Abstract
Long-read sequencing (LRS) techniques are very recent advancements, but they have already been used for transcriptome research in all of the three subfamilies of herpesviruses. These techniques have multiplied the number of known transcripts in each of the examined viruses. Meanwhile, they have revealed a so far hidden complexity of the herpesvirus transcriptome with the discovery of a large number of novel RNA molecules, including coding and non-coding RNAs, as well as transcript isoforms, and polycistronic RNAs. Additionally, LRS techniques have uncovered an intricate meshwork of transcriptional overlaps between adjacent and distally located genes. Here, we review the contribution of LRS to herpesvirus transcriptomics and present the complexity revealed by this technology, while also discussing the functional significance of this phenomenon.
Highlights
Short-read sequencing (SRS) technologies have revolutionized transcriptome studies because of their high throughput nature, precision, sensitivity, and cost-effectiveness
Long-read sequencing (LRS) and ribosome profiling of the herpes transcriptomes have further increased this number with the identification of a number of 5 truncated open reading frames (ORFs), which are located within the ORFs of the larger host genes (Stern-Ginossar et al, 2012; Arias et al, 2014; Moldován et al, 2017; Tombácz et al, 2017b).The tORFs are considered to be separate genes specifying polypeptides with N-terminal deletions compared to the longer protein encoded by the host gene in to which they are embedded
Until recently, the number of known herpesvirus transcript isoforms was comparable to the number of genes
Summary
Long-read sequencing (LRS) techniques are very recent advancements, but they have already been used for transcriptome research in all of the three subfamilies of herpesviruses. These techniques have multiplied the number of known transcripts in each of the examined viruses. They have revealed a so far hidden complexity of the herpesvirus transcriptome with the discovery of a large number of novel RNA molecules, including coding and non-coding RNAs, as well as transcript isoforms, and polycistronic RNAs. LRS techniques have uncovered an intricate meshwork of transcriptional overlaps between adjacent and distally located genes.
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