary Diagnostic Directorate, National Food Chain Safety Office, 1143 Budapest, HungaryDepartment of Genetics, School of Medicine, Stanford University, Stanford, CA 94304, USADepartment of Medical Biology, Faculty of Medicine, University of Szeged, 6720 Szeged, HungaryViral 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.https://www.mdpi.com/2076-0817/10/8/919vaccinia viruslong-read sequencingnanopore sequencingtranscriptome profilinggene expression |
| spellingShingle | Dóra Tombácz István Prazsák Gábor Torma Zsolt Csabai Zsolt Balázs Norbert Moldován Béla Dénes Michael Snyder Zsolt Boldogkői Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay Pathogens vaccinia virus long-read sequencing nanopore sequencing transcriptome profiling gene expression |
| title | Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay |
| title_full | Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay |
| title_fullStr | Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay |
| title_full_unstemmed | Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay |
| title_short | Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay |
| title_sort | time course transcriptome profiling of a poxvirus using long read full length assay |
| topic | vaccinia virus long-read sequencing nanopore sequencing transcriptome profiling gene expression |
| url | https://www.mdpi.com/2076-0817/10/8/919 |
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