Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing

Abstract Third-generation sequencing is able to read full-length transcripts and thus to efficiently identify RNA molecules and transcript isoforms, including transcript length and splice isoforms. In this study, we report the time-course profiling of the effect of bovine alphaherpesvirus type 1 on...

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Autores principales:	Zoltán Maróti, Dóra Tombácz, Norbert Moldován, Gábor Torma, Victoria A. Jefferson, Zsolt Csabai, Gábor Gulyás, Ákos Dörmő, Miklós Boldogkői, Tibor Kalmár, Florencia Meyer, Zsolt Boldogkői
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/af1ae040d093401f85a0a98381764b08
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spelling	oai:doaj.org-article:af1ae040d093401f85a0a98381764b082021-12-02T16:14:55ZTime course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing10.1038/s41598-021-93142-72045-2322https://doaj.org/article/af1ae040d093401f85a0a98381764b082021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93142-7https://doaj.org/toc/2045-2322Abstract Third-generation sequencing is able to read full-length transcripts and thus to efficiently identify RNA molecules and transcript isoforms, including transcript length and splice isoforms. In this study, we report the time-course profiling of the effect of bovine alphaherpesvirus type 1 on the gene expression of bovine epithelial cells using direct cDNA sequencing carried out on MinION device of Oxford Nanopore Technologies. These investigations revealed a substantial up- and down-regulatory effect of the virus on several gene networks of the host cells, including those that are associated with antiviral response, as well as with viral transcription and translation. Additionally, we report a large number of novel bovine transcript isoforms identified by nanopore and synthetic long-read sequencing. This study demonstrates that viral infection causes differential expression of host transcript isoforms. We could not detect an increased rate of transcriptional readthroughs as described in another alphaherpesvirus. According to our knowledge, this is the first report on the use of LoopSeq for the analysis of eukaryotic transcriptomes. This is also the first report on the application of nanopore sequencing for the kinetic characterization of cellular transcriptomes. This study also demonstrates the utility of nanopore sequencing for the characterization of dynamic transcriptomes in any organisms.Zoltán MarótiDóra TombáczNorbert MoldovánGábor TormaVictoria A. JeffersonZsolt CsabaiGábor GulyásÁkos DörmőMiklós BoldogkőiTibor KalmárFlorencia MeyerZsolt BoldogkőiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zoltán Maróti Dóra Tombácz Norbert Moldován Gábor Torma Victoria A. Jefferson Zsolt Csabai Gábor Gulyás Ákos Dörmő Miklós Boldogkői Tibor Kalmár Florencia Meyer Zsolt Boldogkői Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
description	Abstract Third-generation sequencing is able to read full-length transcripts and thus to efficiently identify RNA molecules and transcript isoforms, including transcript length and splice isoforms. In this study, we report the time-course profiling of the effect of bovine alphaherpesvirus type 1 on the gene expression of bovine epithelial cells using direct cDNA sequencing carried out on MinION device of Oxford Nanopore Technologies. These investigations revealed a substantial up- and down-regulatory effect of the virus on several gene networks of the host cells, including those that are associated with antiviral response, as well as with viral transcription and translation. Additionally, we report a large number of novel bovine transcript isoforms identified by nanopore and synthetic long-read sequencing. This study demonstrates that viral infection causes differential expression of host transcript isoforms. We could not detect an increased rate of transcriptional readthroughs as described in another alphaherpesvirus. According to our knowledge, this is the first report on the use of LoopSeq for the analysis of eukaryotic transcriptomes. This is also the first report on the application of nanopore sequencing for the kinetic characterization of cellular transcriptomes. This study also demonstrates the utility of nanopore sequencing for the characterization of dynamic transcriptomes in any organisms.
format	article
author	Zoltán Maróti Dóra Tombácz Norbert Moldován Gábor Torma Victoria A. Jefferson Zsolt Csabai Gábor Gulyás Ákos Dörmő Miklós Boldogkői Tibor Kalmár Florencia Meyer Zsolt Boldogkői
author_facet	Zoltán Maróti Dóra Tombácz Norbert Moldován Gábor Torma Victoria A. Jefferson Zsolt Csabai Gábor Gulyás Ákos Dörmő Miklós Boldogkői Tibor Kalmár Florencia Meyer Zsolt Boldogkői
author_sort	Zoltán Maróti
title	Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
title_short	Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
title_full	Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
title_fullStr	Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
title_full_unstemmed	Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
title_sort	time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/af1ae040d093401f85a0a98381764b08
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Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing

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