In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing
Dóra Tombácz,
Balázs Kakuk,
Gábor Torma,
Zsolt Csabai,
Gábor Gulyás,
Vivien Tamás,
Zoltán Zádori,
Victoria A. Jefferson,
Florencia Meyer,
Zsolt Boldogkői
Affiliations
Dóra Tombácz
Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary
Balázs Kakuk
Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary
Gábor Torma
Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary
Zsolt Csabai
Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary
Gábor Gulyás
Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary
Vivien Tamás
Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, 1143 Budapest, Hungary
Zoltán Zádori
Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, 1143 Budapest, Hungary
Victoria A. Jefferson
Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 408 Dorman P.O. Box 9655, 32 Creelman St., Starkville, MS 39762, USA
Florencia Meyer
Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 408 Dorman P.O. Box 9655, 32 Creelman St., Starkville, MS 39762, USA
Zsolt Boldogkői
Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary
In this work, a long-read sequencing (LRS) technique based on the Oxford Nanopore Technology MinION platform was used for quantifying and kinetic characterization of the poly(A) fraction of bovine alphaherpesvirus type 1 (BoHV-1) lytic transcriptome across a 12-h infection period. Amplification-based LRS techniques frequently generate artefactual transcription reads and are biased towards the production of shorter amplicons. To avoid these undesired effects, we applied direct cDNA sequencing, an amplification-free technique. Here, we show that a single promoter can produce multiple transcription start sites whose distribution patterns differ among the viral genes but are similar in the same gene at different timepoints. Our investigations revealed that the circ gene is expressed with immediate–early (IE) kinetics by utilizing a special mechanism based on the use of the promoter of another IE gene (bicp4) for the transcriptional control. Furthermore, we detected an overlap between the initiation of DNA replication and the transcription from the bicp22 gene, which suggests an interaction between the two molecular machineries. This study developed a generally applicable LRS-based method for the time-course characterization of transcriptomes of any organism.
