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Long-read Assays Shed New Light on the Transcriptome Complexity of a Viral Pathogen and on Virus-Host Interaction

By Dora Tombacz, Istvan Prazsak, Zoltán Maróti, Norbert Moldovan, Zsolt Csabai, Zsolt Balazs, Béla Dénes, Tibor Kalmár, Michael Snyder, Zsolt Boldogkoi

Posted 27 Jan 2020
bioRxiv DOI: 10.1101/2020.01.27.921056

Characterization of global transcriptomes using conventional short-read sequencing is challenging because of the insensitivity of these platforms to transcripts isoforms, multigenic RNA molecules, and transcriptional overlaps, etc. Long-read sequencing (LRS) can overcome these limitations by reading full-length transcripts. Employment of these technologies has led to the redefinition of transcriptional complexities in reported organisms. In this study, we applied LRS platforms from Pacific Biosciences and Oxford Nanopore Technologies to profile the dynamic vaccinia virus (VACV) transcriptome and assess the effect of viral infection on host gene expression. We performed cDNA and direct RNA sequencing analyses and revealed an extremely complex transcriptional landscape of this virus. In particular, VACV genes produce large numbers of transcript isoforms that vary in their start and termination sites. A significant fraction of VACV transcripts start or end within coding regions of neighboring genes. We distinguished five classes of host genes according to their temporal responses to viral infection. This study provides novel insights into the transcriptomic profile of a viral pathogen and the effect of the virus on host gene expression.

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