catalog ͉ evolution ͉ GWAS ͉ polymorphism ͉ disorders

Primary transcripts of certain microRNA (miRNA) genes are subject to RNA editing that converts adenosine to inosine. However, the importance of miRNA editing remains largely undetermined. Here we report that tissue-specific adenosine-to-inosine editing of miR-376 cluster transcripts leads to predominant expression of edited miR-376 isoform RNAs. One highly edited site is positioned in the middle of the 5′-proximal half "seed" region critical for the hybridization of miRNAs to targets. We provide evidence that the edited miR-376 RNA silences specifically a different set of genes. Repression of phosphoribosyl pyrophosphate synthetase 1, a target of the edited miR-376 RNA and an enzyme involved in the uric-acid synthesis pathway, contributes to tight and tissue-specific regulation of uric-acid levels, revealing a previously unknown role for RNA editing in miRNAmediated gene silencing.Many developmental and cellular processes are regulated by microRNA (miRNA)-mediated RNA interference (RNAi) (1-4). After incorporation into the RNA-induced silencing complex, miRNAs guide the RNAi machinery to their target genes by forming RNA duplexes, resulting in sequence-specific mRNA degradation or translational repression (1,2,4). The generation of mature miRNAs requires the processing of primary transcripts (pri-miRNAs) (5), and A → I RNA editing occurs to certain pri-miRNAs (6-8).Human chromosome 14 and syntenic regions of the distal end of mouse chromosome 12 harbor the miR-376 cluster of miRNA genes (9). The six human miR-376 RNAs (miR-376a2, -376b, -368, -B1, and -B2) (Fig. 1A) and three mouse miR-376a-c RNAs ( fig. S1A) have highly similar sequences ( fig. S2). Expression of miR-376 RNAs is detected in the placenta, developing embryos, and adult tissues (9,10).All of the miR-376 RNA cluster members are transcribed into a long primary transcript encompassing the entire region and (except human miR-B1) undergo extensive and * To whom correspondence should be addressed. ykawahara@wistar.org (Y.K.); kazuko@wistar.org (K.N.). † These authors contributed equally to this work. simultaneous A → I editing at one or both of two specific sites (+4 and +44) in select human and mouse tissues and specific subregions of the brain ( Fig. 2 and table S1) (11). The +4 site of some pri-miR-376 cluster genes (e.g., human -376b and -368) is genomically encoded as G and thus not subject to A → I editing (Fig. 1A). Certain miR-376 members, such as primiR-376a2, -376b, and -368, are nearly 100% edited at the +44 site in the human cortex and medulla (Figs. 1B and 2 and table S1), whereas no editing was detected in other tissues (e.g., the +4 site of human pri-miR-376a1 in liver and the +44 site of mouse pri-miR-376a in all tissues). In select members of the cluster, substantial editing (∼20 to 55%) occurs at the −1 site, and infrequent editing occurs at several additional sites (table S1). In contrast, no editing was detected in human pri-miR-654 and mouse pri-miR-300. Although these two pri-miRNAs are located within the miR-376 cluster, t...

MicroRNAs (miRNAs) are~22-nt RNA segments that are involved in the regulation of protein expression primarily by binding to one or more target sites on an mRNA transcript and inhibiting translation. MicroRNAs are likely to factor into multiple developmental pathways, multiple mechanisms of gene regulation, and underlie an array of inherited disease processes and phenotypic determinants. Several computational programs exist to predict miRNA targets in mammals, fruit flies, worms, and plants. However, to date, there is no systematic collection and description of miRNA targets with experimental support. We describe a database, TarBase, which houses a manually curated collection of experimentally tested miRNA targets, in human/ mouse, fruit fly, worm, and zebrafish, distinguishing between those that tested positive and those that tested negative. Each positive target site is described by the miRNA that binds it, the gene in which it occurs, the nature of the experiments that were conducted to test it, the sufficiency of the site to induce translational repression and/or cleavage, and the paper from which all these data were extracted. Additionally, the database is functionally linked to several other useful databases such as Gene Ontology (GO) and UCSC Genome Browser. TarBase reveals significantly more experimentally supported targets than even recent reviews claim, thereby providing a comprehensive data set from which to assess features of miRNA targeting that will be useful for the next generation of target prediction programs. TarBase can be accessed at http://www.diana.pcbi.upenn.edu/ tarbase.

MicroRNAs (miRNAs) are an abundant class of small noncodingRNAs that function as negative gene regulators. miRNA deregulation is involved in the initiation and progression of human cancer; however, the underlying mechanism and its contributions to genome-wide transcriptional changes in cancer are still largely unknown. We studied miRNA deregulation in human epithelial ovarian cancer by integrative genomic approach, including miRNA microarray (n ‫؍‬ 106), array-based comparative genomic hybridization (n ‫؍‬ 109), cDNA microarray (n ‫؍‬ 76), and tissue array (n ‫؍‬ 504). miRNA expression is markedly down-regulated in malignant transformation and tumor progression. Genomic copy number loss and epigenetic silencing, respectively, may account for the downregulation of Ϸ15% and at least Ϸ36% of miRNAs in advanced ovarian tumors and miRNA down-regulation contributes to a genome-wide transcriptional deregulation. Last, eight miRNAs located in the chromosome 14 miRNA cluster (Dlk1-Gtl2 domain) were identified as potential tumor suppressor genes. Therefore, our results suggest that miRNAs may offer new biomarkers and therapeutic targets in epithelial ovarian cancer.Dlk1-Gtl2 domain ͉ noncoding RNA