Identification of microRNAs of the herpesvirus family.
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.
Pfeffer
Sébastien
S
Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA.
Sewer
Alain
A
Lagos-Quintana
Mariana
M
Sheridan
Robert
R
Sander
Chris
C
Grässer
Friedrich A
FA
van Dyk
Linda F
LF
Ho
C Kiong
CK
Shuman
Stewart
S
Chien
Minchen
M
Russo
James J
JJ
Ju
Jingyue
J
Randall
Glenn
G
Lindenbach
Brett D
BD
Rice
Charles M
CM
Simon
Viviana
V
Ho
David D
DD
Zavolan
Mihaela
M
Tuschl
Thomas
T
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*
D035683:MicroRNAs