The viral and cellular microRNA targetome in lymphoblastoid cell lines

Rebecca Skalsky, David L. Corcoran, Eva Gottwein, Christopher L. Frank, Dong Kang, Markus Hafner, Jeffrey D. Nusbaum, Regina Feederle, Henri Jacques Delecluse, Micah A. Luftig, Thomas Tuschl, Uwe Ohler, Bryan R. Cullen

Research output: Contribution to journalArticle

223 Citations (Scopus)

Abstract

Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus linked to a number of B cell cancers and lymphoproliferative disorders. During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) and induces the expression of specific host miRNAs, such as miR-155 and miR-21, which potentially play a role in viral oncogenesis. To date, only a limited number of EBV miRNA targets have been identified; thus, the role of EBV miRNAs in viral pathogenesis and/or lymphomagenesis is not well defined. Here, we used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) combined with deep sequencing and computational analysis to comprehensively examine the viral and cellular miRNA targetome in EBV strain B95-8-infected lymphoblastoid cell lines (LCLs). We identified 7,827 miRNA-interaction sites in 3,492 cellular 3′UTRs. 531 of these sites contained seed matches to viral miRNAs. 24 PAR-CLIP-identified miRNA:3′UTR interactions were confirmed by reporter assays. Our results reveal that EBV miRNAs predominantly target cellular transcripts during latent infection, thereby manipulating the host environment. Furthermore, targets of EBV miRNAs are involved in multiple cellular processes that are directly relevant to viral infection, including innate immunity, cell survival, and cell proliferation. Finally, we present evidence that myc-regulated host miRNAs from the miR-17/92 cluster can regulate latent viral gene expression. This comprehensive survey of the miRNA targetome in EBV-infected B cells represents a key step towards defining the functions of EBV-encoded miRNAs, and potentially, identifying novel therapeutic targets for EBV-associated malignancies.

Original languageEnglish (US)
Article numbere1002484
JournalPLoS Pathogens
Volume8
Issue number1
DOIs
StatePublished - Jan 2012
Externally publishedYes

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MicroRNAs
Human Herpesvirus 4
Cell Line
Ribonucleosides
Immunoprecipitation
B-Lymphocytes
High-Throughput Nucleotide Sequencing
Lymphoproliferative Disorders
Viral Genes
Herpesviridae
Virus Diseases
Infection
Innate Immunity
Neoplasms
Cell Survival
Seeds
Carcinogenesis
Cell Proliferation
Gene Expression

ASJC Scopus subject areas

  • Microbiology
  • Parasitology
  • Virology
  • Immunology
  • Genetics
  • Molecular Biology

Cite this

Skalsky, R., Corcoran, D. L., Gottwein, E., Frank, C. L., Kang, D., Hafner, M., ... Cullen, B. R. (2012). The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathogens, 8(1), [e1002484]. https://doi.org/10.1371/journal.ppat.1002484

The viral and cellular microRNA targetome in lymphoblastoid cell lines. / Skalsky, Rebecca; Corcoran, David L.; Gottwein, Eva; Frank, Christopher L.; Kang, Dong; Hafner, Markus; Nusbaum, Jeffrey D.; Feederle, Regina; Delecluse, Henri Jacques; Luftig, Micah A.; Tuschl, Thomas; Ohler, Uwe; Cullen, Bryan R.

In: PLoS Pathogens, Vol. 8, No. 1, e1002484, 01.2012.

Research output: Contribution to journalArticle

Skalsky, R, Corcoran, DL, Gottwein, E, Frank, CL, Kang, D, Hafner, M, Nusbaum, JD, Feederle, R, Delecluse, HJ, Luftig, MA, Tuschl, T, Ohler, U & Cullen, BR 2012, 'The viral and cellular microRNA targetome in lymphoblastoid cell lines', PLoS Pathogens, vol. 8, no. 1, e1002484. https://doi.org/10.1371/journal.ppat.1002484
Skalsky, Rebecca ; Corcoran, David L. ; Gottwein, Eva ; Frank, Christopher L. ; Kang, Dong ; Hafner, Markus ; Nusbaum, Jeffrey D. ; Feederle, Regina ; Delecluse, Henri Jacques ; Luftig, Micah A. ; Tuschl, Thomas ; Ohler, Uwe ; Cullen, Bryan R. / The viral and cellular microRNA targetome in lymphoblastoid cell lines. In: PLoS Pathogens. 2012 ; Vol. 8, No. 1.
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