Dynamic transcriptome landscape of Vaccinia virus revealed by long-read sequencing approach
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Poxviridae is a large virus family that infects vertebrates and invertebrates with highly pathogenic members, such as the Variola virus, which is the causative agent of smallpox. Vaccinia virus (VACV) is the prototypic member of the Orthopoxvirus genus. It is closely related to the Variola virus that was eradicated as a result of a successful global vaccination program using live VACV. VACV is extensively utilised as an expression and a gene delivery vector, e.g. in oncolytic treatments. It is also known as a model system for the analysis of virus-host interactions. Poxviruses are able to replicate independently in the cytoplasm of the host cell because they encode their own DNA polymerase. The virus has a relatively large (approximately 195 kbp) double-stranded DNA genome coding for about 220 proteins. The VACV genes are divided into two main temporal classes: pre-replicative and post-replicative; they are further grouped into early (E1 and E2), intermediate (I), and late (L) genes, according to Bernard Moss.
Aims
Several traditional methods, including short-read sequencing techniques (SRS), have already been used to resolve transcriptional start and end sites (TSSs, TESs) of VACV, however, variable read-through or polycistronism has remained hidden in the VACV transcriptome. Despite the scientific relevance of VACV, no long-read sequencing techniques (LRS) have been adopted for the VACV transcriptome to date. The aims of this study were the transcriptional reannotation of VACV, description of potential new TSSs and TESs, and discovery of transcript-length isoforms.