Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
Autor: | Miklós Boldogkői, Dóra Tombácz, Gábor Torma, Ákos Dörmő, Tibor Kalmár, Norbert Moldován, Gábor Gulyás, Zsolt Csabai, Victoria A Jefferson, Zsolt Boldogkői, Zoltán Maróti, Florencia Meyer |
---|---|
Jazyk: | angličtina |
Rok vydání: | 2021 |
Předmět: |
0301 basic medicine
Science Computational biology Biology Virus-host interactions Article Transcriptome Nanopores 03 medical and health sciences Gene expression analysis 0302 clinical medicine Transcription (biology) Gene expression Protein Isoforms Transcriptomics Multidisciplinary Sequence Analysis RNA Gene Expression Profiling RNA RNA sequencing Translation (biology) Nanopore 030104 developmental biology Minion Medicine Nanopore sequencing 030217 neurology & neurosurgery |
Zdroj: | Scientific Reports, Vol 11, Iss 1, Pp 1-11 (2021) Scientific Reports |
ISSN: | 2045-2322 |
Popis: | 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. |
Databáze: | OpenAIRE |
Externí odkaz: |