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Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1
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 va...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10336594/ https://www.ncbi.nlm.nih.gov/pubmed/37449092 http://dx.doi.org/10.1016/j.heliyon.2023.e17716 |
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author | Tombácz, Dóra Torma, Gábor Gulyás, Gábor Fülöp, Ádám Dörmő, Ákos Prazsák, István Csabai, Zsolt Mizik, Máté Hornyák, Ákos Zádori, Zoltán Kakuk, Balázs Boldogkői, Zsolt |
author_facet | Tombácz, Dóra Torma, Gábor Gulyás, Gábor Fülöp, Ádám Dörmő, Ákos Prazsák, István Csabai, Zsolt Mizik, Máté Hornyák, Ákos Zádori, Zoltán Kakuk, Balázs Boldogkői, Zsolt |
author_sort | Tombácz, Dóra |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10336594 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-103365942023-07-13 Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 Tombácz, Dóra Torma, Gábor Gulyás, Gábor Fülöp, Ádám Dörmő, Ákos Prazsák, István Csabai, Zsolt Mizik, Máté Hornyák, Ákos Zádori, Zoltán Kakuk, Balázs Boldogkői, Zsolt Heliyon Research Article 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. Elsevier 2023-06-28 /pmc/articles/PMC10336594/ /pubmed/37449092 http://dx.doi.org/10.1016/j.heliyon.2023.e17716 Text en © 2023 Published by Elsevier Ltd. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Article Tombácz, Dóra Torma, Gábor Gulyás, Gábor Fülöp, Ádám Dörmő, Ákos Prazsák, István Csabai, Zsolt Mizik, Máté Hornyák, Ákos Zádori, Zoltán Kakuk, Balázs Boldogkői, Zsolt Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 |
title | Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 |
title_full | Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 |
title_fullStr | Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 |
title_full_unstemmed | Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 |
title_short | Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 |
title_sort | hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10336594/ https://www.ncbi.nlm.nih.gov/pubmed/37449092 http://dx.doi.org/10.1016/j.heliyon.2023.e17716 |
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