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Contemporary Ribonomics Methods for Viral microRNA Target Analysis.

Lauren A Gay1, Peter C Turner2, Rolf Renne3

  • 1Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA. lagay@ufl.edu.

Non-Coding RNA
|November 15, 2018
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Summary

Researchers used cross-linking and immunoprecipitation (CLIP) to identify microRNA (miRNA) targets, revealing crucial interactions for viruses like EBV and KSHV in disease.

Keywords:
AgoCLASHCLIPEBVHITS-CLIPKSHVPAR-CLIPmicroRNAqCLASH

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Area of Science:

  • Molecular Biology
  • Virology
  • Genomics

Background:

  • MicroRNAs (miRNAs) regulate numerous cellular and viral processes.
  • Identifying miRNA targets is crucial for understanding gene regulation.
  • Viral miRNAs play significant roles in host-pathogen interactions.

Purpose of the Study:

  • To elucidate miRNA targets using advanced ribonomics techniques.
  • To investigate miRNA-target interactions in the context of γ-herpesviruses, specifically KSHV and EBV.
  • To review and compare different CLIP-based methods for miRNA target identification.

Main Methods:

  • Cross-linking and Immunoprecipitation (CLIP) coupled with high-throughput sequencing.
  • Utilizing antibodies against Argonaute (Ago) protein within the RISC complex.
  • Employing RNA-RNA ligation techniques for enhanced target identification.

Main Results:

  • CLIP-based methods, particularly Ago-CLIP, have successfully identified numerous miRNA targets.
  • High-throughput sequencing of CLIP data revealed extensive miRNA targetomes for KSHV and EBV.
  • Recent advancements in CLIP protocols, including RNA-RNA ligation, improve miRNA-target linkage.
  • Evidence for biologically significant interactions between miRNAs and long non-coding RNAs (lncRNAs) was reviewed.

Conclusions:

  • Ribonomics-based miRNA targetome analysis significantly enhances our understanding of miRNA-mediated gene regulation.
  • This approach provides valuable insights into the roles of miRNAs in EBV and KSHV pathogenesis and tumorigenesis.
  • CLIP and its variants are powerful tools for comprehensive miRNA target discovery.