title: Identification of microRNAs of the herpesvirus family.
abstract: 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.
authors.affiliation: Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Pfeffer
authors.forename: Alain
authors.initials: A
authors.lastname: Sewer
authors.forename: Mariana
authors.initials: M
authors.lastname: Lagos-Quintana
authors.forename: Robert
authors.initials: R
authors.lastname: Sheridan
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.forename: Friedrich A
authors.initials: FA
authors.lastname: Grässer
authors.forename: Linda F
authors.initials: LF
authors.lastname: van Dyk
authors.forename: C Kiong
authors.initials: CK
authors.lastname: Ho
authors.forename: Stewart
authors.initials: S
authors.lastname: Shuman
authors.forename: Minchen
authors.initials: M
authors.lastname: Chien
authors.forename: James J
authors.initials: JJ
authors.lastname: Russo
authors.forename: Jingyue
authors.initials: J
authors.lastname: Ju
authors.forename: Glenn
authors.initials: G
authors.lastname: Randall
authors.forename: Brett D
authors.initials: BD
authors.lastname: Lindenbach
authors.forename: Charles M
authors.initials: CM
authors.lastname: Rice
authors.forename: Viviana
authors.initials: V
authors.lastname: Simon
authors.forename: David D
authors.initials: DD
authors.lastname: Ho
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D003001:Cloning, Molecular / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D016679:Genome, Viral; D006564:Herpesviridae / Q000145:classification / Q000235:genetics*; D035683:MicroRNAs / Q000032:analysis / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs