Long-read Time-course Profiling of the 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 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 transcripts identified by nanopore and synthetic long-read sequencing. This study demonstrates that viral infection does not lead to a change in the average distance between promoters and transcription start sites, and between polyadenylation signals and transcription end sites. However, it causes differential expression of 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 changes of transcriptomes in any organisms.