We predict regulatory targets for 14 Arabidopsis microRNAs (miRNAs) by identifying mRNAs with near complementarity. Complementary sites within predicted targets are conserved in rice. Of the 49 predicted targets, 34 are members of transcription factor gene families involved in developmental patterning or cell differentiation. The near-perfect complementarity between plant miRNAs and their targets suggests that many plant miRNAs act similarly to small interfering RNAs and direct mRNA cleavage. The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages.

MicroRNAs (miRNAs) are an extensive class of ∼22-nucleotide noncoding RNAs thought to regulate gene expression in metazoans. We find that miRNAs are also present in plants, indicating that this class of noncoding RNA arose early in eukaryotic evolution. In this paper 16 Arabidopsis miRNAs are described, many of which have differential expression patterns in development. Eight are absolutely conserved in the rice genome. The plant miRNA loci potentially encode stem-loop precursors similar to those processed by Dicer (a ribonuclease III) in animals. Mutation of an Arabidopsis Dicer homolog, CARPEL FACTORY, prevents the accumulation of miRNAs, showing that similar mechanisms direct miRNA processing in plants and animals. The previously described roles of CARPEL FACTORY in the development of Arabidopsis embryos, leaves, and floral meristems suggest that the miRNAs could play regulatory roles in the development of plants as well as 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...