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Journal of Virology, June 2006, p. 5499-5508, Vol. 80, No. 11
0022-538X/06/$08.00+0     doi:10.1128/JVI.00200-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Prediction and Identification of Herpes Simplex Virus 1-Encoded MicroRNAs

Can Cui,1 Anthony Griffiths,1 Guanglin Li,2 Lindsey M. Silva,1,{dagger} Martha F. Kramer,1 Terry Gaasterland,3,4,{ddagger} Xiu-Jie Wang,2,3* and Donald M. Coen1*

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115,1 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China,2 Laboratory of Computational Genomics, The Rockefeller University, New York, New York 10021,3 Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 920374

Received 27 January 2006/ Accepted 20 March 2006

MicroRNAs (miRNAs) are key regulators of gene expression in higher eukaryotes. Recently, miRNAs have been identified from viruses with double-stranded DNA genomes. To attempt to identify miRNAs encoded by herpes simplex virus 1 (HSV-1), we applied a computational method to screen the complete genome of HSV-1 for sequences that adopt an extended stem-loop structure and display a pattern of nucleotide divergence characteristic of known miRNAs. Using this method, we identified 11 HSV-1 genomic loci predicted to encode 13 miRNA precursors and 24 miRNA candidates. Eight of the HSV-1 miRNA candidates were predicted to be conserved in HSV-2. The precursor and the mature form of one HSV-1 miRNA candidate, which is encoded ~450 bp upstream of the transcription start site of the latency-associated transcript (LAT), were detected during infection of Vero cells by Northern blot hybridization. These RNAs, which behave as late gene products, are not predicted to be conserved in HSV-2. Additionally, small RNAs, including some that are roughly the expected size of precursor miRNAs, were detected using probes for miRNA candidates derived from sequences encoding the 8.3-kilobase LAT, from sequences complementary to UL15 mRNA, and from the region between ICP4 and US1. However, no species the size of typical mature miRNAs were detected using these probes. Three of these latter miRNA candidates were predicted to be conserved in HSV-2. Thus, HSV-1 encodes at least one miRNA. We hypothesize that HSV-1 miRNAs regulate viral and host gene expression.

* Corresponding author. Mailing address for Donald M. Coen: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Ave., Boston, MA 02115. Phone: (617) 432-1691. Fax: (617) 432-3833. E-mail: Don_Coen{at}hms.harvard.edu. Mailing address for Xiu-Jie Wang: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Andingmenwai, Beijing, 100101, China. Phone: (8610) 6484-0941. Fax: (8610) 6487-3428. E-mail: xjwang{at}genetics.ac.cn.

{dagger} Present address: Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115.

{ddagger} Present address: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037.

Journal of Virology, June 2006, p. 5499-5508, Vol. 80, No. 11
0022-538X/06/$08.00+0     doi:10.1128/JVI.00200-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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