title: Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing.
abstract: Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, and late classes. In this study, a massively parallel sequencing technique that is based on PacBio Single Molecule Real-time sequencing platform, was used for quantifying the poly(A) fraction of the lytic transcriptome of pseudorabies virus (PRV) throughout a 12-hour interval of productive infection on PK-15 cells. Other approaches, including microarray, real-time RT-PCR and Illumina sequencing are capable of detecting only the aggregate transcriptional activity of particular genomic regions, but not individual herpesvirus transcripts. However, SMRT sequencing allows for a distinction between transcript isoforms, including length- and splice variants, as well as between overlapping polycistronic RNA molecules. The non-amplified Isoform Sequencing (Iso-Seq) method was used to analyse the kinetic properties of the lytic PRV transcripts and to then classify them accordingly. Additionally, the present study demonstrates the general utility of long-read sequencing for the time-course analysis of global gene expression in practically any organism.
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary.
authors.forename: Dóra
authors.initials: D
authors.lastname: Tombácz
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Balázs
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Csabai
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary.
authors.forename: Norbert
authors.initials: N
authors.lastname: Moldován
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary.
authors.forename: Attila
authors.initials: A
authors.lastname: Szűcs
authors.affiliation: Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr., Stanford, CA 94305-5120, USA.
authors.forename: Donald
authors.initials: D
authors.lastname: Sharon
authors.affiliation: Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr., Stanford, CA 94305-5120, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Boldogkői
mesh_terms: D000818:Animals; D002460:Cell Line; D005057:Eukaryotic Cells / Q000166:cytology / Q000821:virology; D020869:Gene Expression Profiling; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral / Q000235:genetics; D023281:Genomics / Q000379:methods; D011558:Herpesvirus 1, Suid / Q000235:genetics* / Q000502:physiology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D013552:Swine; D059467:Transcriptome; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins