The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines

PLoS Pathogens

Bryan R. Cullen¹  Eva Gottwein²  Micah A. Luftig³  Dong Kang³  Christopher L. Frank³  Rebecca L. Skalsky³  David L. Corcoran⁴  Uwe Ohler⁴  Regina Feederle⁵  Henri-Jacques Delecluse⁵  Jeffrey D. Nusbaum⁶  Thomas Tuschl⁶  Markus Hafner⁶ 

[1] Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America;Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, United States of America;Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America;Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America;German Cancer Research Center, Department of Virus-Associated Tumours, Heidelberg, Germany;Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, United States of America

关键词: MicroRNAs;    B cells;    Luciferase assay;    Epstein-Barr virus;    Genomic libraries;    Luciferase;    RNA sequencing;    Sequence alignment;   

DOI  :  10.1371/journal.ppat.1002484

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

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.

【 授权许可】

CC BY