Abstract
Viruses, like their metazoan hosts, have evolved to utilize intricate transcriptional mechanisms to generate a vast array of both coding and noncoding RNA transcripts. The resolution of specific noncoding RNA transcripts produced by viruses, particularly herpesviruses, presents a particularly difficult challenge due to their highly dense dsDNA genomes and their complex, overlapping, and context-dependent network of transcripts. While new long read sequencing platforms have facilitated the resolution of some noncoding transcripts from virus genomes, empirical molecular validation of transcripts from individual regions is essential. Herein, we demonstrate that the use of strand specific northern blots is essential for true validation of specific viral noncoding RNAs, and provide here a detailed molecular method for such an approach.
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Acknowledgments
S.A.T. was supported by NIH R01AI108407 and NIH P01CA214091. We thank Dr. Erik Flemington and Dr. Rolf Renne and members of the Renne and Flemington labs for helpful discussions and suggestions.
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Kara, M., Tibbetts, S.A. (2021). Empirical Validation of Overlapping Virus lncRNAs and Coding Transcripts by Northern Blot. In: Navarro, A. (eds) Long Non-Coding RNAs in Cancer. Methods in Molecular Biology, vol 2348. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1581-2_17
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DOI: https://doi.org/10.1007/978-1-0716-1581-2_17
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