title: The viral and cellular microRNA targetome in lymphoblastoid cell lines.
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.
authors.affiliation: Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America.
authors.forename: Rebecca L
authors.initials: RL
authors.lastname: Skalsky
authors.forename: David L
authors.initials: DL
authors.lastname: Corcoran
authors.forename: Eva
authors.initials: E
authors.lastname: Gottwein
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Frank
authors.forename: Dong
authors.initials: D
authors.lastname: Kang
authors.forename: Markus
authors.initials: M
authors.lastname: Hafner
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Nusbaum
authors.forename: Regina
authors.initials: R
authors.lastname: Feederle
authors.forename: Henri-Jacques
authors.initials: HJ
authors.lastname: Delecluse
authors.forename: Micah A
authors.initials: MA
authors.lastname: Luftig
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Cullen
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D001402:B-Lymphocytes / Q000378:metabolism / Q000473:pathology / Q000821:virology; D045744:Cell Line, Tumor; D002472:Cell Transformation, Viral; D020031:Epstein-Barr Virus Infections / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D004854:Herpesvirus 4, Human / Q000502:physiology*; D006801:Humans; D008232:Lymphoproliferative Disorders / Q000235:genetics / Q000378:metabolism* / Q000473:pathology / Q000821:virology*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D017735:Virus Latency / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; C524942:MIRN155 microRNA, human; C524940:MIRN21 microRNA, human; D035683:MicroRNAs