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Identification of host RNAs that interact with EBV noncoding RNA EBER2.

Adalena V Nanni1, Nara Lee1

  • 1a Department of Microbiology and Molecular Genetics, 450 Technology Drive , University of Pittsburgh School of Medicine , Pittsburgh , PA , USA.

RNA Biology
|September 4, 2018
PubMed
Summary

Epstein-Barr virus EBER2 RNA guides the PAX5 protein to specific DNA sites. This novel method identifies EBER2-interacting RNAs, revealing new interactions with host RNAs and potential regulatory roles.

Keywords:
Epstein-Barr virusRNA-RNA interactionnext-generation sequencingnoncoding RNA

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Area of Science:

  • Molecular Biology
  • Virology
  • RNA Biology

Background:

  • Epstein-Barr virus (EBV) nuclear noncoding RNA EBER2 interacts with host transcription factor PAX5.
  • This ribonucleoprotein complex targets EBV genome's terminal repeat (TR) regions via RNA-RNA interactions.

Purpose of the Study:

  • To develop a method for identifying EBER2-interacting RNAs transcriptome-wide.
  • To investigate the RNA-RNA interactions mediated by EBER2 and PAX5.

Main Methods:

  • Psoralen-mediated crosslinking.
  • Selection using EBER2-targeting antisense oligonucleotides.
  • RNase V1 digestion coupled with next-generation sequencing.

Main Results:

  • The method successfully identified known EBER2-TR RNA interactions.
  • Identified host noncoding RNAs (MRP, H1, 7SL) and enhancer RNAs as novel EBER2 interactors.
  • Observed PAX5 occupancy at these host gene loci.

Conclusions:

  • The developed approach efficiently identifies specific RNA-RNA interactions.
  • EBER2, via PAX5, may interact with nascent transcripts at host gene loci.
  • This study provides a novel tool for RNA-RNA interaction discovery.