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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HIV-1 TAR element is processed by Dicer to yield a viral micro-RNA involved in chromatin remodeling of the viral LTR
Zachary Klase,Prachee Kale,Rafael Winograd,Madhur V Gupta,Mohammad Heydarian,Reem Berro,Timothy A. McCaffrey,Fatah Kashanchi,Fatah Kashanchi +8 more
TL;DR: The possibility that the HIV-1 TAR element, a hairpin structure of ~50 nucleotides found at the 5' end of the HIV viral mRNA, is recognized by the RNAi machinery and processed to yield a viral miRNA is investigated.
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Exosomes/miRNAs as mediating cell-based therapy of stroke.
Hongqi Xin,Yi Li,Michael Chopp +2 more
TL;DR: The present review focuses on the paracrine mechanism of MSC exosomes, and the regulation and transfer of exosome content, especially the packaging andTransfer of miRNAs which enhance tissue repair and functional recovery.
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Attomolar ultrasensitive microRNA detection by DNA-scaffolded silver-nanocluster probe based on isothermal amplification.
TL;DR: A novel method to quantify miRNA expression levels as low as attomolar sensitivity by target-assisted isothermal exponential amplification coupled with fluorescent DNA-scaffolded AgNCs and shows the high selectivity for discriminating differences between miRNA family members, providing a promising alternative to standard approaches for quantitative detection of miRNA.
Journal ArticleDOI
The interplay between transcription factors and microRNAs in genome-scale regulatory networks.
TL;DR: How trans‐regulators interact with each other in the context of gene regulatory networks to coordinate gene expression at the genome‐scale level is described, and future challenges of integrating these networks with other types of functional networks are discussed.
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miRNP:mRNA association in polyribosomes in a human neuronal cell line
TL;DR: In a human neuronal cell line, the miRNP proteins eIF2C2 (a member of the Argonaute family of proteins), Gemin3, and Gemin4 along with miRNAs cosediment with polyribosomes suggest that miR NP proteins may play important roles in target mRNA recognition and translational repression.
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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.
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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.