Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells

J Virol. 2010 Dec;84(24):13053-8. doi: 10.1128/JVI.01521-10. Epub 2010 Oct 13.


RNA-seq provides a rich source of transcriptome information with high qualitative and quantitative value. Here, we provide a pipeline for Epstein-Barr virus (EBV) transcriptome analysis using RNA-seq and we apply it to two type I latency cell lines, Mutu I and Akata. This analysis revealed substantial average expression levels of many lytic genes in predominantly latent cell populations. The lytic transcripts BHLF1 and LF3 were expressed at levels greater than those for 98% of all cellular polyadenylated transcripts. Exon junction mapping accurately identified the Qp-derived EBNA1 splicing pattern, lytic gene splicing, and a complex splicing pattern within the BamHI A region.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biomarkers / metabolism
  • Burkitt Lymphoma / genetics
  • Burkitt Lymphoma / virology*
  • Epstein-Barr Virus Infections / genetics
  • Epstein-Barr Virus Infections / virology*
  • Epstein-Barr Virus Nuclear Antigens / genetics*
  • Epstein-Barr Virus Nuclear Antigens / metabolism
  • Gene Expression Profiling*
  • Gene Expression Regulation, Viral
  • Genome, Viral
  • Herpesvirus 4, Human / genetics*
  • Herpesvirus 4, Human / pathogenicity
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • RNA Splicing
  • RNA, Messenger / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Transcription, Genetic
  • Viral Proteins / genetics
  • Virus Latency / genetics


  • Biomarkers
  • Epstein-Barr Virus Nuclear Antigens
  • LF3 protein, Epstein-Barr virus
  • RNA, Messenger
  • Viral Proteins