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Article
Nature Methods - 2, 269 - 276 (2005)
Published online: 16 February 2005; | doi:10.1038/nmeth746

Identification of microRNAs of the herpesvirus family

Sébastien Pfeffer1, 12, Alain Sewer2, 12, Mariana Lagos-Quintana1, Robert Sheridan3, Chris Sander3, Friedrich A Grässer4, Linda F van Dyk5, C Kiong Ho6, 11, Stewart Shuman6, Minchen Chien7, James J Russo7, Jingyue Ju7, 8, Glenn Randall9, Brett D Lindenbach9, Charles M Rice9, Viviana Simon10, David D Ho10, Mihaela Zavolan2 & Thomas Tuschl1

1  Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA.

2  Biozentrum der Universität Basel, Klingelbergstr 50-70, CH-4056 Basel, Switzerland.

3  Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA.

4  Institut für Mikrobiologie und Hygiene, Abteilung Virologie, Haus 47, Universitätskliniken, D-66421 Homburg/Saar, Germany.

5  Microbiology and Immunology Departments, University of Colorado Health Science Center, Aurora, Colorado 80045, USA.

6  Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA.

7  Columbia Genome Center, Russ Berrie Pavilion, 1150 St. Nicholas Avenue, New York, New York 10032, USA.

8  Department of Chemical Engineering, Columbia University, 500 West 120 Street, New York, New York 10027, USA.

9  Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.

10  Aaron Diamond AIDS Research Center, The Rockefeller University, 455 First Avenue, New York, New York 10016, USA.

11  Present address: Department of Biological Sciences, 648 Cooke Hall, North Campus, State University of New York at Buffalo, Buffalo, New York 14260, USA.

12  These authors contributed equally to this work.

Correspondence should be addressed to Mihaela Zavolan mihaela.zavolan@unibas.ch or Thomas Tuschl ttuschl@rockefeller.edu

Epstein-Barr virus (EBV or HHV4), a member of the human herpesvirus (HHV) family, has recently been shown to encode microRNAs (miRNAs). In contrast to most eukaryotic miRNAs, these viral miRNAs do not have close homologs in other viral genomes or in the genome of the human host. To identify other miRNA genes in pathogenic viruses, we combined a new miRNA gene prediction method with small-RNA cloning from several virus-infected cell types. We cloned ten miRNAs in the Kaposi sarcoma–associated virus (KSHV or HHV8), nine miRNAs in the mouse gammaherpesvirus 68 (MHV68) and nine miRNAs in the human cytomegalovirus (HCMV or HHV5). These miRNA genes are expressed individually or in clusters from either polymerase (pol) II or pol III promoters, and share no substantial sequence homology with one another or with the known human miRNAs. Generally, we predicted miRNAs in several large DNA viruses, and we could neither predict nor experimentally identify miRNAs in the genomes of small RNA viruses or retroviruses.

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Nature Methods
ISSN: 1548-7091
EISSN: 1548-7105
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