201
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Burgyán J, Havelda Z. Viral suppressors of RNA silencing. TRENDS IN PLANT SCIENCE 2011; 16:265-72. [PMID: 21439890 DOI: 10.1016/j.tplants.2011.02.010] [Citation(s) in RCA: 299] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 02/14/2011] [Accepted: 02/22/2011] [Indexed: 05/03/2023]
Abstract
The infection and replication of viruses in the host induce diverse mechanisms for combating viral infection. One of the best-studied antiviral defence mechanisms is based on RNA silencing. Consistently, several viral suppressors of RNA silencing (VSRs) have been identified from almost all plant virus genera, which are surprisingly diverse within and across kingdoms, exhibiting no obvious sequence similarities. VSRs efficiently inhibit host antiviral responses by interacting with the key components of cellular silencing machinery, often mimicking their normal cellular functions. Recent findings have revealed that the impact of VSRs on endogenous pathways is more complex and profound than had been estimated thus far. This review highlights the current understanding of and new insights into the mechanisms and functions of plant VSRs.
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Affiliation(s)
- József Burgyán
- Istituto di Virologia Vegetale, CNR, Strada Delle Cacce 73, Torino, Italy.
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202
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Frank F, Fabian MR, Stepinski J, Jemielity J, Darzynkiewicz E, Sonenberg N, Nagar B. Structural analysis of 5'-mRNA-cap interactions with the human AGO2 MID domain. EMBO Rep 2011; 12:415-20. [PMID: 21475248 DOI: 10.1038/embor.2011.48] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Revised: 02/25/2011] [Accepted: 03/01/2011] [Indexed: 12/15/2022] Open
Abstract
In RNA silencing, microRNA (miRNA)-mediated translational repression occurs through mechanisms that do not invoke messenger-RNA (mRNA) target cleavage by Argonaute proteins. The nature of these mechanisms is unclear, but several recent studies have proposed that a direct interaction between the mRNA-cap and the middle (MID) domain of Argonautes is involved. Here, we present crystallographic and NMR data demonstrating that cap analogues do not bind significantly to the isolated MID domain of human Argonaute 2 (hAGO2) and are found in the miRNA 5'-nucleotide binding site in an implausible binding mode. Additionally, in vitro pull-down experiments with full-length hAGO2 indicate that the interaction with cap analogues is nonspecific.
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Affiliation(s)
- Filipp Frank
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
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203
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Ceman S, Saugstad J. MicroRNAs: Meta-controllers of gene expression in synaptic activity emerge as genetic and diagnostic markers of human disease. Pharmacol Ther 2011; 130:26-37. [PMID: 21256154 PMCID: PMC3043141 DOI: 10.1016/j.pharmthera.2011.01.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 01/05/2011] [Indexed: 12/18/2022]
Abstract
MicroRNAs are members of the non-protein-coding family of RNAs. They serve as regulators of gene expression by modulating the translation and/or stability of messenger RNA targets. The discovery of microRNAs has revolutionized the field of cell biology, and has permanently altered the prevailing view of a linear relationship between gene and protein expression. The increased complexity of gene regulation is both exciting and daunting, as emerging evidence supports a pervasive role for microRNAs in virtually every cellular process. This review briefly describes microRNA processing and formation of RNA-induced silencing complexes, with a focus on the role of RNA binding proteins in this process. We also discuss mechanisms for microRNA-mediated regulation of translation, particularly in dendritic spine formation and function, and the role of microRNAs in synaptic plasticity. We then discuss the evidence for altered microRNA function in cognitive brain disorders, and the effect of gene mutations revealed by single nucleotide polymorphism analysis on altered microRNA function and human disease. Further, we present evidence that altered microRNA expression in circulating fluids such as plasma/serum can correlate with, and serve as, novel diagnostic biomarkers of human disease.
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Affiliation(s)
- Stephanie Ceman
- University of Illinois, Department of Cell & Developmental Biology, Urbana IL 61801, United States
| | - Julie Saugstad
- Legacy Research Institute, RS Dow Neurobiology Labs, Portland, OR 97232, United States
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204
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Jafarifar F, Yao P, Eswarappa SM, Fox PL. Repression of VEGFA by CA-rich element-binding microRNAs is modulated by hnRNP L. EMBO J 2011; 30:1324-34. [PMID: 21343907 DOI: 10.1038/emboj.2011.38] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 01/21/2011] [Indexed: 12/27/2022] Open
Abstract
Expression of vascular endothelial growth factor-A (VEGFA) by tumour-associated macrophages is critical for tumour progression and metastasis. Hypoxia, a common feature of the neoplastic microenvironment, induces VEGFA expression by increased transcription, translation, and mRNA stabilization. Here, we report a new mechanism of VEGFA regulation by hypoxia that involves reversal of microRNA (miRNA)-mediated silencing of VEGFA expression. We show that the CA-rich element (CARE) in the human VEGFA 3'-UTR is targeted by at least four miRNAs. Among these miRNAs, miR-297 and -299 are endogenously expressed in monocytic cells and negatively regulate VEGFA expression. Unexpectedly, hypoxia completely reverses miRNA-mediated repression of VEGFA expression. We show that heterogeneous nuclear ribonucleoprotein L (hnRNP L), which also binds the VEGFA 3'-UTR CARE, prevents miRNA silencing activity. Hypoxia induces translocation of nuclear hnRNP L to the cytoplasm, which markedly increases hnRNP L binding to VEGFA mRNA thereby inhibiting miRNA activity. In summary, we describe a novel regulatory mechanism in which the interplay between miRNAs and RNA-binding proteins influences expression of a critical hypoxia-inducible angiogenic protein. These studies may contribute to provide miRNA-based anticancer therapeutic tools.
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Affiliation(s)
- Faegheh Jafarifar
- Department of Cell Biology, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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205
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Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 2011; 12:99-110. [PMID: 21245828 DOI: 10.1038/nrg2936] [Citation(s) in RCA: 1763] [Impact Index Per Article: 125.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite their widespread roles as regulators of gene expression, important questions remain about target regulation by microRNAs. Animal microRNAs were originally thought to repress target translation, with little or no influence on mRNA abundance, whereas the reverse was thought to be true in plants. Now, however, it is clear that microRNAs can induce mRNA degradation in animals and, conversely, translational repression in plants. Recent studies have made important advances in elucidating the relative contributions of these two different modes of target regulation by microRNAs. They have also shed light on the specific mechanisms of target silencing, which, although it differs fundamentally between plants and animals, shares some common features between the two kingdoms.
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206
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Abstract
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) act with the Argonaute family of proteins to regulate target messenger RNAs (mRNAs) posttranscriptionally. SiRNAs typically induce endonucleolytic cleavage of mRNA with near-perfect complementarity. For targets with less complementarity, both translational repression and mRNA destabilization mechanisms have been implicated in miRNA-mediated gene repression, although the timing, coupling, and relative importance of these events have not been determined. Here, we review gene-specific and global approaches that probe miRNA function and mechanism, looking for a unifying model. More systematic analyses of the molecular specificities of the core components coupled with analysis of the relative timing of the different events will ultimately shed light on the mechanism of miRNA-mediated repression.
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Affiliation(s)
- Sergej Djuranovic
- Howard Hughes Medical Institute (HHMI), Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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207
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Khong A, Jan E. Modulation of stress granules and P bodies during dicistrovirus infection. J Virol 2011; 85:1439-51. [PMID: 21106737 PMCID: PMC3028890 DOI: 10.1128/jvi.02220-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 11/16/2010] [Indexed: 11/20/2022] Open
Abstract
Stress granules (SGs) are dynamic cytosolic aggregates composed of ribonucleoproteins that are induced during cellular stress when protein synthesis is inhibited. The function of SGs is poorly understood, but they are thought to be sites for reorganizing mRNA and protein. Several viruses can modulate SG formation, suggesting that SGs have an impact on virus infection. In this study, we have investigated the relationship of SG formation in Drosophila S2 cells infected by cricket paralysis virus (CrPV), a member of the Dicistroviridae family. Despite a rapid shutoff of host translation during CrPV infection, several hallmark SG markers such as the Drosophila TIA-1 and G3BP (RasGAP-SH3-binding protein) homologs, Rox8 and Rin, respectively, do not aggregate in CrPV-infected cells, even when challenged with potent SG inducers such as heat shock, oxidative stress, and pateamine A treatment. Furthermore, we demonstrate that a subset of P body markers become moderately dispersed at late times of infection. In contrast, as shown by fluorescent in situ hybridization, poly(A)(+) RNA granules still form at late times of infection. These poly(A)(+) RNA granules do not contain viral RNA nor do they colocalize with P body markers. Finally, our results demonstrate that the CrPV viral 3C protease is sequestered to SGs under cellular stress but not during virus infection. In summary, we propose that dicistrovirus infection leads to the selective inhibition of distinct SGs so that viral proteins are available for viral processing.
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Affiliation(s)
- Anthony Khong
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
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208
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Lindquist RA, Ottina KA, Wheeler DB, Hsu PP, Thoreen CC, Guertin DA, Ali SM, Sengupta S, Shaul YD, Lamprecht MR, Madden KL, Papallo AR, Jones TR, Sabatini DM, Carpenter AE. Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1-S6K pathway signaling. Genome Res 2011; 21:433-46. [PMID: 21239477 DOI: 10.1101/gr.111492.110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The evolutionarily conserved target of rapamycin complex 1 (TORC1) controls cell growth in response to nutrient availability and growth factors. TORC1 signaling is hyperactive in cancer, and regulators of TORC1 signaling may represent therapeutic targets for human diseases. To identify novel regulators of TORC1 signaling, we performed a genome-scale RNA interference screen on microarrays of Drosophila melanogaster cells expressing human RPS6, a TORC1 effector whose phosphorylated form we detected by immunofluorescence. Our screen revealed that the TORC1-S6K-RPS6 signaling axis is regulated by many subcellular components, including the Class I vesicle coat (COPI), the spliceosome, the proteasome, the nuclear pore, and the translation initiation machinery. Using additional RNAi reagents, we confirmed 70 novel genes as significant on-target regulators of RPS6 phosphorylation, and we characterized them with extensive secondary assays probing various arms of the TORC1 pathways, identifying functional relationships among those genes. We conclude that cell-based microarrays are a useful platform for genome-scale and secondary screening in Drosophila, revealing regulators that may represent drug targets for cancers and other diseases of deregulated TORC1 signaling.
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Affiliation(s)
- Robert A Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
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209
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Giovannini-Chami L, Grandvaux N, Zaragosi LE, Robbe-Sermesant K, Marcet B, Cardinaud B, Coraux C, Berthiaume Y, Waldmann R, Mari B, Barbry P. Impact of microRNA in normal and pathological respiratory epithelia. Methods Mol Biol 2011; 741:171-91. [PMID: 21594785 PMCID: PMC7121186 DOI: 10.1007/978-1-61779-117-8_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Extensive sequencing efforts, combined with ad hoc bioinformatics developments, have now led to the identification of 1222 distinct miRNAs in human (derived from 1368 distinct genomic loci) and of many miRNAs in other multicellular organisms. The present chapter is aimed at describing a general experimental strategy to identify specific miRNA expression profiles and to highlight the functional networks operating between them and their mRNA targets, including several miRNAs deregulated in cystic fibrosis and during differentiation of airway epithelial cells.
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210
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Eckhardt S, Szostak E, Yang Z, Pillai R. Artificial tethering of Argonaute proteins for studying their role in translational repression of target mRNAs. Methods Mol Biol 2011; 725:191-206. [PMID: 21528455 DOI: 10.1007/978-1-61779-046-1_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Small RNAs such as microRNAs (miRNAs) and small-interfering RNAs (siRNAs) associate with members of the RNA-binding Argonaute family proteins. Together they participate in transcriptional and posttranscriptional gene silencing mechanisms. The fate of the target mRNA is determined, in part, by the degree of complementarity with the small RNA. To examine the exact role of the Argonaute protein in the silencing complex, human Argonautes were artificially recruited to reporter mRNAs in a small RNA-independent manner by the BoxB-N-peptide tethering system. Tethering of Argonaute proteins to a reporter mRNA leads to the inhibition of translation, mimicking the repression seen with miRNAs. Similar tethering experiments were performed with fly and fission yeast Argonaute proteins and other components of the small RNP (ribonucleoprotein) complex, uncovering their specific roles in the silencing complexes containing them.
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211
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Fabian MR, Svitkin YV, Sonenberg N. An efficient system for let-7 microRNA and GW182 protein-mediated deadenylation in vitro. Methods Mol Biol 2011; 725:207-17. [PMID: 21528456 DOI: 10.1007/978-1-61779-046-1_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Experiments with cell cultures have been useful in analyzing microRNA action. However, miRNA-mediated effects are often assayed many hours or days after miRNA target recognition. Consequently, this has made it difficult to analyze early events of miRNA-mediated repression. The development of cell-free systems that recapitulate miRNA action in vitro has been instrumental in dissecting the molecular mechanisms of miRNA action. Here we describe such a system, derived from mouse Krebs II ascites carcinoma cells, termed Krebs cell-free system. As an example, the protocol for assaying let-7 and GW182 (TNRC6) protein-mediated deadenylation of mRNA in vitro is described.
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Affiliation(s)
- Marc R Fabian
- Department of Biochemistry, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada.
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212
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Nicolas FE. Experimental validation of microRNA targets using a luciferase reporter system. Methods Mol Biol 2011; 732:139-52. [PMID: 21431711 DOI: 10.1007/978-1-61779-083-6_11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding transcripts that repress gene expression by pairing with their target messenger RNAs (mRNAs). The human genome codes for hundreds of different miRNAs and it is predicted that they target thousands of mRNAs involved in a wide variety of physiological processes such as development and cell identity. In animals, the identification of mRNA targets is complex because most miRNAs and their target mRNAs do not have exact or nearly exact complementarity. This tendency of animal miRNAs to bind their mRNA targets with imperfect sequence homology represents a considerable challenge to identifying miRNA targets. Computational algorithms based on conservation and experimental approaches based on expression profiles are flooding the literature with lists of candidate genes containing a large number of false-positive and false-negative predictions and indirect targets that cover the real list of direct targets for each miRNA. Currently, the only available tools to validate a sequence as a direct target of an miRNA are the systems based on a reporter gene carrying the candidate sequence. Here, an miRNA target validation reporter gene system based on the luminescence generated by the luciferase protein is described in detail, including the design of the reporter constructs, its expression in a model cell line and its measurement using a luciferase assay.
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213
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Yao B, Li S, Jung HM, Lian SL, Abadal GX, Han F, Fritzler MJ, Chan EKL. Divergent GW182 functional domains in the regulation of translational silencing. Nucleic Acids Res 2010; 39:2534-47. [PMID: 21131274 PMCID: PMC3074120 DOI: 10.1093/nar/gkq1099] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNA (miRNA)-mediated gene regulation has become a major focus in many biological processes. GW182 and its long isoform TNGW1 are marker proteins of GW/P bodies and bind to Argonaute proteins of the RNA induced silencing complex. The goal of this study is to further define and distinguish the repression domain(s) in human GW182/TNGW1. Two non-overlapping regions, Δ12 (amino acids 896–1219) containing the Ago hook and Δ5 (amino acids 1670–1962) containing the RRM, both induced comparable silencing in a tethering assay. Mapping data showed that the RRM and its flanking sequences in Δ5, but not the Ago hook in Δ12, were important for silencing. Repression mediated by Δ5 or Δ12 was not differentially affected when known endogenous repressors RCK/p54, GW182/TNGW1, TNRC6B were depleted. Transfected Δ5, but not Δ12, enhanced Ago2-mediated repression in a tethering assay. Transfected Δ12, but not Δ5, released endogenous miRNA reporter silencing without affecting siRNA function. Alanine substitution showed that GW/WG motifs in Δ12 (Δ12a, amino acids 896–1045) were important for silencing activity. Although Δ12 appeared to bind PABPC1 more efficiently than Δ5, neither Δ5 nor Δ12 significantly enhanced reporter mRNA degradation. These different functional characteristics of Δ5 and Δ12 suggest that their roles are distinct, and possibly dynamic, in human GW182-mediated silencing.
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Affiliation(s)
- Bing Yao
- Department of Oral Biology, University of Florida, Gainesville, FL 32610-0424, USA
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214
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Moretti F, Thermann R, Hentze MW. Mechanism of translational regulation by miR-2 from sites in the 5' untranslated region or the open reading frame. RNA (NEW YORK, N.Y.) 2010; 16:2493-2502. [PMID: 20966199 PMCID: PMC2995410 DOI: 10.1261/rna.2384610] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 09/08/2010] [Indexed: 05/30/2023]
Abstract
MicroRNAs (miRs) commonly regulate translation from target mRNA 3' untranslated regions (UTRs). While effective miR-binding sites have also been identified in 5' untranslated regions (UTRs) or open reading frames (ORFs), the mechanism(s) of miR-mediated regulation from these sites has not been defined. Here, we systematically investigate how the position of miR-binding sites influences translational regulation and characterize their mechanistic basis. We show that specific translational regulation is elicited in vitro and in vivo not only from the 3'UTR, but equally effectively from six Drosophila miR-2-binding sites in the 5'UTR or the ORF. In all cases, miR-2 triggers mRNA deadenylation and inhibits translation initiation in a cap-dependent fashion. In contrast, single or dual miR-2-binding sites in the 5'UTR or the ORF yield rather inefficient or no regulation. This work represents the first demonstration that 5'UTR and ORF miR-binding sites can function mechanistically similarly to the intensively investigated 3'UTR sites. Using single or dual binding sites, it also reveals a biological rationale for the high prevalence of miR regulatory sites in the 3'UTR.
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Affiliation(s)
- Francesca Moretti
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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215
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Huntzinger E, Braun JE, Heimstädt S, Zekri L, Izaurralde E. Two PABPC1-binding sites in GW182 proteins promote miRNA-mediated gene silencing. EMBO J 2010; 29:4146-60. [PMID: 21063388 PMCID: PMC3018788 DOI: 10.1038/emboj.2010.274] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Accepted: 10/12/2010] [Indexed: 12/14/2022] Open
Abstract
Previous studies have suggested that the mechanism of miRNA-mediated silencing may differ between human and Drosophila cells. Here, a direct comparison demonstrates that the mechanism is conserved and the GW182–PABP interaction is required for silencing in vivo. miRNA-mediated gene silencing requires the GW182 proteins, which are characterized by an N-terminal domain that interacts with Argonaute proteins (AGOs), and a C-terminal silencing domain (SD). In Drosophila melanogaster (Dm) GW182 and a human (Hs) orthologue, TNRC6C, the SD was previously shown to interact with the cytoplasmic poly(A)-binding protein (PABPC1). Here, we show that two regions of GW182 proteins interact with PABPC1: the first contains a PABP-interacting motif 2 (PAM2; as shown before for TNRC6C) and the second contains the M2 and C-terminal sequences in the SD. The latter mediates indirect binding to the PABPC1 N-terminal domain. In D. melanogaster cells, the second binding site dominates; however, in HsTNRC6A–C the PAM2 motif is essential for binding to both Hs and DmPABPC1. Accordingly, a single amino acid substitution in the TNRC6A–C PAM2 motif abolishes the interaction with PABPC1. This mutation also impairs TNRC6s silencing activity. Our findings reveal that despite species-specific differences in the relative strength of the PABPC1-binding sites, the interaction between GW182 proteins and PABPC1 is critical for miRNA-mediated silencing in animal cells.
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Affiliation(s)
- Eric Huntzinger
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
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216
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Abstract
Metazoan cells form cytoplasmic mRNA granules such as stress granules (SG) and processing bodies (P bodies) that are proposed to be sites of aggregated, translationally silenced mRNAs and mRNA degradation. Poliovirus (PV) is a plus-strand RNA virus containing a genome that is a functional mRNA; thus, we investigated if PV antagonizes the processes that lead to formation of these structures. We have previously shown that PV infection inhibits the ability of cells to form stress granules by cleaving RasGAP-SH3-binding protein (G3BP). Here, we show that P bodies are also disrupted during PV infection in cells by 4 h postinfection. The disruption of P bodies is more rapid and more complete than disruption of stress granules. The kinetics of P body disruption correlated with production of viral proteinases and required substantial viral gene product expression. The organizing mechanism that forms P body foci in cells is unknown; however, potential scaffolding, aggregating, or other regulatory proteins found in P bodies were investigated for degradation. Two factors involved in 5'-end mRNA decapping and degradation, Xrn1 and Dcp1a, and the 3' deadenylase complex component Pan3 underwent accelerated degradation during infection, and Dcp1a may be a direct substrate of PV 3C proteinase. Several other key factors proposed to be essential for P body formation, GW182, Edc3, and Edc4, were unaffected by poliovirus infection. Since deadenylation has been reported to be required for P body formation, viral inhibition of deadenylation, through Pan3 degradation, is a potential mechanism of P body disruption.
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217
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Moser JJ, Fritzler MJ. The microRNA and messengerRNA profile of the RNA-induced silencing complex in human primary astrocyte and astrocytoma cells. PLoS One 2010; 5:e13445. [PMID: 20976148 PMCID: PMC2956662 DOI: 10.1371/journal.pone.0013445] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 09/14/2010] [Indexed: 12/18/2022] Open
Abstract
Background GW/P bodies are cytoplasmic ribonucleoprotein-rich foci involved in microRNA (miRNA)-mediated messenger RNA (mRNA) silencing and degradation. The mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 that bind miRNA in the RNA-induced silencing complex (RISC). To date there are no published reports of the profile of miRNA and mRNA targeted to the RISC or a comparison of the RISC-specific miRNA/mRNA profile differences in malignant and non-malignant cells. Methodology/Principal Findings RISC mRNA and miRNA components were profiled by microarray analysis of malignant human U-87 astrocytoma cells and its non-malignant counterpart, primary human astrocytes. Total cell RNA as well as RNA from immunoprecipitated RISC was analyzed. The novel findings were fourfold: (1) miRNAs were highly enriched in astrocyte RISC compared to U-87 astrocytoma RISC, (2) astrocytoma and primary astrocyte cells each contained unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3) miR-195, 10b, 29b, 19b, 34a and 455-3p levels were increased and the miR-181b level was decreased in U-87 astrocytoma RISC as compared to astrocyte RISC, and (4) the RISC contained decreased levels of mRNAs in primary astrocyte and U-87 astrocytoma cells. Conclusions/Significance The observation that miR-34a and miR-195 levels were increased in the RISC of U-87 astrocytoma cells suggests an oncogenic role for these miRNAs. Differential regulation of mRNAs by specific miRNAs is evidenced by the observation that three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated while one miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in malignancy and other conditions. This study points to the importance of the RISC and ultimately GW/P body composition and function in miRNA and mRNA deregulation in astrocytoma cells and possibly in other malignancies.
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Affiliation(s)
- Joanna J. Moser
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Marvin J. Fritzler
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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218
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Affiliation(s)
- Christine Ender
- Center for Integrated Protein Science Munich (CIPS), Laboratory of RNA Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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219
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Abstract
Small RNA molecules regulating gene expression received a status of omnipresent master regulators of eukaryotic lives with almost supernatural powers. Mammals hold at least three mechanisms employing small RNA molecules for regulating gene expression. One of these mechanisms, the microRNA (miRNA) pathway, involves currently over a thousand of genome-encoded different miRNAs that are claimed to extend their control over more than a half of a genome. Here, I discuss how and why mouse oocytes and early embryos ignore the regulatory power of miRNAs, adding another surprising feature to the field of small RNAs.
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Affiliation(s)
- Petr Svoboda
- Institute of Molecular Genetics AS CR, Prague, Czech Republic.
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220
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The microRNAs of Caenorhabditis elegans. Semin Cell Dev Biol 2010; 21:728-37. [DOI: 10.1016/j.semcdb.2010.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 07/02/2010] [Indexed: 11/21/2022]
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221
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Sossin WS, Lacaille JC. Mechanisms of translational regulation in synaptic plasticity. Curr Opin Neurobiol 2010; 20:450-6. [PMID: 20430610 PMCID: PMC3006486 DOI: 10.1016/j.conb.2010.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 03/24/2010] [Accepted: 03/28/2010] [Indexed: 12/19/2022]
Abstract
The plasticity of the nervous system is due to the ability of neurons to change their properties by altering the function of their proteome. A major mechanism for this is through altering the amount of proteins by regulating their translation. In this review, we focus on recent advances in the elucidation of the mechanisms by which neurons regulate translation during synaptic plasticity. Particular focus will be on the different transduction mechanisms that selectively target distinct elements of the mRNA in the regulation of translation during plasticity.
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Affiliation(s)
- Wayne S Sossin
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada.
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222
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Giraldez AJ. microRNAs, the cell's Nepenthe: clearing the past during the maternal-to-zygotic transition and cellular reprogramming. Curr Opin Genet Dev 2010; 20:369-75. [PMID: 20452200 PMCID: PMC2908189 DOI: 10.1016/j.gde.2010.04.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 04/07/2010] [Accepted: 04/12/2010] [Indexed: 12/18/2022]
Abstract
The maternal-to-zygotic transition (MZT) is a universal step in animal development characterized by two major events: activation of zygotic transcription and degradation of maternally provided mRNAs. How zygotic gene products instruct the degradation of maternal messages remains a long-standing question in biology. MicroRNAs (miRNAs) have recently emerged as widespread regulators of gene expression. miRNAs control temporal and spatial gene expression by both accelerating the decay of mRNAs from previous developmental stages and modulating the levels of actively transcribed genes. In this review, I discuss recent studies of the roles of miRNAs during the maternal-to-zygotic transition and cellular reprogramming, where they reshape transcriptional landscapes to facilitate the establishment of novel cellular states.
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Affiliation(s)
- Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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223
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Olive V, Jiang I, He L. mir-17-92, a cluster of miRNAs in the midst of the cancer network. Int J Biochem Cell Biol 2010; 42:1348-54. [PMID: 20227518 PMCID: PMC3681296 DOI: 10.1016/j.biocel.2010.03.004] [Citation(s) in RCA: 360] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 11/19/2009] [Accepted: 03/08/2010] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs (ncRNAs) that function to regulate gene expression at the post-transcriptional level. Although their functions were originally described during normal development, miRNAs have emerged as integral components of the oncogenic and tumor suppressor network, regulating nearly all cellular processes altered during tumor formation. In particular, mir-17-92, a miRNA polycistron also known as oncomir-1, is among the most potent oncogenic miRNAs. Genomic amplification and elevated expression of mir-17-92 were both found in several human B-cell lymphomas, and its enforced expression exhibits strong tumorigenic activity in multiple mouse tumor models. mir-17-92 carries out pleiotropic functions during both normal development and malignant transformation, as it acts to promote proliferation, inhibit differentiation, increase angiogenesis, and sustain cell survival. Unlike most protein coding genes, mir-17-92 is a polycistronic miRNA cluster that contains multiple miRNA components, each of which has a potential to regulate hundreds of target mRNAs. This unique gene structure of mir-17-92 may underlie the molecular basis for its pleiotropic functions in a cell type- and context-dependent manner. Here we review the recent literature on the functional studies of mir-17-92 and highlight its potential impacts on the oncogene network. These findings on mir-17-92 indicate that miRNAs are integrated components of the molecular pathways that regulate tumor development and tumor maintenance.
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Affiliation(s)
- Virginie Olive
- 535 LSA, Division of Cell and Developmental Biology, MCB Department, University of California at Berkeley, Berkeley, CA 94720-3200
| | - Iris Jiang
- 535 LSA, Division of Cell and Developmental Biology, MCB Department, University of California at Berkeley, Berkeley, CA 94720-3200
| | - Lin He
- 535 LSA, Division of Cell and Developmental Biology, MCB Department, University of California at Berkeley, Berkeley, CA 94720-3200
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224
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Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010; 11:597-610. [PMID: 20661255 DOI: 10.1038/nrg2843] [Citation(s) in RCA: 3647] [Impact Index Per Article: 243.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are a large family of post-transcriptional regulators of gene expression that are approximately 21 nucleotides in length and control many developmental and cellular processes in eukaryotic organisms. Research during the past decade has identified major factors participating in miRNA biogenesis and has established basic principles of miRNA function. More recently, it has become apparent that miRNA regulators themselves are subject to sophisticated control. Many reports over the past few years have reported the regulation of miRNA metabolism and function by a range of mechanisms involving numerous protein-protein and protein-RNA interactions. Such regulation has an important role in the context-specific functions of miRNAs.
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Affiliation(s)
- Jacek Krol
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
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225
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Svoboda P, Flemr M. The role of miRNAs and endogenous siRNAs in maternal-to-zygotic reprogramming and the establishment of pluripotency. EMBO Rep 2010; 11:590-7. [PMID: 20651740 DOI: 10.1038/embor.2010.102] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 06/18/2010] [Indexed: 12/18/2022] Open
Abstract
RNA silencing is a complex of mechanisms that regulate gene expression through small RNA molecules. The microRNA (miRNA) pathway is the most common of these in mammals. Genome-encoded miRNAs suppress translation in a sequence-specific manner and facilitate shifts in gene expression during developmental transitions. Here, we discuss the role of miRNAs in oocyte-to-zygote transition and in the control of pluripotency. Existing data suggest a common principle involving miRNAs in defining pluripotent and differentiated cells. RNA silencing pathways also rapidly evolve, resulting in many unique features of RNA silencing in different taxonomic groups. This is exemplified in the mouse model of oocyte-to-zygote transition, in which the endogenous RNA interference pathway has acquired a novel role in regulating protein-coding genes, while the miRNA pathway has become transiently suppressed.
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Affiliation(s)
- Petr Svoboda
- Institute of Molecular Genetics AS CR, Praha, Czech Republic.
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226
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Giner A, Lakatos L, García-Chapa M, López-Moya JJ, Burgyán J. Viral protein inhibits RISC activity by argonaute binding through conserved WG/GW motifs. PLoS Pathog 2010; 6:e1000996. [PMID: 20657820 PMCID: PMC2904775 DOI: 10.1371/journal.ppat.1000996] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/11/2010] [Indexed: 11/24/2022] Open
Abstract
RNA silencing is an evolutionarily conserved sequence-specific gene-inactivation system that also functions as an antiviral mechanism in higher plants and insects. To overcome antiviral RNA silencing, viruses express silencing-suppressor proteins. These viral proteins can target one or more key points in the silencing machinery. Here we show that in Sweet potato mild mottle virus (SPMMV, type member of the Ipomovirus genus, family Potyviridae), the role of silencing suppressor is played by the P1 protein (the largest serine protease among all known potyvirids) despite the presence in its genome of an HC-Pro protein, which, in potyviruses, acts as the suppressor. Using in vivo studies we have demonstrated that SPMMV P1 inhibits si/miRNA-programmed RISC activity. Inhibition of RISC activity occurs by binding P1 to mature high molecular weight RISC, as we have shown by immunoprecipitation. Our results revealed that P1 targets Argonaute1 (AGO1), the catalytic unit of RISC, and that suppressor/binding activities are localized at the N-terminal half of P1. In this region three WG/GW motifs were found resembling the AGO-binding linear peptide motif conserved in metazoans and plants. Site-directed mutagenesis proved that these three motifs are absolutely required for both binding and suppression of AGO1 function. In contrast to other viral silencing suppressors analyzed so far P1 inhibits both existing and de novo formed AGO1 containing RISC complexes. Thus P1 represents a novel RNA silencing suppressor mechanism. The discovery of the molecular bases of P1 mediated silencing suppression may help to get better insight into the function and assembly of the poorly explored multiprotein containing RISC. RNA silencing is an evolutionarily conserved sequence-specific gene-inactivation system that also functions as a major antiviral mechanism in higher plants and insects. Viral RNAs are processed by Dicer-like proteins into small interfering (si) RNAs, which trigger the RNA-induced silencing complex (RISC) assembly. Then siRNA loaded RISC inactivates cognate viral RNA. However, viral silencing suppressors evolved to counteract with RNA silencing targeting one or more key points in the silencing machinery. Here we show that in Sweet potato mild mottle virus, the role of silencing suppressor is played by P1 protein and it works by inhibiting si/miRNA-loaded RISC through targeting Argonaute 1 (AGO1). We confirmed using immunoprecipitation and in vitro binding assays that the interaction between P1 and small RNA loaded AGO1 is specific and direct. The suppression activity mapped to the N-terminal part of P1 containing three WG/GW motifs that resemble the AGO-binding linear peptide motif conserved in metazoans and plants. Site-directed mutagenesis proved that these three motifs are essential for both binding and suppression of AGO1 function. P1 protein is the only silencing suppressor identified so far that inhibits active RISC and this is the first demonstration of a WG/GW protein having negative effect on RNA silencing.
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Affiliation(s)
- Ana Giner
- Centre for Research in Agricultural Genomics, CRAG, CSIC-IRTA-UAB, Barcelona, Spain
| | - Lóránt Lakatos
- Agricultural Biotechnology Centre, Gödöllő, Hungary
- * E-mail: (LL); (JJLM); or (JB)
| | | | - Juan José López-Moya
- Centre for Research in Agricultural Genomics, CRAG, CSIC-IRTA-UAB, Barcelona, Spain
- * E-mail: (LL); (JJLM); or (JB)
| | - József Burgyán
- Agricultural Biotechnology Centre, Gödöllő, Hungary
- Instituto di Virologia Vegetale, Torino, Italy
- * E-mail: (LL); (JJLM); or (JB)
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227
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James V, Zhang Y, Foxler DE, de Moor CH, Kong YW, Webb TM, Self TJ, Feng Y, Lagos D, Chu CY, Rana TM, Morley SJ, Longmore GD, Bushell M, Sharp TV. LIM-domain proteins, LIMD1, Ajuba, and WTIP are required for microRNA-mediated gene silencing. Proc Natl Acad Sci U S A 2010; 107:12499-504. [PMID: 20616046 PMCID: PMC2906597 DOI: 10.1073/pnas.0914987107] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In recent years there have been major advances with respect to the identification of the protein components and mechanisms of microRNA (miRNA) mediated silencing. However, the complete and precise repertoire of components and mechanism(s) of action remain to be fully elucidated. Herein we reveal the identification of a family of three LIM domain-containing proteins, LIMD1, Ajuba and WTIP (Ajuba LIM proteins) as novel mammalian processing body (P-body) components, which highlight a novel mechanism of miRNA-mediated gene silencing. Furthermore, we reveal that LIMD1, Ajuba, and WTIP bind to Ago1/2, RCK, Dcp2, and eIF4E in vivo, that they are required for miRNA-mediated, but not siRNA-mediated gene silencing and that all three proteins bind to the mRNA 5' m(7)GTP cap-protein complex. Mechanistically, we propose the Ajuba LIM proteins interact with the m(7)GTP cap structure via a specific interaction with eIF4E that prevents 4EBP1 and eIF4G interaction. In addition, these LIM-domain proteins facilitate miRNA-mediated gene silencing by acting as an essential molecular link between the translationally inhibited eIF4E-m(7)GTP-5(')cap and Ago1/2 within the miRISC complex attached to the 3'-UTR of mRNA, creating an inhibitory closed-loop complex.
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Affiliation(s)
- Victoria James
- School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Yining Zhang
- School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Daniel E. Foxler
- School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Cornelia H. de Moor
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Yi Wen Kong
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Thomas M. Webb
- School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Tim J. Self
- Institute of Cell Signalling, School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Yungfeng Feng
- Washington University School of Medicine, Campus Box 8086, Room 770 McDonnell Sciences Building, 660 South Euclid Avenue, St. Louis, MO 63110
| | - Dimitrios Lagos
- Cancer Research UK Viral Oncology Group, University College London Cancer Institute, Paul O’Gorman Building, Huntley Street, University College London, London WC1E 6BT, United Kingdom
| | - Chia-Ying Chu
- Institute of Zoology, School of Life Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Tariq M. Rana
- Program for RNA Biology, Sandford–Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037; and
| | - Simon J. Morley
- Department of Biochemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
| | - Gregory D. Longmore
- Washington University School of Medicine, Campus Box 8086, Room 770 McDonnell Sciences Building, 660 South Euclid Avenue, St. Louis, MO 63110
| | - Martin Bushell
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Tyson V. Sharp
- School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
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228
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Wahid F, Shehzad A, Khan T, Kim YY. MicroRNAs: synthesis, mechanism, function, and recent clinical trials. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:1231-43. [PMID: 20619301 DOI: 10.1016/j.bbamcr.2010.06.013] [Citation(s) in RCA: 605] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 06/30/2010] [Accepted: 06/30/2010] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are a class of small, endogenous RNAs of 21-25 nucleotides (nts) in length. They play an important regulatory role in animals and plants by targeting specific mRNAs for degradation or translation repression. Recent scientific advances have revealed the synthesis pathways and the regulatory mechanisms of miRNAs in animals and plants. miRNA-based regulation is implicated in disease etiology and has been studied for treatment. Furthermore, several preclinical and clinical trials have been initiated for miRNA-based therapeutics. In this review, the existing knowledge about miRNAs synthesis, mechanisms for regulation of the genome, and their widespread functions in animals and plants is summarized. The current status of preclinical and clinical trials regarding miRNA therapeutics is also reviewed. The recent findings in miRNA studies, summarized in this review, may add new dimensions to small RNA biology and miRNA therapeutics.
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Affiliation(s)
- Fazli Wahid
- School of life Sciences and Biotechnology, College of Natural sciences, Kyungpook National University, Buk-ku, Taegu, Korea
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229
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Dekanty A, Romero NM, Bertolin AP, Thomas MG, Leishman CC, Perez-Perri JI, Boccaccio GL, Wappner P. Drosophila genome-wide RNAi screen identifies multiple regulators of HIF-dependent transcription in hypoxia. PLoS Genet 2010; 6:e1000994. [PMID: 20585616 PMCID: PMC2891703 DOI: 10.1371/journal.pgen.1000994] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/19/2010] [Indexed: 01/08/2023] Open
Abstract
Hypoxia-inducible factors (HIFs) are a family of evolutionary conserved alpha-beta heterodimeric transcription factors that induce a wide range of genes in response to low oxygen tension. Molecular mechanisms that mediate oxygen-dependent HIF regulation operate at the level of the alpha subunit, controlling protein stability, subcellular localization, and transcriptional coactivator recruitment. We have conducted an unbiased genome-wide RNA interference (RNAi) screen in Drosophila cells aimed to the identification of genes required for HIF activity. After 3 rounds of selection, 30 genes emerged as critical HIF regulators in hypoxia, most of which had not been previously associated with HIF biology. The list of genes includes components of chromatin remodeling complexes, transcription elongation factors, and translational regulators. One remarkable hit was the argonaute 1 (ago1) gene, a central element of the microRNA (miRNA) translational silencing machinery. Further studies confirmed the physiological role of the miRNA machinery in HIF–dependent transcription. This study reveals the occurrence of novel mechanisms of HIF regulation, which might contribute to developing novel strategies for therapeutic intervention of HIF–related pathologies, including heart attack, cancer, and stroke. Adaptation of cells to low oxygen (hypoxia) is a physiological response related to important diseases, including heart attacks, stroke, cancer, and diabetes. The mechanisms that mediate adaptation to hypoxia in humans are almost identical to those operating in diverse animal species, including mice, worms, and insects. The master regulator of cellular responses to hypoxia is a transcription factor named HIF, which induces a set of genes that mediate adaptation to oxygen starvation. Although it is known that regulation of HIF occurs mainly at the level of protein degradation and transcriptional coactivator recruitment, a comprehensive screen for HIF regulators has not been performed before. In this work, we have conducted an RNAi-based screen of the genome of the fruit fly Drosophila melanogaster, searching for genes that are required for HIF activity. This screen carried out in a cell culture system led to the definition of 30 critical regulators of HIF, most of which have not been associated with hypoxia biology before. The hits of the screen included components of chromatin remodeling complexes, transcription elongation factors, and translational regulators. Our results open the possibility of performing detailed studies on HIF regulation that may lead to novel therapeutic strategies for important human diseases.
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Affiliation(s)
- Andrés Dekanty
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nuria M. Romero
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Agustina P. Bertolin
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - María G. Thomas
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | | | | | - Graciela L. Boccaccio
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Pablo Wappner
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- * E-mail:
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230
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Miller BH, Wahlestedt C. MicroRNA dysregulation in psychiatric disease. Brain Res 2010; 1338:89-99. [PMID: 20303342 PMCID: PMC2891055 DOI: 10.1016/j.brainres.2010.03.035] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Revised: 02/04/2010] [Accepted: 03/11/2010] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs that individually regulate up to several hundred genes, and collectively may regulate as much as two-thirds of the transcriptome. Recent evidence supports a role for miRNA dysregulation in psychiatric and neurological disorders, including schizophrenia, bipolar disorder, and autism. Small changes in miRNA expression can fine-tune the expression of multiple genes within a biological network, suggesting that miRNA dysregulation may underlie many of the molecular changes observed in psychiatric disease, and that therapeutic regulation of miRNA levels may represent a novel treatment option.
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Affiliation(s)
- Brooke H. Miller
- Department of Neuroscience, Scripps Florida, Jupiter, FL 33458 USA
| | - Claes Wahlestedt
- Department of Neuroscience, Scripps Florida, Jupiter, FL 33458 USA
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231
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Crystal structure and ligand binding of the MID domain of a eukaryotic Argonaute protein. EMBO Rep 2010; 11:522-7. [PMID: 20539312 PMCID: PMC2897117 DOI: 10.1038/embor.2010.81] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 05/10/2010] [Accepted: 05/12/2010] [Indexed: 11/08/2022] Open
Abstract
Argonaute (AGO) proteins are core components of RNA-induced silencing complexes and have essential roles in RNA-mediated gene silencing. They are characterized by a bilobal architecture, consisting of one lobe containing the amino-terminal and PAZ domains and another containing the MID and PIWI domains. Except for the PAZ domain, structural information on eukaryotic AGO domains is not yet available. In this study, we report the crystal structure of the MID domain of the eukaryotic AGO protein QDE-2 from Neurospora crassa. This domain adopts a Rossmann-like fold and recognizes the 5'-terminal nucleotide of a guide RNA in a manner similar to its prokaryotic counterparts. The 5'-nucleotide-binding site shares common residues with a second, adjacent ligand-binding site, suggesting a mechanism for the cooperative binding of ligands to the MID domain of eukaryotic AGOs.
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232
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Hurschler BA, Ding XC, Grosshans H. Translational control of endogenous microRNA target genes in C. elegans. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2010; 50:21-40. [PMID: 19841879 DOI: 10.1007/978-3-642-03103-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
lin-4 and let-7 are the founding members of the large microRNA (miRNA) family of regulatory RNAs and were originally identified as components of a C. elegans developmental pathway that controls temporal cell fates. Consistent with their pioneering role, lin-4 and let-7 were studied widely as "model miRNAs" in efforts to reveal the mode of action of miRNAs. Early work on lin-4 thus established a paradigm that miRNAs inhibit translation of their target mRNAs at a step downstream from initiation, without affecting mRNA stability. Although some studies on mammalian miRNAs in cell culture reached similar conclusions, most of those studies indicated that miRNAs repressed translation initiation and frequently also promoted target mRNA degradation. We will discuss here what is known about modes of miRNA target gene repression in C. elegans, highlighting recent work that demonstrates that both mRNA degradation and repression of translation initiation are mechanisms employed in vivo by let-7 and, unexpectedly, lin-4 to silence their endogenous targets. We will also discuss the roles of the GW182 homologous AIN-1 and AIN-2 proteins in this process.
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Affiliation(s)
- Benjamin A Hurschler
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, WRO-1066.1.38, CH-4002, Basel, Switzerland
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233
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Chekulaeva M, Parker R, Filipowicz W. The GW/WG repeats of Drosophila GW182 function as effector motifs for miRNA-mediated repression. Nucleic Acids Res 2010; 38:6673-83. [PMID: 20530530 PMCID: PMC2965232 DOI: 10.1093/nar/gkq501] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The control of messenger RNA (mRNA) function by micro RNAs (miRNAs) in animal cells requires the GW182 protein. GW182 is recruited to the miRNA repression complex via interaction with Argonaute protein, and functions downstream to repress protein synthesis. Interaction with Argonaute is mediated by GW/WG repeats, which are conserved in many Argonaute-binding proteins involved in RNA interference and miRNA silencing, from fission yeast to mammals. GW182 contains at least three effector domains that function to repress target mRNA. Here, we analyze the functions of the N-terminal GW182 domain in repression and Argonaute1 binding, using tethering and immunoprecipitation assays in Drosophila cultured cells. We demonstrate that its function in repression requires intact GW/WG repeats, but does not involve interaction with the Argonaute1 protein, and is independent of the mRNA polyadenylation status. These results demonstrate a novel role for the GW/WG repeats as effector motifs in miRNA-mediated repression.
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Affiliation(s)
- Marina Chekulaeva
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland.
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234
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Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA Translation and Stability by microRNAs. Annu Rev Biochem 2010; 79:351-79. [PMID: 20533884 DOI: 10.1146/annurev-biochem-060308-103103] [Citation(s) in RCA: 2427] [Impact Index Per Article: 161.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marc Robert Fabian
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland;
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235
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Abstract
miRNAs post-transcriptionally regulate gene expression in many eukaryotes and thereby affect a wide range of biological processes. GW182 is a key factor in translation repression and mRNA degradation by miRNAs. In this study we investigate the potential interaction of GW182 and translation or mRNA degradation factors in Drosophila S2 cells. We have identified the decapping activator HP at as a novel factor co-purifying with GW182. Furthermore, we show that the C-terminal domain of GW182, important for gene silencing, is sufficient to form a complex with HP at. Our findings implicate a potential interaction of the miRNA effector component GW182 with the decapping machinery.
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Affiliation(s)
- Elisabeth Jäger
- Max F. Perutz Laboratories, University of Vienna, Department of Biochemistry and Cell Biology, Dr. Bohr-Gasse 9/5, A-1030 Vienna, Austria
| | - Silke Dorner
- Max F. Perutz Laboratories, University of Vienna, Department of Biochemistry and Cell Biology, Dr. Bohr-Gasse 9/5, A-1030 Vienna, Austria
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236
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Minshall N, Allison R, Marnef A, Wilczynska A, Standart N. Translational control assessed using the tethered function assay in Xenopus oocytes. Methods 2010; 51:165-9. [PMID: 20188836 DOI: 10.1016/j.ymeth.2010.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 02/18/2010] [Accepted: 02/20/2010] [Indexed: 10/19/2022] Open
Abstract
The tethered function assay is a method designed to address the role of an RNA-binding protein upon the metabolism of a reporter RNA. The basis of this assay is to artificially tether a test protein to a reporter mRNA by employing an unrelated bacteriophage MS2 or lambda N RNA-protein interaction, and to assess the effects of the test protein on the reporter RNA. In this chapter, we first discuss the principles and validity of the tethered function approach, drawing on appropriate examples from several cell types and of many proteins that regulate RNA in a variety of processes, including RNA processing (splicing, polyadenylation/deadenylation, decay), localisation and protein synthesis. Secondly, we will focus on the use of this approach to monitor translational activation and repression in Xenopus oocytes, giving a detailed protocol, and discussing possible optimizations we have explored.
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Affiliation(s)
- Nicola Minshall
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
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237
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Roberts R, Steer CJ. Disease Genes and Gene Regulation by microRNAs. J Cardiovasc Transl Res 2010; 3:169-72. [DOI: 10.1007/s12265-010-9186-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 04/05/2010] [Indexed: 01/08/2023]
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238
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Abstract
The coding sequence of a protein must contain the information required for the canonical amino acid sequence. However, the redundancy of the genetic code creates potential for embedding other types of information within coding regions as well. In a genome-wide computational screen for functional motifs within coding regions based on evolutionary conservation, highly conserved motifs included some expected motifs, some novel motifs and coding region target sites for known microRNAs, which are generally presumed to target 3' untranslated regions (UTRs) (www.SiteSifter.org). We report here an analysis of published proteomics experiments that further support a functional role for coding region microRNA binding sites, though the effects are weaker than for sites in the 3' UTR. We also demonstrate a positional bias with greater conservation for sites at the end of the coding region, and the beginning and end of the 3' UTR. An increased effectiveness of microRNA binding sites at the 3' end of transcripts could reflect proximity to the poly(A) tail or interactions with the 5' terminal 7mGpppN "cap", which is physically adjacent to this region once the message is circularized. The effectiveness of 3' UTR sites could reflect a cooperative role for RNA binding proteins. Finally, increased microRNA conservation near the stop codon suggests to us the possible involvement of proteins that execute nonsense-mediated decay, since this process is activated by tagging of termination codons with factors that induce transcript degradation.
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239
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Role of GW182 proteins and PABPC1 in the miRNA pathway: a sense of déjà vu. Nat Rev Mol Cell Biol 2010; 11:379-84. [PMID: 20379206 DOI: 10.1038/nrm2885] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
GW182 proteins have emerged as key components of microRNA (miRNA) silencing complexes in animals. Although the precise molecular function of GW182 proteins is not fully understood, new findings indicate that they act as poly(A)-binding protein (PABP)-interacting proteins (PAIPs) that promote gene silencing, at least in part, by interfering with cytoplasmic PABP1 (PABPC1) function during translation and mRNA stabilization. This recent discovery paves the way for future studies of miRNA silencing mechanisms.
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240
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Fischer SEJ. Small RNA-mediated gene silencing pathways in C. elegans. Int J Biochem Cell Biol 2010; 42:1306-15. [PMID: 20227516 DOI: 10.1016/j.biocel.2010.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 09/23/2009] [Accepted: 03/08/2010] [Indexed: 12/14/2022]
Abstract
Small RNA pathways, including the RNA interference (RNAi) pathway and the microRNA (miRNA) pathway, regulate gene expression, defend against transposable elements and viruses, and, in some organisms, guide genome rearrangements. The nematode Caenorhabditis elegans (C. elegans) has been at the forefront of small RNA research; not only were the first miRNAs and their function as regulators of gene expression discovered in C. elegans, but also double-stranded RNA-induced gene silencing by RNAi was discovered in this model organism. Since then, genetic and RNAi-mediated screens, candidate gene approaches, and biochemical studies have uncovered numerous factors in the small RNA pathways and painted a rich palette of interacting pathways. Here we review the different small RNAs that have been discovered in C. elegans and discuss our understanding of their biogenesis pathways and mechanisms of action.
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Affiliation(s)
- Sylvia E J Fischer
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114, USA.
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241
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Johnston M, Geoffroy MC, Sobala A, Hay R, Hutvagner G. HSP90 protein stabilizes unloaded argonaute complexes and microscopic P-bodies in human cells. Mol Biol Cell 2010; 21:1462-9. [PMID: 20237157 PMCID: PMC2861606 DOI: 10.1091/mbc.e09-10-0885] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The cancer drug geldanamycin, an HSP90 inhibitor, decreases the stability of key components of the miRNA regulatory pathway, the efficacy of siRNAs, and the formation of P-bodies without affecting endogenous miRNA function. Key components of the miRNA-mediated gene regulation pathway are localized in cytoplasmic processing bodies (P-bodies). Mounting evidence suggests that the presence of microscopic P-bodies are not always required for miRNA-mediated gene regulation. Here we have shown that geldanamycin, a well-characterized HSP90 inhibitor, abolishes P-bodies and significantly reduces Argonaute and GW182 protein levels but does not affect the miRNA level and the efficiency of miRNA-mediated gene repression; however, it significantly impairs siRNA loading and the efficacy of exogenous siRNA. Our data suggests that HSP90 protein chaperones Argonautes before binding RNA and may facilitate efficient loading of small RNA.
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Affiliation(s)
- Michael Johnston
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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242
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Wilson R, Purcell D, Netter HJ, Revill PA. Does RNA interference provide new hope for control of chronic hepatitis B infection? Antivir Ther 2010; 14:879-89. [PMID: 19918092 DOI: 10.3851/imp1424] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hepatitis B virus (HBV) infection is a global human health problem, with an estimated 350 million people having chronic hepatitis B (CHB) infection worldwide. The majority of infections acquired during adulthood are resolved without intervention; however, infections acquired at birth or during early childhood have a 90% chance of progressing to CHB, leading to a host of adverse effects on the liver, including cirrhosis and cancer. CHB is currently treated with a combination of cytokines and/or nucleoside/nucleotide analogues; however, adverse side effects to cytokine therapy and the selection of resistance mutations to nucleoside analogues often abrogate the efficacy of treatment. The recent discovery that small interfering RNA and microRNA are active in mammalian cells suggests it might be possible to supplement existing HBV therapies with small RNA-based therapeutic(s).
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Affiliation(s)
- Rachel Wilson
- Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
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243
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Jackson RJ, Hellen CUT, Pestova TV. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 2010; 11:113-27. [PMID: 20094052 DOI: 10.1038/nrm2838] [Citation(s) in RCA: 1999] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein synthesis is principally regulated at the initiation stage (rather than during elongation or termination), allowing rapid, reversible and spatial control of gene expression. Progress over recent years in determining the structures and activities of initiation factors, and in mapping their interactions in ribosomal initiation complexes, have advanced our understanding of the complex translation initiation process. These developments have provided a solid foundation for studying the regulation of translation initiation by mechanisms that include the modulation of initiation factor activity (which affects almost all scanning-dependent initiation) and through sequence-specific RNA-binding proteins and microRNAs (which affect individual mRNAs).
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Affiliation(s)
- Richard J Jackson
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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244
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Jinek M, Fabian MR, Coyle SM, Sonenberg N, Doudna JA. Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation. Nat Struct Mol Biol 2010; 17:238-40. [PMID: 20098421 PMCID: PMC2920127 DOI: 10.1038/nsmb.1768] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 12/23/2009] [Indexed: 12/28/2022]
Abstract
GW182-family proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells. Here we show that a conserved motif in the human GW182 paralog TNRC6C interacts with the C-terminal domain of polyadenylate binding protein 1 (PABC) and present the crystal structure of the complex. Mutations at the complex interface impair mRNA deadenylation in mammalian cell extracts, suggesting that the GW182-PABC interaction contributes to microRNA-mediated gene silencing.
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Affiliation(s)
- Martin Jinek
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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245
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Flemr M, Ma J, Schultz RM, Svoboda P. P-body loss is concomitant with formation of a messenger RNA storage domain in mouse oocytes. Biol Reprod 2010; 82:1008-17. [PMID: 20075394 DOI: 10.1095/biolreprod.109.082057] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In mammalian somatic cells, several pathways that converge on deadenylation, decapping, and 5'-3' degradation are found in cytoplasmic foci known as P-bodies. Because controlled mRNA stability is essential for oocyte-to-zygote transition, we examined the dynamics of P-body components in mouse oocytes. We report that oocyte growth is accompanied by loss of P-bodies and a subcortical accumulation of several RNA-binding proteins, including DDX6, CPEB, YBX2 (MSY2), and the exon junction complex. These proteins form transient RNA-containing aggregates in fully grown oocytes with a surrounded nucleolus chromatin configuration. These aggregates disperse during oocyte maturation, consistent with recruitment of maternal mRNAs that occurs during this time. In contrast, levels of DCP1A are low during oocyte growth, and DCP1A does not colocalize with DDX6 in the subcortical aggregates. The amount of DCP1A markedly increases during meiosis, which correlates with the first wave of destabilization of maternal mRNAs. We propose that the cortex of growing oocytes serves as an mRNA storage compartment, which contains a novel type of RNA granule related to P-bodies.
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Affiliation(s)
- Matyas Flemr
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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246
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Djuranovic S, Zinchenko MK, Hur JK, Nahvi A, Brunelle JL, Rogers EJ, Green R. Allosteric regulation of Argonaute proteins by miRNAs. Nat Struct Mol Biol 2010; 17:144-50. [PMID: 20062058 DOI: 10.1038/nsmb.1736] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 11/16/2009] [Indexed: 01/11/2023]
Abstract
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) bind to Argonaute (AGO) family proteins to form a related set of effector complexes that have diverse roles in post-transcriptional gene regulation throughout the eukaryotic lineage. Here sequence and structural analysis of the MID domain of the AGO proteins identified similarities with a family of allosterically regulated bacterial ligand-binding domains. We used in vitro and in vivo approaches to show that certain AGO proteins (those involved in translational repression) have conserved this functional allostery between two distinct sites, one involved in binding miRNA-target duplex and the other in binding the 5' cap feature (m(7)GpppG) of eukaryotic mRNAs. This allostery provides an explanation for how miRNA-bound effector complexes may avoid indiscriminate repressive action (mediated through binding interactions with the cap) before full target recognition.
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Affiliation(s)
- Sergej Djuranovic
- Howard Hughes Medical Institute and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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247
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Beilharz TH, Humphreys DT, Preiss T. miRNA Effects on mRNA closed-loop formation during translation initiation. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2010; 50:99-112. [PMID: 19841884 DOI: 10.1007/978-3-642-03103-8_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A flurry of recent studies, carried out primarily in transfected cells or in vitro translation systems, have attempted to reveal the molecular means by which animal microRNAs (miRNAs) attenuate mRNA translation. Despite these intense efforts it has not yet been possible to derive a consensus model for such a mechanism. Here we summarise our own experimental contributions to this topic, which led us to propose that miRNAs control early translation initiation by affecting eukaryotic initiation factor 4E/cap structure and poly(A) tail function, and place them in a current context of this rapidly moving and challenging field.
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Affiliation(s)
- Traude H Beilharz
- Molecular Genetics Division, Victor Chang Cardiac Research Institute (VCCRI), Darlinghurst, Sydney, NSW, 2010, Australia
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248
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Ketting RF. microRNA Biogenesis and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 700:1-14. [DOI: 10.1007/978-1-4419-7823-3_1] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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249
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Fabian MR, Sundermeier TR, Sonenberg N. Understanding How miRNAs Post-Transcriptionally Regulate Gene Expression. MIRNA REGULATION OF THE TRANSLATIONAL MACHINERY 2010; 50:1-20. [DOI: 10.1007/978-3-642-03103-8_1] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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250
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Cao Q, Padmanabhan K, Richter JD. Pumilio 2 controls translation by competing with eIF4E for 7-methyl guanosine cap recognition. RNA (NEW YORK, N.Y.) 2010; 16:221-7. [PMID: 19933321 PMCID: PMC2802031 DOI: 10.1261/rna.1884610] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Pumilio 2 (Pum2) interacts with the 3' UTR-containing pumilio binding element (PBE) of RINGO/SPY mRNA to repress translation in Xenopus oocytes. Here, we show that Pum2 also binds directly to the 5' 7mG cap structure; in so doing, it precludes eIF4E from binding the cap. Using deletion analysis, we have mapped the cap interaction domain of Pum2 to the amino terminus of the protein and identified a conserved tryptophan residue that mediates this specific interaction. Reporter mRNA-based assays demonstrate that Pum2 requires the conserved tryptophan to repress translation in injected Xenopus oocytes. Thus, in addition to its suggested role in regulating poly(A) tail length and mRNA stability, our results suggest that vertebrate Pumilio can repress translation by blocking the assembly of the essential initiation complex on the cap.
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Affiliation(s)
- Quiping Cao
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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