MicroRNAs (miRNAs) are a class of noncoding RNAs that post-transcriptionally regulate gene expression in plants and animals. To investigate the influence of miRNAs on transcript levels, we transfected miRNAs into human cells and used microarrays to examine changes in the messenger RNA profile. Here we show that delivering miR-124 causes the expression profile to shift towards that of brain, the organ in which miR-124 is preferentially expressed, whereas delivering miR-1 shifts the profile towards that of muscle, where miR-1 is preferentially expressed. In each case, about 100 messages were downregulated after 12 h. The 3' untranslated regions of these messages had a significant propensity to pair to the 5' region of the miRNA, as expected if many of these messages are the direct targets of the miRNAs. Our results suggest that metazoan miRNAs can reduce the levels of many of their target transcripts, not just the amount of protein deriving from these transcripts. Moreover, miR-1 and miR-124, and presumably other tissue-specific miRNAs, seem to downregulate a far greater number of targets than previously appreciated, thereby helping to define tissue-specific gene expression in humans.

Two small temporal RNAs (stRNAs), lin-4 and let-7, control developmental timing in Caenorhabditis elegans. We find that these two regulatory RNAs are members of a large class of 21- to 24-nucleotide noncoding RNAs, called microRNAs (miRNAs). We report on 55 previously unknown miRNAs in C. elegans. The miRNAs have diverse expression patterns during development: a let-7 paralog is temporally coexpressed with let-7; miRNAs encoded in a single genomic cluster are coexpressed during embryogenesis; and still other miRNAs are expressed constitutively throughout development. Potential orthologs of several of these miRNA genes were identified in Drosophila and human genomes. The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals.

MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to identify miRNA genes conserved in more than one genome. Applying this program, known as MiRscan, together with molecular identification and validation methods, we have identified most of the miRNA genes in the nematode Caenorhabditis elegans. The total number of validated miRNA genes stands at 88, with no more than 35 genes remaining to be detected or validated. These 88 miRNA genes represent 48 gene families; 46 of these families (comprising 86 of the 88 genes) are conserved in Caenorhabditis briggsae, and 22 families are conserved in humans. More than a third of the worm miRNAs, including newly identified members of the lin-4 and let-7 gene families, are differentially expressed during larval development, suggesting a role for these miRNAs in mediating larval developmental transitions. Most are present at very high steady-state levels-more than 1000 molecules per cell, with some exceeding 50,000 molecules per cell. Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species.[Keywords: miRNA; noncoding RNA; computational gene identification; Dicer] Supplemental material is available at http://www.genesdev.org. Noncoding RNAs (ncRNAs) of ∼22 nucleotides (nt) in length are increasingly recognized as playing important roles in regulating gene expression in animals, plants, and fungi. The first such tiny regulatory RNA to be identified was the lin-4 RNA, which controls the timing of Caenorhabditis elegans larval development (Lee et al. 1993;Wightman et al. 1993). This 21-nt RNA pairs to sites within the 3Ј untranslated region (UTR) of target mRNAs, specifying the translational repression of these mRNAs and triggering the transition to the next developmental stage (Lee et al. 1993;Wightman et al. 1993;Ha et al. 1996;Moss et al. 1997;Olsen and Ambros 1999). A second tiny riboregulator, let-7 RNA, is expressed later in development and appears to act in a similar manner to trigger the transition to late-larval and adult stages Slack et al. 2000). The lin-4 and let-7 RNAs are sometimes called small temporal RNAs (stRNAs) because of their important roles in regulating the timing of larval development . The lin-4 and let-7 stRNAs are now recognized as the founding members of a large class of ∼22-nt ncRNAs termed microRNAs (miRNAs), which resemble stRNAs but do not necessarily control developmental timing (Lagos-Quintana et al. 2001;Lau et al. 2001;Lee and Ambros 2001).Understanding the biogenesis and function of miRNAs has been greatly facilitated by analogy and contrast to another class of tiny ncRNAs known as small interfering RNAs (siRNAs), first identified because of their roles in mediating RNA interference (RNAi) in animals and posttranscriptional ge...