The microRNAs of Caenorhabditis elegans
Lee P. Lim,Nelson C. Lau,Earl G. Weinstein,Aliaa Abdelhakim,Soraya Yekta,Matthew W. Rhoades,Christopher B. Burge,David P. Bartel +7 more
TLDR
The 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.Abstract:
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.read more
Citations
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MicroRNA miR-199a-3p regulates cell proliferation and survival by targeting caveolin-2.
Tatiana Shatseva,Tatiana Shatseva,Daniel Y. Lee,Daniel Y. Lee,Zhaoqun Deng,Zhaoqun Deng,Burton B. Yang,Burton B. Yang +7 more
TL;DR: The findings suggest that MiR-199a-3p targeting of caveolin-2 might have an important role in breast cancer tumor progression, making it a potential candidate for intervention in cancer.
Journal ArticleDOI
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans
TL;DR: A computational learning method SVM (support vector machine) was implemented to build a high throughput and good performance computational pre-miRNA prediction tool called MiRFinder, designed for genome-wise, pair-wise sequences from two related species.
Journal ArticleDOI
microRNA-guided posttranscriptional gene regulation
Po Yu Chen,Gunter Meister +1 more
TL;DR: Identification of miRNAs along with a comprehensive description of the miRNA/target-mRNA interaction network will add a new level to knowledge of gene regulation and provide new insights into the biology of so far poorly understood diseases, including various forms of cancer.
Journal ArticleDOI
Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans.
TL;DR: This study suggests that sncRNAs including miRNAs contribute to lifespan regulation in C. elegans, and indicates new connections between aging, stress responses, and the small RNA world.
Journal ArticleDOI
The evolution and functional diversification of animal microRNA genes.
TL;DR: Some of the many strategies that allow novel miRNA functions to emerge are described, with particular emphasis on how miRNA genes evolve in animals.
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
TL;DR: Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin- 4 regulates lin- 14 translation via an antisense RNA-RNA interaction.
Journal ArticleDOI
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Todd M. Lowe,Sean R. Eddy +1 more
TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
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Role for a bidentate ribonuclease in the initiation step of RNA interference
TL;DR: Dicer is a member of the RNase III family of nucleases that specifically cleave double-stranded RNAs, and is evolutionarily conserved in worms, flies, plants, fungi and mammals, and has a distinctive structure, which includes a helicase domain and dualRNase III motifs.