1751
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Preall JB, He Z, Gorra JM, Sontheimer EJ. Short interfering RNA strand selection is independent of dsRNA processing polarity during RNAi in Drosophila. Curr Biol 2006; 16:530-5. [PMID: 16527750 DOI: 10.1016/j.cub.2006.01.061] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 01/17/2006] [Accepted: 01/20/2006] [Indexed: 11/21/2022]
Abstract
Short interfering RNAs (siRNAs) guide mRNA cleavage during RNA interference (RNAi). Only one siRNA strand assembles into the RNA-induced silencing complex (RISC), with preference given to the strand whose 5' terminus has lower base-pairing stability. In Drosophila, Dcr-2/R2D2 processes siRNAs from longer double-stranded RNAs (dsRNAs) and also nucleates RISC assembly, suggesting that nascent siRNAs could remain bound to Dcr-2/R2D2. In vitro, Dcr-2/R2D2 senses base-pairing asymmetry of synthetic siRNAs and dictates strand selection by asymmetric binding to the duplex ends. During dsRNA processing, Dicer (Dcr) liberates siRNAs from dsRNA ends in a manner dictated by asymmetric enzyme-substrate interactions. Because Dcr-2/R2D2 is unlikely to sense base-pairing asymmetry of an siRNA that is embedded within a precursor, it is not clear whether processed siRNAs strictly follow the thermodynamic asymmetry rules or whether processing polarity can affect strand selection. We use a Drosophila in vitro system in which defined siRNAs with known asymmetry can be generated from longer dsRNA precursors. These dsRNAs permit processing specifically from either the 5' or the 3' end of the thermodynamically favored strand of the incipient siRNA. Combined dsRNA-processing/mRNA-cleavage assays indicate that siRNA strand selection is independent of dsRNA processing polarity during Drosophila RISC assembly in vitro.
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Affiliation(s)
- Jonathan B Preall
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208, USA
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1752
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Abstract
Inhibition of gene expression through RNA interference (RNAi) is emerging as a powerful experimental tool for gene function and target validation studies. The potential uses of this technology seem unlimited, extending to the prevention and therapy of human diseases. However, recent work demonstrating that there are unanticipated, different nonspecific effects associated with the use of small interfering RNAs in mammals has raised concerns about the safe use of RNAi in vivo. These nonspecific effects include activation of the immune system, potentially harming the individual. The application of screening assays for nonspecific activation of both innate and acquired immunity will be necessary for further development of RNAi as a therapeutic tool.
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Affiliation(s)
- Joao T Marques
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
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1753
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Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. RNA editing of human microRNAs. Genome Biol 2006; 7:R27. [PMID: 16594986 PMCID: PMC1557993 DOI: 10.1186/gb-2006-7-4-r27] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Revised: 01/30/2005] [Accepted: 03/06/2006] [Indexed: 12/31/2022] Open
Abstract
A survey of RNA editing of miRNAs from ten human tissues indicates that RNA editing increases the diversity of miRNAs and their targets. Background MicroRNAs (miRNAs) are short RNAs of around 22 nucleotides that regulate gene expression. The primary transcripts of miRNAs contain double-stranded RNA and are therefore potential substrates for adenosine to inosine (A-to-I) RNA editing. Results We have conducted a survey of RNA editing of miRNAs from ten human tissues by sequence comparison of PCR products derived from matched genomic DNA and total cDNA from the same individual. Six out of 99 (6%) miRNA transcripts from which data were obtained were subject to A-to-I editing in at least one tissue. Four out of seven edited adenosines were in the mature miRNA and were predicted to change the target sites in 3' untranslated regions. For a further six miRNAs, we identified A-to-I editing of transcripts derived from the opposite strand of the genome to the annotated miRNA. These miRNAs may have been annotated to the wrong genomic strand. Conclusion Our results indicate that RNA editing increases the diversity of miRNAs and their targets, and hence may modulate miRNA function.
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Affiliation(s)
- Matthew J Blow
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Russell J Grocock
- Computational and Functional Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stijn van Dongen
- Computational and Functional Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anton J Enright
- Computational and Functional Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ed Dicks
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - P Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Richard Wooster
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
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1754
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Abstract
The Human Immunodeficiency Virus type 1 (HIV-1), a member of the lentivirus subfamily, infects both dividing and nondividing cells and, following reverse transcription of the viral RNA genome, integrates into the host chromatin where it enters into a latent state. Many of the factors governing viral latency remain unresolved and current antiviral treatment regimens are largely ineffective at eliminating cellular reservoirs of latent virus. The recent identification of microRNA (miRNA) encoding sequences embedded in the HIV-1 genome, and the discovery of functional virus-derived miRNAs, suggests a role for RNA Interference (RNAi) in the regulation of HIV-1 gene expression. Recently, the mammalian RNAi machinery was shown to regulate gene expression epigenetically by transcriptional modulation, providing a direct link between RNAi and a mechanism for inducing latency. Interestingly, both HIV-1 Tat, and the host TAR RNA-binding protein (TRBP), bind to the transactivating response (TAR) RNA of HIV-1 and affect the function of RNAi in human cells. Specifically, TRBP, a cofactor in Tat-TAR interactions, is a vital component of Dicer-mediated dsRNA processing. These novel observations support a central role for HIV-1 and associated host factors in regulating cellular RNAi and viral gene expression through RNA directed processes. Thus, HIV-1 may have evolved mechanisms to exploit the RNAi pathway at both the transcriptional and posttranscriptional level to affect and/or maintain a latent infection.
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Affiliation(s)
- Marc S Weinberg
- Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, South Africa
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1755
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Behlke MA. Progress towards in vivo use of siRNAs. Mol Ther 2006; 13:644-70. [PMID: 16481219 PMCID: PMC7106286 DOI: 10.1016/j.ymthe.2006.01.001] [Citation(s) in RCA: 325] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 01/11/2006] [Accepted: 01/11/2006] [Indexed: 01/28/2023] Open
Abstract
RNA interference (RNAi) has become the method of choice to suppress gene expression in vitro. It is also emerging as a powerful tool for in vivo research with over 90 studies published using synthetic small interfering RNAs in mammals. These reports demonstrate the potential for use of synthetic small interfering RNAs (siRNAs) as therapeutic agents, especially in the areas of cancer and viral infection. The number of reports using siRNAs for functional genomics applications, for validation of targets for small-molecule drug development programs, and to address questions of basic biology will rapidly grow as methods and protocols for use in animals become more established. This review will first discuss aspects of RNAi biochemistry and biology that impact in vivo use, especially as relates to experimental design, and will then provide an overview of published work with a focus on methodology.
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Affiliation(s)
- Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA.
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1756
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Das RM, Van Hateren NJ, Howell GR, Farrell ER, Bangs FK, Porteous VC, Manning EM, McGrew MJ, Ohyama K, Sacco MA, Halley PA, Sang HM, Storey KG, Placzek M, Tickle C, Nair VK, Wilson SA. A robust system for RNA interference in the chicken using a modified microRNA operon. Dev Biol 2006; 294:554-63. [PMID: 16574096 DOI: 10.1016/j.ydbio.2006.02.020] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 02/13/2006] [Accepted: 02/15/2006] [Indexed: 11/24/2022]
Abstract
RNA interference (RNAi) provides an effective method to silence gene expression and investigate gene function. However, RNAi tools for the chicken embryo have largely been adapted from vectors designed for mammalian cells. Here we present plasmid and retroviral RNAi vectors specifically designed for optimal gene silencing in chicken cells. The vectors use a chicken U6 promoter to express RNAs modelled on microRNA30, which are embedded within chicken microRNA operon sequences to ensure optimal Drosha and Dicer processing of transcripts. The chicken U6 promoter works significantly better than promoters of mammalian origin and in combination with a microRNA operon expression cassette (MOEC), achieves up to 90% silencing of target genes. By using a MOEC, we show that it is also possible to simultaneously silence two genes with a single vector. The vectors express either RFP or GFP markers, allowing simple in vivo tracking of vector delivery. Using these plasmids, we demonstrate effective silencing of Pax3, Pax6, Nkx2.1, Nkx2.2, Notch1 and Shh in discrete regions of the chicken embryonic nervous system. The efficiency and ease of use of this RNAi system paves the way for large-scale genetic screens in the chicken embryo.
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Affiliation(s)
- Raman M Das
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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1757
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Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 2006; 20:515-24. [PMID: 16510870 DOI: 10.1101/gad.1399806] [Citation(s) in RCA: 1570] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The control of translation and mRNA degradation is an important part of the regulation of gene expression. It is now clear that small RNA molecules are common and effective modulators of gene expression in many eukaryotic cells. These small RNAs that control gene expression can be either endogenous or exogenous micro RNAs (miRNAs) and short interfering RNAs (siRNAs) and can affect mRNA degradation and translation, as well as chromatin structure, thereby having impacts on transcription rates. In this review, we discuss possible mechanisms by which miRNAs control translation and mRNA degradation. An emerging theme is that miRNAs, and siRNAs to some extent, target mRNAs to the general eukaryotic machinery for mRNA degradation and translation control.
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Affiliation(s)
- Marco Antonio Valencia-Sanchez
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona 85721, USA
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1758
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Nair V, Zavolan M. Virus-encoded microRNAs: novel regulators of gene expression. Trends Microbiol 2006; 14:169-75. [PMID: 16531046 DOI: 10.1016/j.tim.2006.02.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Revised: 02/02/2006] [Accepted: 02/22/2006] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs that have recently been recognized as major regulators of gene expression. They influence diverse cellular processes ranging from cellular differentiation, proliferation, apoptosis and metabolism to cancer. Bioinformatic approaches and direct cloning methods have identified >3500 miRNAs, including orthologues from various species. Experiments to identify the targets and potential functions of miRNAs in various species are continuing but the recent discovery of virus-encoded miRNAs indicates that viruses also use this fundamental mode of gene regulation. Virus-encoded miRNAs seem to evolve rapidly and regulate both the viral life cycle and the interaction between viruses and their hosts.
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Affiliation(s)
- Venugopal Nair
- Viral Oncogenesis Group, Division of Microbiology, Institute for Animal Health, Compton, Berkshire, UK, RG20 7NN.
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1759
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Abstract
Much remains to be learnt about the in vivo function of specific microRNAs. Recently, the conserved microRNA miR-1 has been found to be essential for Drosophila development. miR-1 mutants die during the rapid larval growth phase with severe muscle defects.
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Affiliation(s)
- Michael V Taylor
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, UK
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1760
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Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006; 34:D140-4. [PMID: 16381832 PMCID: PMC1347474 DOI: 10.1093/nar/gkj112] [Citation(s) in RCA: 3449] [Impact Index Per Article: 191.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry and fulfils three main roles: the miRBase Registry acts as an independent arbiter of microRNA gene nomenclature, assigning names prior to publication of novel miRNA sequences. miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at .
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Affiliation(s)
- Sam Griffiths-Jones
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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1761
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Varki A, Altheide TK. Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome Res 2006; 15:1746-58. [PMID: 16339373 DOI: 10.1101/gr.3737405] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The chimpanzee genome sequence is a long-awaited milestone, providing opportunities to explore primate evolution and genetic contributions to human physiology and disease. Humans and chimpanzees shared a common ancestor approximately 5-7 million years ago (Mya). The difference between the two genomes is actually not approximately 1%, but approximately 4%--comprising approximately 35 million single nucleotide differences and approximately 90 Mb of insertions and deletions. The challenge is to identify the many evolutionarily, physiologically, and biomedically important differences scattered throughout these genomes while integrating these data with emerging knowledge about the corresponding "phenomes" and the relevant environmental influences. It is logical to tackle the genetic aspects via both genome-wide analyses and candidate gene studies. Genome-wide surveys could eliminate the majority of genomic sequence differences from consideration, while simultaneously identifying potential targets of opportunity. Meanwhile, candidate gene approaches can be based on such genomic surveys, on genes that may contribute to known differences in phenotypes or disease incidence/severity, or on mutations in the human population that impact unique aspects of the human condition. These two approaches will intersect at many levels and should be considered complementary. We also cite some known genetic differences between humans and great apes, realizing that these likely represent only the tip of the iceberg.
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Affiliation(s)
- Ajit Varki
- Glycobiology Research and Training Center, Departments of Medicine and Cellular & Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.
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1762
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Neely LA, Patel S, Garver J, Gallo M, Hackett M, McLaughlin S, Nadel M, Harris J, Gullans S, Rooke J. A single-molecule method for the quantitation of microRNA gene expression. Nat Methods 2006; 3:41-6. [PMID: 16369552 DOI: 10.1038/nmeth825] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Accepted: 11/02/2005] [Indexed: 01/06/2023]
Abstract
MicroRNAs (miRNA) are short endogenous noncoding RNA molecules that regulate fundamental cellular processes such as cell differentiation, cell proliferation and apoptosis through modulation of gene expression. Critical to understanding the role of miRNAs in this regulation is a method to rapidly and accurately quantitate miRNA gene expression. Existing methods lack sensitivity, specificity and typically require upfront enrichment, ligation and/or amplification steps. The Direct miRNA assay hybridizes two spectrally distinguishable fluorescent locked nucleic acid (LNA)-DNA oligonucleotide probes to the miRNA of interest, and then tagged molecules are directly counted on a single-molecule detection instrument. In this study, we show the assay is sensitive to femtomolar concentrations of miRNA (500 fM), has a three-log linear dynamic range and is capable of distinguishing among miRNA family members. Using this technology, we quantified expression of 45 human miRNAs within 16 different tissues, yielding a quantitative differential expression profile that correlates and expands upon published results.
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Affiliation(s)
- Lori A Neely
- US Genomics, 12 Gill Street, Suite 4700, Woburn, Massachusetts 01801, USA.
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1763
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Conaco C, Otto S, Han JJ, Mandel G. Reciprocal actions of REST and a microRNA promote neuronal identity. Proc Natl Acad Sci U S A 2006; 103:2422-7. [PMID: 16461918 PMCID: PMC1413753 DOI: 10.1073/pnas.0511041103] [Citation(s) in RCA: 557] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) are implicated in both tissue differentiation and maintenance of tissue identity. In most cases, however, the mechanisms underlying their regulation are not known. One brain-specific miRNA, miR-124a, decreases the levels of hundreds of nonneuronal transcripts, such that its introduction into HeLa cells promotes a neuronal-like mRNA profile. The transcriptional repressor, RE1 silencing transcription factor (REST), has a reciprocal activity, inhibiting the expression of neuronal genes in nonneuronal cells. Here, we show that REST regulates the expression of a family of miRNAs, including brain-specific miR-124a. In nonneuronal cells and neural progenitors, REST inhibits miR-124a expression, allowing the persistence of nonneuronal transcripts. As progenitors differentiate into mature neurons, REST leaves miR-124a gene loci, and nonneuronal transcripts are degraded selectively. Thus, the combined transcriptional and posttranscriptional consequences of REST action maximize the contrast between neuronal and nonneuronal cell phenotypes.
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Affiliation(s)
- Cecilia Conaco
- Department of Neurobiology and Behavior, Howard Hughes Medical Institute, State University of New York, Stony Brook, NY 11794
| | - Stefanie Otto
- Department of Neurobiology and Behavior, Howard Hughes Medical Institute, State University of New York, Stony Brook, NY 11794
| | - Jong-Jin Han
- Department of Neurobiology and Behavior, Howard Hughes Medical Institute, State University of New York, Stony Brook, NY 11794
| | - Gail Mandel
- Department of Neurobiology and Behavior, Howard Hughes Medical Institute, State University of New York, Stony Brook, NY 11794
- To whom correspondence should be addressed. E-mail:
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1764
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Yi R, O'Carroll D, Pasolli HA, Zhang Z, Dietrich FS, Tarakhovsky A, Fuchs E. Morphogenesis in skin is governed by discrete sets of differentially expressed microRNAs. Nat Genet 2006; 38:356-62. [PMID: 16462742 DOI: 10.1038/ng1744] [Citation(s) in RCA: 418] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 01/10/2006] [Indexed: 01/07/2023]
Abstract
During embryogenesis, multipotent progenitors within the single-layered surface epithelium differentiate to form the epidermis and its appendages. Here, we show that microRNAs (miRNAs) have an essential role in orchestrating these events. We cloned more than 100 miRNAs from skin and show that epidermis and hair follicles differentially express discrete miRNA families. To explore the functional significance of this finding, we conditionally targeted Dicer1 gene ablation in embryonic skin progenitors. Within the first week after loss of miRNA expression, cell fate specification and differentiation were not markedly impaired, and in the interfollicular epidermis, apoptosis was not markedly increased. Notably, however, developing hair germs evaginate rather than invaginate, thereby perturbing the epidermal organization. Here we characterize miRNAs in skin, the existence of which was hitherto unappreciated, and demonstrate their differential expression and importance in the morphogenesis of epithelial tissues within this vital organ.
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Affiliation(s)
- Rui Yi
- Howard Hughes Medical Institute, Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, New York 10021, USA
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1765
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1766
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Haase AD, Jaskiewicz L, Zhang H, Lainé S, Sack R, Gatignol A, Filipowicz W. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep 2006; 6:961-7. [PMID: 16142218 PMCID: PMC1369185 DOI: 10.1038/sj.embor.7400509] [Citation(s) in RCA: 487] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 07/13/2005] [Accepted: 07/15/2005] [Indexed: 12/11/2022] Open
Abstract
Dicer is a key enzyme involved in RNA interference (RNAi) and microRNA (miRNA) pathways. It is required for biogenesis of miRNAs and small interfering RNAs (siRNAs), and also has a role in the effector steps of RNA silencing. Apart from Argonautes, no proteins are known to associate with Dicer in mammalian cells. In this work, we describe the identification of TRBP (human immunodeficiency virus (HIV-1) transactivating response (TAR) RNA-binding protein) as a protein partner of human Dicer. We show that TRBP is required for optimal RNA silencing mediated by siRNAs and endogenous miRNAs, and that it facilitates cleavage of pre-miRNA in vitro. TRBP had previously been assigned several functions, including inhibition of the interferon-induced double-stranded RNA-regulated protein kinase PKR and modulation of HIV-1 gene expression by association with TAR. The TRBP-Dicer interaction shown raises interesting questions about the potential interplay between RNAi and interferon-PKR pathways.
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Affiliation(s)
- Astrid D Haase
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4508 Basel, Switzerland
| | - Lukasz Jaskiewicz
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4508 Basel, Switzerland
| | - Haidi Zhang
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4508 Basel, Switzerland
| | - Sébastien Lainé
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, McGill University, 3755 Côte Ste Catherine, Montréal, Québec H3T 1E2, Canada
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4508 Basel, Switzerland
| | - Anne Gatignol
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, McGill University, 3755 Côte Ste Catherine, Montréal, Québec H3T 1E2, Canada
| | - Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4508 Basel, Switzerland
- Tel: +41 61 6976993; Fax: +41 61 6973976; E-mail:
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1767
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Yang Z, Ebright YW, Yu B, Chen X. HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. Nucleic Acids Res 2006; 34:667-75. [PMID: 16449203 PMCID: PMC1356533 DOI: 10.1093/nar/gkj474] [Citation(s) in RCA: 283] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
microRNAs (miRNAs) and small interfering RNAs (siRNAs) in plants bear a methyl group on the ribose of the 3′ terminal nucleotide. We showed previously that the methylation of miRNAs and siRNAs requires the protein HEN1 in vivo and that purified HEN1 protein methylates miRNA/miRNA* duplexes in vitro. In this study, we show that HEN1 methylates both miRNA/miRNA* and siRNA/siRNA* duplexes in vitro with a preference for 21–24 nt RNA duplexes with 2 nt overhangs. We also demonstrate that HEN1 deposits the methyl group on to the 2′ OH of the 3′ terminal nucleotide. Among various modifications that can occur on the ribose of the terminal nucleotide, such as 2′-deoxy, 3′-deoxy, 2′-O-methyl and 3′-O-methyl, only 2′-O-methyl on a small RNA inhibits the activity of yeast poly(A) polymerase (PAP). These findings indicate that HEN1 specifically methylates miRNAs and siRNAs and implicate the importance of the 2′-O-methyl group in the biology of RNA silencing.
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Affiliation(s)
| | - Yon W. Ebright
- Waksman Institute, Rutgers UniversityPiscataway, NJ 08854, USA
| | | | - Xuemei Chen
- To whom correspondence should be addressed. Tel: +1 951 827 3988; Fax: +1 951 827 4437;
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1768
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Colvis CM, Pollock JD, Goodman RH, Impey S, Dunn J, Mandel G, Champagne FA, Mayford M, Korzus E, Kumar A, Renthal W, Theobald DEH, Nestler EJ. Epigenetic mechanisms and gene networks in the nervous system. J Neurosci 2006; 25:10379-89. [PMID: 16280577 PMCID: PMC6725821 DOI: 10.1523/jneurosci.4119-05.2005] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Christine M Colvis
- Division of Basic Neurosciences and Behavioral Research, National Institute on Drug Abuse, Bethesda, Maryland 20892, USA.
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1769
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Tkaczuk KL, Obarska A, Bujnicki JM. Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol 2006; 6:6. [PMID: 16433904 PMCID: PMC1397878 DOI: 10.1186/1471-2148-6-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 01/24/2006] [Indexed: 11/17/2022] Open
Abstract
Background Recently, HEN1 protein from Arabidopsis thaliana was discovered as an essential enzyme in plant microRNA (miRNA) biogenesis. HEN1 transfers a methyl group from S-adenosylmethionine to the 2'-OH or 3'-OH group of the last nucleotide of miRNA/miRNA* duplexes produced by the nuclease Dicer. Previously it was found that HEN1 possesses a Rossmann-fold methyltransferase (RFM) domain and a long N-terminal extension including a putative double-stranded RNA-binding motif (DSRM). However, little is known about the details of the structure and the mechanism of action of this enzyme, and about its phylogenetic origin. Results Extensive database searches were carried out to identify orthologs and close paralogs of HEN1. Based on the multiple sequence alignment a phylogenetic tree of the HEN1 family was constructed. The fold-recognition approach was used to identify related methyltransferases with experimentally solved structures and to guide the homology modeling of the HEN1 catalytic domain. Additionally, we identified a La-like predicted RNA binding domain located C-terminally to the DSRM domain and a domain with a peptide prolyl cis/trans isomerase (PPIase) fold, but without the conserved PPIase active site, located N-terminally to the catalytic domain. Conclusion The bioinformatics analysis revealed that the catalytic domain of HEN1 is not closely related to any known RNA:2'-OH methyltransferases (e.g. to the RrmJ/fibrillarin superfamily), but rather to small-molecule methyltransferases. The structural model was used as a platform to identify the putative active site and substrate-binding residues of HEN and to propose its mechanism of action.
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Affiliation(s)
- Karolina L Tkaczuk
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Agnieszka Obarska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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1770
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Lee Y, Hur I, Park SY, Kim YK, Suh MR, Kim VN. The role of PACT in the RNA silencing pathway. EMBO J 2006; 25:522-32. [PMID: 16424907 PMCID: PMC1383527 DOI: 10.1038/sj.emboj.7600942] [Citation(s) in RCA: 480] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 12/09/2005] [Indexed: 11/09/2022] Open
Abstract
Small RNA-mediated gene silencing (RNA silencing) has emerged as a major regulatory pathway in eukaryotes. Identification of the key factors involved in this pathway has been a subject of rigorous investigation in recent years. In humans, small RNAs are generated by Dicer and assembled into the effector complex known as RNA-induced silencing complex (RISC) by multiple factors including hAgo2, the mRNA-targeting endonuclease, and TRBP (HIV-1 TAR RNA-binding protein), a dsRNA-binding protein that interacts with both Dicer and hAgo2. Here we describe an additional dsRNA-binding protein known as PACT, which is significant in RNA silencing. PACT is associated with an approximately 500 kDa complex that contains Dicer, hAgo2, and TRBP. The interaction with Dicer involves the third dsRNA-binding domain (dsRBD) of PACT and the N-terminal region of Dicer containing the helicase motif. Like TRBP, PACT is not required for the pre-microRNA (miRNA) cleavage reaction step. However, the depletion of PACT strongly affects the accumulation of mature miRNA in vivo and moderately reduces the efficiency of small interfering RNA-induced RNA interference. Our study indicates that, unlike other RNase III type proteins, human Dicer may employ two different dsRBD-containing proteins that facilitate RISC assembly.
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Affiliation(s)
- Yoontae Lee
- Department of Biological Sciences and Research Center for Functional Cellulomics, Seoul National University, Seoul, Korea
| | - Inha Hur
- Department of Biological Sciences and Research Center for Functional Cellulomics, Seoul National University, Seoul, Korea
| | - Seong-Yeon Park
- Department of Biological Sciences and Research Center for Functional Cellulomics, Seoul National University, Seoul, Korea
| | - Young-Kook Kim
- Department of Biological Sciences and Research Center for Functional Cellulomics, Seoul National University, Seoul, Korea
| | - Mi Ra Suh
- Department of Biological Sciences and Research Center for Functional Cellulomics, Seoul National University, Seoul, Korea
| | - V Narry Kim
- Department of Biological Sciences and Research Center for Functional Cellulomics, Seoul National University, Seoul, Korea
- Institute of Biological Sciences and Research Center for Functional Cellulomics, Seoul National University, Seoul 151-742, Korea. Tel.: +82 2 880 9120; Fax: +82 2 887 0244; E-mail:
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1771
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Abstract
It has become clear in the past few years that eukaryotic organisms possess different genetic systems to counter viruses, transposons and other repeated elements such as transgenes that could otherwise accumulate in the genome. In addition to serving as a model organism for genetic, biochemical and molecular studies, Neurospora crassa has proved to be a paradigm for the study of gene-silencing mechanisms. Indeed, its genome can be protected from expansion of selfish nucleic acids by a variety of mechanisms that inactivate duplicated sequences. Studies of these mechanisms have made a fundamental contribution to the understanding of the gene-silencing field.
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Affiliation(s)
- Caterina Catalanotto
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Policlinico Umberto I, Universita' degli Studi di Roma 'La Sapienza', Roma, Italy
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1772
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Leung AKL, Sharp PA. Function and localization of microRNAs in mammalian cells. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2006; 71:29-38. [PMID: 17381277 DOI: 10.1101/sqb.2006.71.049] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
microRNAs (miRNAs) represent a large set of master regulators of gene expression. They constitute 1-4% of human genes and probably regulate 30% of protein-encoding genes. These small regulatory RNAs act at a posttranscriptional level-mediating translational repression and/or mRNA degradation-through their association with Argonaute protein and target mRNAs. In this paper, we discuss various mechanisms by which miRNAs regulate posttranscriptionally, including their subcellular localization. Recent results indicate that the majority of miRNA-targeted and thus translationally repressed mRNA is probably distributed in the diffuse cytoplasm, even though a small fraction is concentrated in subcellular compartments, such as processing bodies or stress granules; notably, the stress granule localization of Argonaute depends on the presence of miRNAs. Here we discuss the structural requirement of these subcellular compartments in light of their potential miRNA functions.
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Affiliation(s)
- A K L Leung
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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1773
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Verschure PJ, Visser AE, Rots MG. Step out of the Groove: Epigenetic Gene Control Systems and Engineered Transcription Factors. ADVANCES IN GENETICS 2006; 56:163-204. [PMID: 16735158 DOI: 10.1016/s0065-2660(06)56005-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
At the linear DNA level, gene activity is believed to be driven by binding of transcription factors, which subsequently recruit the RNA polymerase to the gene promoter region. However, it has become clear that transcriptional activation involves large complexes of many different proteins, which not only directly recruit components of the transcription machinery but also affect the DNA folding. Such proteins, including various chromatin-modifying enzymes, alter among other processes nucleosome positioning and histone modifications and are potentially involved in changing the overall structure of the chromatin and/or the position of chromatin in the nucleus. These epigenetic regulatory features are now known to control and regulate gene expression, although the molecular mechanisms still need to be clarified in more detail. Several diseases are characterized by aberrant gene-expression patterns. Many of these diseases are linked to dysregulation of epigenetic gene-regulatory systems. To interfere with aberrant gene expression, a novel approach is emerging as a disease therapy, involving engineered transcription factors. Engineered transcription factors are based on, for example, zinc-finger proteins (ZFP) that bind DNA in a sequence-specific manner. Engineered transcription factors based on ZFP are fused to effector domains that function to normalize disrupted gene-expression levels. Zinc-finger proteins most likely also influence epigenetic regulatory systems, such as the complex set of chemical histone and DNA modifications, which control chromatin compaction and nuclear organization. In this chapter, we review how epigenetic regulation systems acting at various levels of packaging the genome in the cell nucleus add to gene-expression control at the DNA level. Since an increasing number of diseases are described to have a clear link to epigenetic dysregulation, we here highlight 10 examples of such diseases. In the second part, we describe the different effector domains that have been fused to ZFPs and are capable of activating or silencing endogenous genes, and we illustrate how these effector domains influence epigenetic control mechanisms. Finally, we speculate how accumulating knowledge about epigenetics can be exploited to make such zinc-finger-transcription factors (ZF-TF) even more effective.
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Affiliation(s)
- Pernette J Verschure
- Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, 1098SM Amsterdam, The Netherlands.
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1774
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Abstract
RNA interference (RNAi) mediates gene silencing in a sequence-specific manner and has proven to be an exceptionally valuable discovery for bench scientists. In the laboratory, RNAi technologies provide efficient means for validating drug targets and for performing reverse genetics to study gene function (Friedman and Perrimon, 2004). Patients may also benefit from RNAi as applications extend to potential human therapies. RNAi-based treatments are being investigated and may provide hope for patients suffering from cancer, viral infections, or genetic diseases for which effective therapies are currently lacking. Notably, several independent studies have demonstrated that RNAi therapy can improve disease phenotypes in various mouse models of human disease. In this chapter, we focus on the potential of RNAi in treating neurologic diseases for which reduction of mutant or toxic gene expression may provide therapeutic benefit. We discuss approaches to achieving RNAi in vivo, progress in the field, and the potential pitfalls associated with RNAi-based therapies.
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Affiliation(s)
- Ryan L Boudreau
- Program in Gene Therapy, Department of Internal Medicine, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA
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1775
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Fatica A, Rosa A, Fazi F, Ballarino M, Morlando M, De Angelis FG, Caffarelli E, Nervi C, Bozzoni I. MicroRNAs and hematopoietic differentiation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2006; 71:205-10. [PMID: 17381298 DOI: 10.1101/sqb.2006.71.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The discovery of microRNAS (miRNAs) and of their mechanism of action has provided some very new clues on how gene expression is regulated. These studies established new concepts on how posttranscriptional control can fine-tune gene expression during differentiation and allowed the identification of new regulatory circuitries as well as factors involved therein. Because of the wealth of information available about the transcriptional and cellular networks involved in hematopoietic differentiation, the hematopoietic system is ideal for studying cell lineage specification. An interesting interplay between miRNAs and lineage-specific transcriptional factors has been found, and this can help us to understand how terminal differentiation is accomplished.
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Affiliation(s)
- A Fatica
- Institute Pasteur Cenci-Bolognetti, Department of Genetics and Molecular Biology and I.B.P.M., University of Rome La Sapienza, Rome, Italy
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1776
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Seyhan AA, Vlassov AV, Johnston BH. RNA interference from multimeric shRNAs generated by rolling circle transcription. Oligonucleotides 2006; 16:353-63. [PMID: 17155910 DOI: 10.1089/oli.2006.16.353] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Methods most commonly used for producing small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) are chemical synthesis and intracellular expression from engineered vectors. For shRNAs, chemical synthesis is very costly and construction of vectors is laborious. Synthesis by phage RNA polymerases from their natural promoters results in a 5 -terminal triphosphate that can trigger an interferon (IFN) response. Moreover, due to the requirement of phage promoters for 5 - GPuPuPu sequences for transcription initiation, shRNA transcripts may have extra 5 -nucleotides that can constrain the sequences that can be targeted. Also, the 3 ends may have an additional n + 1 nucleotide not encoded by the template. Here we present a novel approach for synthesizing functional shRNAs via rolling circle transcription (RCT) of small (approximately 70 nt) single-stranded DNA circles using T7 RNA polymerase, which avoids these issues. Due to internal pairing, these circles are dumbbell-shaped. RCT produces large transcripts (>10 kb in length) consisting of multimers (>150 copies) of shRNAs in the absence of promoter, terminator, or primer sequences. Dumbbells targeting red fluorescent protein (DsRed), human tumor necrosis factor-alpha (TNF-alpha) and hepatitis C virus (HCV) internal ribosome entry site (IRES) were prepared and transcribed. The resulting long transcripts are substrates for Dicer. When introduced into 293FT and Huh7 cells, the multimeric transcripts inhibited their target genes at levels similar to an equivalent mass of monomeric shRNAs, indicating that they can enter the RNAi pathway. Thus, rolling circle transcription of small DNA dumbbells provides a new source of biologically active interfering RNA.
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1777
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Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. RNA editing of human microRNAs. Genome Biol 2006. [PMID: 16594986 DOI: 10.1186/gb-2006-7-4-r17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short RNAs of around 22 nucleotides that regulate gene expression. The primary transcripts of miRNAs contain double-stranded RNA and are therefore potential substrates for adenosine to inosine (A-to-I) RNA editing. RESULTS We have conducted a survey of RNA editing of miRNAs from ten human tissues by sequence comparison of PCR products derived from matched genomic DNA and total cDNA from the same individual. Six out of 99 (6%) miRNA transcripts from which data were obtained were subject to A-to-I editing in at least one tissue. Four out of seven edited adenosines were in the mature miRNA and were predicted to change the target sites in 3' untranslated regions. For a further six miRNAs, we identified A-to-I editing of transcripts derived from the opposite strand of the genome to the annotated miRNA. These miRNAs may have been annotated to the wrong genomic strand. CONCLUSION Our results indicate that RNA editing increases the diversity of miRNAs and their targets, and hence may modulate miRNA function.
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Affiliation(s)
- Matthew J Blow
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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1778
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Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. RNA editing of human microRNAs. Genome Biol 2006. [PMID: 16594986 DOI: 10.1186/gb-20060704-r27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short RNAs of around 22 nucleotides that regulate gene expression. The primary transcripts of miRNAs contain double-stranded RNA and are therefore potential substrates for adenosine to inosine (A-to-I) RNA editing. RESULTS We have conducted a survey of RNA editing of miRNAs from ten human tissues by sequence comparison of PCR products derived from matched genomic DNA and total cDNA from the same individual. Six out of 99 (6%) miRNA transcripts from which data were obtained were subject to A-to-I editing in at least one tissue. Four out of seven edited adenosines were in the mature miRNA and were predicted to change the target sites in 3' untranslated regions. For a further six miRNAs, we identified A-to-I editing of transcripts derived from the opposite strand of the genome to the annotated miRNA. These miRNAs may have been annotated to the wrong genomic strand. CONCLUSION Our results indicate that RNA editing increases the diversity of miRNAs and their targets, and hence may modulate miRNA function.
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Affiliation(s)
- Matthew J Blow
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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1779
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Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs that function as endogenous triggers of the RNA interference pathway. Originally discovered in Caenorhabditis elegans, this group of tiny RNAs has moved to the forefront of biology. With over 300 miRNA genes identified in the human genome, and a plethora of predicted mRNA targets, it is believed that these small RNAs have a central role in diverse cellular and developmental processes. Concordant with this, aberrant expression of miRNA genes could lead to human disease, including cancer. Although the connection of miRNAs with cancer has been suspected for several years, four recent studies have confirmed the suspicion that miRNAs regulate cell proliferation and apoptosis, and play a role in cancer.
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Affiliation(s)
- Scott M Hammond
- Department of Cell and Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
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1780
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Abstract
MicroRNAs are sequence-specific regulators of post-transcriptional gene expression in many eukaryotes. They are believed to control the expression of thousands of target mRNAs, with each mRNA believed to be targeted by multiple microRNAs. Recent studies have uncovered various mechanisms by which microRNAs down-regulate their target mRNAs and have linked a well-known subcellular structure, the cytoplasmic processing bodies (PBs) to the microRNA pathway. The finding that microRNAs are misexpressed in cancers has reinforced the idea that their regulatory roles are very important.
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Affiliation(s)
- Ramesh S Pillai
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland.
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1781
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Klein ME, Impey S, Goodman RH. Role reversal: the regulation of neuronal gene expression by microRNAs. Curr Opin Neurobiol 2005; 15:507-13. [PMID: 16150590 DOI: 10.1016/j.conb.2005.08.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Accepted: 08/25/2005] [Indexed: 01/07/2023]
Abstract
In a similar fashion to transcription factors, non-coding RNAs can be essential regulators of gene expression. The largest class of non-coding RNAs is the microRNAs. These approximately 22 nt double-stranded RNA molecules can repress translation or target mRNA degradation. There has been a surge of research in the past year stimulated by the recent availability of specialized techniques, both in vitro and in silico, for predicting and characterizing microRNAs. The accumulating evidence suggests that microRNAs are ubiquitous regulators of gene expression during development. The combined actions of microRNAs and transcription factors are able to tune the expression of proteins on a global level in a manner that cannot be achieved by transcription factors alone.
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Affiliation(s)
- Matthew E Klein
- Reed College and Vollum Institute, Oregon Health and Sciences University, Portland OR, USA
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1782
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Abstract
MicroRNAs (miRNAs) play a pivotal role in the regulation of genes involved in diverse processes such as development, differentiation, and cellular growth control. Recently, many viral-encoded miRNAs have been discovered, for the most part in viruses transcribed from double-stranded DNA genomes. As with their cellular counterparts, the functions of most viral-derived miRNAs are unknown; however, functions have been documented or proposed for viral miRNAs from three different viral families-herpesviruses, polyomaviruses, and retroviruses. Several virus-encoded miRNAs have unique aspects to their biogenesis, such as the polymerase that transcribes them or their location within the precursor transcript. Additionally, viral interactions with cellular miRNAs have also been identified, and these have substantially expanded our appreciation of miRNA functions.
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Affiliation(s)
- Christopher S Sullivan
- Howard Hughes Medical Institute, Department of Microbiology, University of California, San Francisco, CA 94143, USA
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1783
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Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 2005; 123:631-40. [PMID: 16271387 DOI: 10.1016/j.cell.2005.10.022] [Citation(s) in RCA: 1071] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 09/02/2005] [Accepted: 10/21/2005] [Indexed: 02/08/2023]
Abstract
RNA interference is implemented through the action of the RNA-induced silencing complex (RISC). Although Argonaute2 has been identified as the catalytic center of RISC, the RISC polypeptide composition and assembly using short interfering RNA (siRNA) duplexes has remained elusive. Here we show that RISC is composed of Dicer, the double-stranded RNA binding protein TRBP, and Argonaute2. We demonstrate that this complex can cleave target RNA using precursor microRNA (pre-miRNA) hairpin as the source of siRNA. Although RISC can also utilize duplex siRNA, it displays a nearly 10-fold greater activity using the pre-miRNA Dicer substrate. RISC distinguishes the guide strand of the siRNA from the passenger strand and specifically incorporates the guide strand. Importantly, ATP is not required for miRNA processing, RISC assembly, or multiple rounds of target-RNA cleavage. These results define the composition of RISC and demonstrate that miRNA processing and target-RNA cleavage are coupled.
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1784
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Miyoshi K, Tsukumo H, Nagami T, Siomi H, Siomi MC. Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev 2005; 19:2837-48. [PMID: 16287716 PMCID: PMC1315391 DOI: 10.1101/gad.1370605] [Citation(s) in RCA: 305] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Argonaute proteins play important yet distinct roles in RNA silencing. Human Argonaute2 (hAgo2) was shown to be responsible for target RNA cleavage ("Slicer") activity in RNA interference (RNAi), whereas other Argonaute subfamily members do not exhibit the Slicer activity in humans. In Drosophila, AGO2 was shown to possess the Slicer activity. Here we show that AGO1, another member of the Drosophila Argonaute subfamily, immunopurified from Schneider2 (S2) cells associates with microRNA (miRNA) and cleaves target RNA completely complementary to the miRNA. Slicer activity is reconstituted with recombinant full-length AGO1. Thus, in Drosophila, unlike in humans, both AGO1 and AGO2 have Slicer functions. Further, reconstitution of Slicer activity with recombinant PIWI domains of AGO1 and AGO2 demonstrates that other regions in the Argonautes are not strictly necessary for small interfering RNA (siRNA)-binding and cleavage activities. It has been shown that in circumstances with AGO2-lacking, the siRNA duplex is not unwound and consequently an RNA-induced silencing complex (RISC) is not formed. We show that upon addition of an siRNA duplex in S2 lysate, the passenger strand is cleaved in an AGO2-dependent manner, and nuclease-resistant modification of the passenger strand impairs RISC formation. These findings give rise to a new model in which AGO2 is directly involved in RISC formation as "Slicer" of the passenger strand of the siRNA duplex.
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Affiliation(s)
- Keita Miyoshi
- Institute for Genome Research, University of Tokushima, Tokushima 770-8503, Japan
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1785
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Abstract
Recent findings show that the Tat protein of human immunodeficiency virus (HIV) can suppress the host's RNA-silencing pathway and may thus counteract host antiviral RNAs. RNA silencing has a known role in the antiviral responses of plants and insects. Recent evidence, including the finding that the Tat protein of human immunodeficiency virus (HIV) can suppress the host's RNA-silencing pathway and may thus counteract host antiviral RNAs, suggests that RNA-silencing pathways could also have key roles in mammalian virus-host interactions.
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Affiliation(s)
- Edward P Browne
- Molecular Pathogenesis Program and Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Junjie Li
- Molecular Pathogenesis Program and Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Mark Chong
- Molecular Pathogenesis Program and Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Dan R Littman
- Molecular Pathogenesis Program and Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
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1786
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Vo N, Klein ME, Varlamova O, Keller DM, Yamamoto T, Goodman RH, Impey S. A cAMP-response element binding protein-induced microRNA regulates neuronal morphogenesis. Proc Natl Acad Sci U S A 2005; 102:16426-31. [PMID: 16260724 PMCID: PMC1283476 DOI: 10.1073/pnas.0508448102] [Citation(s) in RCA: 662] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) regulate cellular fate by controlling the stability or translation of mRNA transcripts. Although the spatial and temporal patterning of miRNA expression is tightly controlled, little is known about signals that induce their expression nor mechanisms of their transcriptional regulation. Furthermore, few miRNA targets have been validated experimentally. The miRNA, miR132, was identified through a genome-wide screen as a target of the transcription factor, cAMP-response element binding protein (CREB). miR132 is enriched in neurons and, like many neuronal CREB targets, is highly induced by neurotrophins. Expression of miR132 in cortical neurons induced neurite outgrowth. Conversely, inhibition of miR132 function attenuated neuronal outgrowth. We provide evidence that miR132 regulates neuronal morphogenesis by decreasing levels of the GTPase-activating protein, p250GAP. These data reveal that a CREB-regulated miRNA regulates neuronal morphogenesis by responding to extrinsic trophic cues.
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Affiliation(s)
- Ngan Vo
- Vollum Institute, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
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1787
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Biemar F, Zinzen R, Ronshaugen M, Sementchenko V, Manak JR, Levine MS. Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc Natl Acad Sci U S A 2005; 102:15907-11. [PMID: 16249329 PMCID: PMC1276093 DOI: 10.1073/pnas.0507817102] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) regulate posttranscriptional gene activity by binding to specific sequences in the 3' UTRs of target mRNAs. A number of metazoan miRNAs have been shown to exhibit tissue-specific patterns of expression. Here, we investigate the possibility that localized expression is mediated by tissue-specific enhancers, comparable to those seen for protein-coding genes. Two miRNA loci in Drosophila melanogaster are investigated, the mir-309-6 polycistron (8-miR) and the mir-1 gene. The 8-miR locus contains a cluster of eight distinct miRNAs that are transcribed in a common precursor RNA. The 8-miR primary transcript displays a dynamic pattern of expression in early embryos, including repression at the anterior and posterior poles. An 800-bp 5' enhancer was identified that recapitulates this complex pattern when attached to a RNA polymerase II core promoter fused to a lacZ-reporter gene. The miR-1 locus is specifically expressed in the mesoderm of gastrulating embryos. Bioinformatics methods were used to identify a mesoderm-specific enhancer located approximately 5 kb 5' of the miR-1 transcription unit. Evidence is presented that the 8-miR enhancer is regulated by the localized Huckebein repressor, whereas miR-1 is activated by Dorsal and Twist. These results provide evidence that restricted activities of the 8-miR and miR-1 miRNAs are mediated by classical tissue-specific enhancers.
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Affiliation(s)
- Frédéric Biemar
- Division of Genetics and Development, Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
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1788
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Berezikov E, Plasterk RHA. Camels and zebrafish, viruses and cancer: a microRNA update. Hum Mol Genet 2005; 14 Spec No. 2:R183-90. [PMID: 16244316 DOI: 10.1093/hmg/ddi271] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) form an extensive class of RNA molecules that regulate gene expression at post-transcriptional level. In recent years, much progress has been made in dissection of biogenesis and functions of miRNAs. There are at least several hundred miRNA genes in the human genome, and the emerging evidence suggests that miRNAs are broadly implicated in gene regulation. Here, we review some recent advances, and particularly we discuss how comparative genomics helps to identify novel miRNA genes, how studies in zebrafish reveal roles of miRNAs in morphogenesis, how changes in miRNA expression patterns are connected with cancer and how host-virus coevolution exploits miRNA regulatory pathways.
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Affiliation(s)
- Eugene Berezikov
- Hubrecht Laboratory, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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1789
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Hammond SM. Dicing and slicing: the core machinery of the RNA interference pathway. FEBS Lett 2005; 579:5822-9. [PMID: 16214139 DOI: 10.1016/j.febslet.2005.08.079] [Citation(s) in RCA: 361] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Revised: 08/25/2005] [Accepted: 08/28/2005] [Indexed: 12/30/2022]
Abstract
RNA interference (RNAi) is broadly defined as a gene silencing pathway that is triggered by double-stranded RNA (dsRNA). Many variations have been described on this theme. The dsRNA trigger can be supplied exogenously, as an experimental tool, or can derive from the genome in the form of microRNAs. Gene silencing can be the result of nucleolytic degradation of the mRNA, or by translational suppression. At the heart of the pathway are two ribonuclease machines. The ribonuclease III enzyme Dicer initiates the RNAi pathway by generating the active short interfering RNA trigger. Silencing is effected by the RNA-induced silencing complex and its RNaseH core enzyme Argonaute. This review describes the discovery of these machines and discusses future lines of work on this amazing biochemical pathway.
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Affiliation(s)
- Scott M Hammond
- Department of Cell and Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
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1790
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Abstract
Small RNA guides--microRNAs, small interfering RNAs, and repeat-associated small interfering RNAs, 21 to 30 nucleotides in length--shape diverse cellular pathways, from chromosome architecture to stem cell maintenance. Fifteen years after the discovery of RNA silencing, we are only just beginning to understand the depth and complexity of how these RNAs regulate gene expression and to consider their role in shaping the evolutionary history of higher eukaryotes.
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Affiliation(s)
- Phillip D Zamore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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1791
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Abstract
As knowledge of microRNAs (miRNA) grows from a compendium of sequences to annotated functional data it has become increasingly clear that a highly significant segment of regulatory biology depends on these approximately 22 nucleotide noncoding transcripts. The expression of many miRNAs in the nervous system, some with a high degree of temporal and spatial specificity, suggests that understanding miRNAs in the nervous system will yield rewarding neurobiological insights. High on the list of insights that microRNAs promise is a deeper understanding of the remarkable cellular diversity found among neurons. This review examines the interface between an emerging biology of miRNAs and their role in nervous systems.
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Affiliation(s)
- Kenneth S Kosik
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California 93106, USA.
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1792
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Chen X. MicroRNA biogenesis and function in plants. FEBS Lett 2005; 579:5923-31. [PMID: 16144699 PMCID: PMC5127707 DOI: 10.1016/j.febslet.2005.07.071] [Citation(s) in RCA: 339] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 07/18/2005] [Accepted: 07/19/2005] [Indexed: 11/15/2022]
Abstract
A microRNA (miRNA) is a 21-24 nucleotide RNA product of a non-protein-coding gene. Plants, like animals, have a large number of miRNA-encoding genes in their genomes. The biogenesis of miRNAs in Arabidopsis is similar to that in animals in that miRNAs are processed from primary precursors by at least two steps mediated by RNAse III-like enzymes and that the miRNAs are incorporated into a protein complex named RISC. However, the biogenesis of plant miRNAs consists of an additional step, i.e., the miRNAs are methylated on the ribose of the last nucleotide by the miRNA methyltransferase HEN1. The high degree of sequence complementarity between plant miRNAs and their target mRNAs has facilitated the bioinformatic prediction of miRNA targets, many of which have been subsequently validated. Plant miRNAs have been predicted or confirmed to regulate a variety of processes, such as development, metabolism, and stress responses. A large category of miRNA targets consists of genes encoding transcription factors that play important roles in patterning the plant form.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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1793
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Abstract
MicroRNAs (miRNAs) are endogenously expressed non-coding RNAs of 20-24 nucleotides, which post-transcriptionally regulate gene expression in plants and animals. Recently it has been recognized that miRNAs comprise one of the abundant gene families in multicellular species, and their regulatory functions in various biological processes are widely spread. There has been a surge in the research activities in this field in the past few years. From the very beginning, computational methods have been utilized as indispensable tools, and many discoveries have been obtained through combination of experimental and computational approaches. In this review, both biological and computational aspects of miRNA will be discussed. A brief history of the discovery of miRNA and discussion of microarray applications in miRNA research are also included.
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Affiliation(s)
- Yong Kong
- Department of Mathematics, National University of Singapore.
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