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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...

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Autores principales: Tombácz, Dóra, Torma, Gábor, Gulyás, Gábor, Fülöp, Ádám, Dörmő, Ákos, Prazsák, István, Csabai, Zsolt, Mizik, Máté, Hornyák, Ákos, Zádori, Zoltán, Kakuk, Balázs, Boldogkői, Zsolt
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
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.
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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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