Genes and Mechanisms Related to RNA Interference Regulate Expression of the Small Temporal RNAs that Control C. elegans Developmental Timing

Grishok, Alla; Pasquinelli, Amy E.; Conte, Darryl; Li, Na; Parrish, Susan; Ha, Ilho; Baillie, David L.; Fire, Andrew; Ruvkun, Gary; Mello, Craig C.

doi:10.1016/s0092-8674(01)00431-7

Cited by 1,716 publications

(1,434 citation statements)

References 41 publications

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“…In present day eukaryotes both Argonaute-like proteins and Piwi-like proteins have been implicated in a variety of RNAi-related phenomena and several subfamily members appear to have distinct functions (Grishok et al 2001;Lee et al 2003;Okamura et al 2004). For instance, a Piwi-like protein, Twi1, is required for the conjugation-induced accumulation of small RNAs involved in programmed DNA elimination in T. thermophila (Lee and Collins 2006;Liu et al 2004b).…”

Section: Nature Of the Ancestral Rnai Machinerymentioning

confidence: 99%

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On the origin and functions of RNA-mediated silencing: from protists to man

2006

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Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways. We have examined the taxonomic distribution and the phylogenetic relationship of key components of the RNA interference (RNAi) machinery in members of five eukaryotic supergroups. On the basis of the parsimony principle, our analyses suggest that a relatively complex RNAi machinery was already present in the last common ancestor of eukaryotes and consisted, at a minimum, of one Argonautelike polypeptide, one Piwi-like protein, one Dicer, and one RNAdependent RNA polymerase. As proposed before, the ancestral (but non-essential) role of these components may have been in defense responses against genomic parasites such as transposable elements and viruses. From a mechanistic perspective, the RNAi machinery in the eukaryotic ancestor may have been capable of both small-RNA-guided transcript degradation as well as transcriptional repression, most likely through histone modifications. Both roles appear to be widespread among living eukaryotes and this diversification of function could account for the evolutionary conservation of duplicated Argonaute-Piwi proteins. In contrast, additional RNAi-mediated pathways such as RNA-directed DNA methylation, programmed genome rearrangements, meiotic silencing by unpaired DNA, and miRNA-mediated gene regulation may have evolved independently in specific lineages.

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Section: Nature Of the Ancestral Rnai Machinerymentioning

confidence: 99%

“…However, several other Ago paralogs are not endonucleolytically active (Liu et al 2004a;Rivas et al 2005). In fact, in several species, there is evidence for functional specialization of Ago-Piwi proteins (Grishok et al 2001;Lee et al 2003;Matzke and Birchler 2005;Okamura et al 2004).…”

Section: Introductionmentioning

confidence: 99%

On the origin and functions of RNA-mediated silencing: from protists to man

2006

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“…The Droshagenerated pre-miRNA is a 70-to 80-nt RNA with a typical stem-loop structure. It is transported to the cytoplasm by Exportin-5 (Yi et al, 2003;Lund et al, 2004) where it is processed by another RNaseIII type protein, Dicer, to generate the mature (20-to 22-nt) miRNA (Grishok et al, 2001;Hutvagner et al, 2001;Ketting et al, 2001;Knight and Bass, 2001). miRNAs have partially complementary sequences to certain mRNAs and guide a protein complex, RISC (RNA induced silencing complex), to the target mRNAs (Khvorova et al, 2003;Schwarz et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

FGF‐4 signaling is involved in mir‐206 expression in developing somites of chicken embryos

Sweetman

Rathjen

Jefferson

et al. 2006

Developmental Dynamics

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The microRNAs (miRNAs) are recently discovered short, noncoding RNAs, that regulate gene expression in metazoans. We have cloned short RNAs from chicken embryos and identified five new chicken miRNA genes. Genome analysis identified 17 new chicken miRNA genes based on sequence homology to previously characterized mouse miRNAs. Developmental Northern blots of chick embryos showed increased accumulation of most miRNAs analyzed from 1.5 days to 5 days except, the stem cell-specific mir-302, which was expressed at high levels at early stages and then declined. In situ analysis of mature miRNAs revealed the restricted expression of mir-124 in the central nervous system and of mir-206 in developing somites, in particular the developing myotome. In addition, we investigated how miR-206 expression is controlled during somite development using bead implants. These experiments demonstrate that fibroblast growth factor (FGF) -mediated signaling negatively regulates the initiation of mir-206 gene expression. This may be mediated through the effects of FGF on somite differentiation. These data provide the first demonstration that developmental signaling pathways affect miRNA expression. Thus far, miRNAs have not been studied extensively in chicken embryos, and our results show that this system can complement other model organisms to investigate the regulation of many other miRNAs. Developmental Dynamics 235:2185-2191, 2006.

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“…In plants, the sizes of miRNA precursors range from 60 to a few hundred nt [5,8]. Mature miRNAs are processed from their precursors by Dicer-like enzymes [9,10]. These short, single-stranded RNAs are incorporated into the RNA-induced silencing complex (RISC, [11]) and used as a guide to direct posttranscriptional regulation either by cleaving the target mRNA when identical to the pairing site or by repressing protein translation when the miRNA has mismatches with the target sequences [4].…”

Section: Introductionmentioning

confidence: 99%

Molecular evolution of the rice miR395 gene family

et al. 2005

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MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.

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Genes and Mechanisms Related to RNA Interference Regulate Expression of the Small Temporal RNAs that Control C. elegans Developmental Timing

Cited by 1,716 publications

References 41 publications

On the origin and functions of RNA-mediated silencing: from protists to man

On the origin and functions of RNA-mediated silencing: from protists to man

FGF‐4 signaling is involved in mir‐206 expression in developing somites of chicken embryos

Molecular evolution of the rice miR395 gene family

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