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
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DMP1 is a target of let-7 in dental pulp cells.
TL;DR: It is discovered that dentin matrix protein 1 (DMP1), which is a non-collagenous protein essential in the mineralization of dentin and bone, has a let-7 binding site in its 3'-untranslated region, and results suggest that DMP1 is regulated post-transcriptionally byLet-7 during odontoblast differentiation.
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Stage-Specific Timing of the microRNA Regulation of lin-28 by the Heterochronic Gene lin-14 in Caenorhabditis elegans.
TL;DR: It is demonstrated that three let-7 family miRNAs—miR-48, miR-84, andMiR-241—inhibit lin-28 expression, making them the first known targets of lin-14 that act in the heterochronic pathway.
Journal ArticleDOI
A high-throughput 3' UTR reporter screening identifies microRNA interactomes of cancer genes.
Gert Van Peer,Evelien Mets,Shana Claeys,Ines De Punt,Steve Lefever,Maté Ongenaert,Pieter Rondou,Franki Speleman,Pieter Mestdagh,Jo Vandesompele +9 more
TL;DR: The cancer gene-miRNA interactome data set represents a unique resource that will aid in the unraveling of regulatory miRNA networks and the dynamic regulation of key protein-coding cancer genes.
Journal ArticleDOI
Acquired Glucocorticoid Resistance Due to Homologous Glucocorticoid Receptor Downregulation: A Modern Look at an Age-Old Problem.
TL;DR: In this paper, the major role players in the homologous downregulation of the glucocorticoid receptor alpha (GRα) pool are discussed, with a specific focus on previously reported GC-mediated reductions in GRα mRNA and protein levels, the molecular mechanisms through which the GRα functional pool is maintained and the possible impact of receptor conformation on GC-induced downregulation.
Journal ArticleDOI
Computational approaches to discovering noncoding RNA
TL;DR: It is expected that imminent breakthroughs will include the classification of newer types of ncRNA and new insights into miRNA and piRNA biology, eventually leading toward the completion of a catalog of all human ncRNAs.
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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
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
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.