Tandem array-based expression screens identify host mRNA targets of virus-encoded microRNAs.
MicroRNAs (miRNAs) are short noncoding RNAs of cellular and viral origin that post-transcriptionally regulate gene expression through imperfect base pairing to their mRNA targets. Because the recognition sequences of miRNAs for their targets are short and may be discontinuous, bioinformatic prediction of targets is difficult. Here we present an approach to the experimental identification of the mRNA targets of miRNAs encoded by the Kaposi's sarcoma-associated herpesvirus (KSHV). KSHV encodes 17 miRNAs, derived from 12 pre-miRNAs expressed from a single locus during viral latency. We conducted multiple screens that examine small changes in transcript abundance under different conditions of miRNA expression or inhibition and then searched the identified transcripts for seed sequence matches. Using this strategy, we identified BCLAF1, encoding Bcl2-associated factor, as a target for miR-K5, and further analysis revealed that several other KSHV miRNAs also target this gene product. Our results support that this type of expression profiling provides a potentially general approach to the identification of miRNA targets.
Ziegelbauer
Joseph M
JM
Howard Hughes Medical Institute, GW Hooper Foundation, University of California San Francisco, San Francisco, California 94143, USA.
Sullivan
Christopher S
CS
Ganem
Don
D
D017209:Apoptosis; D001483:Base Sequence; D002460:Cell Line; D004268:DNA-Binding Proteins; D042783:Endothelial Cells / Q000166:cytology / Q000378:metabolism; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D019288:Herpesvirus 8, Human / Q000235:genetics; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics*; D012097:Repressor Proteins; D025521:Tumor Suppressor Proteins
C119386:BCLAF1 protein, human; D004268:DNA-Binding Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; D012367:RNA, Viral; D012097:Repressor Proteins; D025521:Tumor Suppressor Proteins