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.
Fig: The effect of viral infection on transcript start and end sites. (a) The distance of TATA boxes from TSSs and (b) the distance of polyadenylation signals from TESs in base pairs. The sequence motif of the (c) TSSs and the (d) TESs in the mock infected cells, 4 h and 12 h following infection. Panels (a) and (b) were created using R v. 3.6.3 and ggplot2 v. 3.3.3. Panels (c) and (d) were created using the online tool WebLogo3. The figure was created using Inkscape v. 0.92.
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.
Maróti, Z., Tombácz, D., Moldován, N. et al. Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing. Sci Rep 11, 14219 (2021). https://doi.org/10.1038/s41598-021-93142-7