Integrative functional genomics decodes herpes simplex virus 1

Abstract

<jats:title>Summary</jats:title><jats:p>Since the genome of herpes simplex virus 1 (HSV-1) was first sequenced more than 30 years ago, its predicted 80 genes have been intensively studied. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identified a total of 201 viral transcripts and 284 open reading frames (ORFs) including all known and 46 novel large ORFs. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of novel viral ORFs as well as N-terminal extensions (NTEs) and truncations thereof. We show that key viral regulators and structural proteins possess NTEs, which initiate from non-canonical start codons and govern subcellular protein localization and packaging. We validated a novel non-canonical large spliced ORF in the ICP0 locus and identified a 93 aa ORF overlapping ICP34.5 that is thus also deleted in the FDA-approved oncolytic virus Imlygic. Finally, we extend the current nomenclature to include all novel viral gene products. Taken together, this work provides a valuable resource for future functional studies, vaccine design and oncolytic therapies.</jats:p>

Demand for Multiplatform and Meta-analytic Approaches in Transcriptome Profiling

“…In this study, we employed an integrated approach based on the meta-analysis of the HSV-1 transcriptome data published by Depledge and colleagues (using ONT dRNA-Seq and Illumina RNA-Seq) 7 10 , and our laboratory (Tombácz and colleagues using PacBio RSII 11 , as well as Boldogkői et al 12 and Tombácz et al 13 using PacBio Sequel, ONT dRNA-Seq and cDNA sequencing with multiple library preparation methods; Supplementary Table 1). This analysis led to the discovery of novel transcripts, especially of novel multigenic transcripts ( Supplementary Figure 1), and splice sites (Figure 1, Supplementary Figure 2).…”

“…The LoRTIA tool was used to annotate introns and TSSs, and TESs from the LRS data, whereas we used the STAR software was used to detect introns from the SRS samples. The previously published introns (Tang et al 8 , Wishnant et al 10 , and Tombácz et al 11,13 ) were compared with each other, reanalyzed, and validated by using the datasets from all of the aforementioned publications.…”

“…The datasets generated by Depledge et al 7 and five other datasets (Tombácz et al 11,13 ; Tang et al 8 ; Rutkowski et al 9 , and Whisnant et al 10 ) were reanalyzed in order to define the complete HSV transcriptome.…”

“…The datasets used in this work were obtained from the original publications: Depledge et al, 7 , Whisnant et al 10 , Tang et al 8 , Rutkowski et al 9 , and from Tombácz et al 11,13 . All data generated in this study are included in Supplementary Table 1.…”

“…The 378 putative introns identified in our earlier study 11,13 are already multiplatform-based (various combination of library preparation techniques of Pacific Biosciences RSII and Sequel, and Oxford Nanopore Technologies MinION sequencing). These datasets were compared with the intron datasets generated by Tang et al 8 and Whisnant et al 10 . We also used the raw sequencing reads from Depledge's direct RNA-Seq study.…”