Empirical Validation of Overlapping Virus lncRNAs and Coding Transcripts by Northern Blot

KARA M. , Tibbetts S. A.

LONG NON-CODING RNAS IN CANCER, vol.2348, pp.243-253, 2021 (Journal Indexed in SCI) identifier identifier

  • Publication Type: Article / Article
  • Volume: 2348
  • Publication Date: 2021
  • Doi Number: 10.1007/978-1-0716-1581-2_17
  • Page Numbers: pp.243-253
  • Keywords: Viral lncRNAs, Herpesviruses, Strand specific northern blot, NONCODING RNAS


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.