51
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Niinuma S, Fukaya T, Tomari Y. CCR4 and CAF1 deadenylases have an intrinsic activity to remove the post-poly(A) sequence. RNA (NEW YORK, N.Y.) 2016; 22:1550-1559. [PMID: 27484313 PMCID: PMC5029453 DOI: 10.1261/rna.057679.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/21/2016] [Indexed: 05/31/2023]
Abstract
MicroRNAs (miRNAs) recruit the CCR4-NOT complex, which contains two deadenylases, CCR4 and CAF1, to promote shortening of the poly(A) tail. Although both CCR4 and CAF1 generally have a strong preference for poly(A) RNA substrates, it has been reported from yeast to humans that they can also remove non-A residues in vitro to various degrees. However, it remains unknown how CCR4 and CAF1 remove non-A sequences. Herein we show that Drosophila miRNAs can promote the removal of 3'-terminal non-A residues in an exonucleolytic manner, but only if an upstream poly(A) sequence exists. This non-A removing reaction is directly catalyzed by both CCR4 and CAF1 and depends on the balance between the length of the internal poly(A) sequence and that of the downstream non-A sequence. These results suggest that the CCR4-NOT complex has an intrinsic activity to remove the 3'-terminal non-A modifications downstream from the poly(A) tail.
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Affiliation(s)
- Sho Niinuma
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, JapanDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Fukaya
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, JapanDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, JapanDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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52
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Powers JT, Tsanov KM, Pearson DS, Roels F, Spina CS, Ebright R, Seligson M, de Soysa Y, Cahan P, Theiβen J, Tu HC, Han A, Kurek KC, LaPier GS, Osborne JK, Ross SJ, Cesana M, Collins JJ, Berthold F, Daley GQ. Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma. Nature 2016; 535:246-51. [PMID: 27383785 PMCID: PMC4947006 DOI: 10.1038/nature18632] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/08/2016] [Indexed: 02/06/2023]
Abstract
Poor prognosis in neuroblastoma is associated with genetic amplification of MYCN. MYCN is itself a target of let-7, a tumour suppressor family of microRNAs implicated in numerous cancers. LIN28B, an inhibitor of let-7 biogenesis, is overexpressed in neuroblastoma and has been reported to regulate MYCN. Here we show, however, that LIN28B is dispensable in MYCN-amplified neuroblastoma cell lines, despite de-repression of let-7. We further demonstrate that MYCN messenger RNA levels in amplified disease are exceptionally high and sufficient to sponge let-7, which reconciles the dispensability of LIN28B. We found that genetic loss of let-7 is common in neuroblastoma, inversely associated with MYCN amplification, and independently associated with poor outcomes, providing a rationale for chromosomal loss patterns in neuroblastoma. We propose that let-7 disruption by LIN28B, MYCN sponging, or genetic loss is a unifying mechanism of neuroblastoma development with broad implications for cancer pathogenesis.
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Affiliation(s)
- John T Powers
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Kaloyan M Tsanov
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Daniel S Pearson
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Frederik Roels
- Department of Pediatric Oncology, University Hospital Koln, Cologne, Germany
| | - Catherine S Spina
- Department of Biological Engineering, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard; Wyss Institute for Biologically Inspired Engineering; Boston, MA 02115, USA
| | - Richard Ebright
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Marc Seligson
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Yvanka de Soysa
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Patrick Cahan
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Jessica Theiβen
- Department of Pediatric Oncology, University Hospital Koln, Cologne, Germany
| | - Ho-Chou Tu
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Areum Han
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Kyle C Kurek
- Department of Pathology, Boston Children’s Hospital, Boston MA 02215, USA
| | - Grace S LaPier
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Jihan K Osborne
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Samantha J Ross
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Marcella Cesana
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard; Wyss Institute for Biologically Inspired Engineering; Boston, MA 02115, USA
| | - Frank Berthold
- Department of Pediatric Oncology, University Hospital Koln, Cologne, Germany
| | - George Q Daley
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
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53
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Sokolowski TR, Walczak AM, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. Phys Rev E 2016; 93:022404. [PMID: 26986359 PMCID: PMC5221721 DOI: 10.1103/physreve.93.022404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 11/07/2022]
Abstract
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression.
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Affiliation(s)
- Thomas R. Sokolowski
- Institute of Science and Technology Austria, Am Campus 1, A-3400
Klosterneuburg, Austria
| | - Aleksandra M. Walczak
- CNRS-Laboratoire de Physique Théorique de
l’École Normale Supérieure, 24 rue Lhomond, F-75005 Paris,
France
| | - William Bialek
- Joseph Henry Laboratories of Physics, Lewis-Sigler Institute for
Integrative Genomics, Princeton University Princeton, New Jersey 08544, USA
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Am Campus 1, A-3400
Klosterneuburg, Austria
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54
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Iwakawa HO, Tomari Y. The Functions of MicroRNAs: mRNA Decay and Translational Repression. Trends Cell Biol 2015; 25:651-665. [PMID: 26437588 DOI: 10.1016/j.tcb.2015.07.011] [Citation(s) in RCA: 552] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs, which regulate complementary mRNAs by inducing translational repression and mRNA decay. Although this dual repression system seems to operate in both animals and plants, genetic and biochemical studies suggest that the mechanism underlying the miRNA-mediated silencing is different in the two kingdoms. Here, we review the recent progress in our understanding of how miRNAs mediate translational repression and mRNA decay, and discuss the contributions of the two silencing modes to the overall silencing effect in both kingdoms.
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Affiliation(s)
- Hiro-Oki Iwakawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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55
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Karaiskos S, Naqvi AS, Swanson KE, Grigoriev A. Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets. Biol Direct 2015; 10:51. [PMID: 26374501 PMCID: PMC4572633 DOI: 10.1186/s13062-015-0081-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 09/07/2015] [Indexed: 12/20/2022] Open
Abstract
Background Development of sequencing technologies and supporting computation enable discovery of small RNA molecules that previously escaped detection or were ignored due to low count numbers. While the focus in the analysis of small RNA libraries has been primarily on microRNAs (miRNAs), recent studies have reported findings of fragments of transfer RNAs (tRFs) across a range of organisms. Results Here we describe Drosophila melanogaster tRFs, which appear to have a number of structural and functional features similar to those of miRNAs but are less abundant. As is the case with miRNAs, (i) tRFs seem to have distinct isoforms preferentially originating from 5’ or 3’ end of a precursor molecule (in this case, tRNA), (ii) ends of tRFs appear to contain short “seed” sequences matching conserved regions across 12 Drosophila genomes, preferentially in 3’ UTRs but also in introns and exons; (iii) tRFs display specific isoform loading into Ago1 and Ago2 and thus likely function in RISC complexes; (iii) levels of loading in Ago1 and Ago2 differ considerably; and (iv) both tRF expression and loading appear to be age-dependent, indicating potential regulatory changes from young to adult organisms. Conclusions We found that Drosophila tRF reads mapped to both nuclear and mitochondrial tRNA genes for all 20 amino acids, while previous studies have usually reported fragments from only a few tRNAs. These tRFs show a number of similarities with miRNAs, including seed sequences. Based on complementarity with conserved Drosophila regions we identified such seed sequences and their possible targets with matches in the 3’UTR regions. Strikingly, the potential target genes of the most abundant tRFs show significant Gene Ontology enrichment in development and neuronal function. The latter suggests that involvement of tRFs in the RNA interfering pathway may play a role in brain activity or brain changes with age. Reviewers This article was reviewed by Eugene Koonin, Neil Smalheiser and Alexander Kel. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0081-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Spyros Karaiskos
- Department of BiologyCenter for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA.
| | - Ammar S Naqvi
- Department of BiologyCenter for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA.
| | - Karl E Swanson
- Department of BiologyCenter for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA.
| | - Andrey Grigoriev
- Department of BiologyCenter for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA.
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56
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Jonas S, Izaurralde E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet 2015; 16:421-33. [PMID: 26077373 DOI: 10.1038/nrg3965] [Citation(s) in RCA: 1400] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are a conserved class of small non-coding RNAs that assemble with Argonaute proteins into miRNA-induced silencing complexes (miRISCs) to direct post-transcriptional silencing of complementary mRNA targets. Silencing is accomplished through a combination of translational repression and mRNA destabilization, with the latter contributing to most of the steady-state repression in animal cell cultures. Degradation of the mRNA target is initiated by deadenylation, which is followed by decapping and 5'-to-3' exonucleolytic decay. Recent work has enhanced our understanding of the mechanisms of silencing, making it possible to describe in molecular terms a continuum of direct interactions from miRNA target recognition to mRNA deadenylation, decapping and 5'-to-3' degradation. Furthermore, an intricate interplay between translational repression and mRNA degradation is emerging.
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Affiliation(s)
- Stefanie Jonas
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany
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57
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Besnard-Guérin C, Jacquier C, Pidoux J, Deddouche S, Antoniewsk C. The cricket paralysis virus suppressor inhibits microRNA silencing mediated by the Drosophila Argonaute-2 protein. PLoS One 2015; 10:e0120205. [PMID: 25793377 PMCID: PMC4368812 DOI: 10.1371/journal.pone.0120205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/20/2015] [Indexed: 11/25/2022] Open
Abstract
Small RNAs are potent regulators of gene expression. They also act in defense pathways against invading nucleic acids such as transposable elements or viruses. To counteract these defenses, viruses have evolved viral suppressors of RNA silencing (VSRs). Plant viruses encoded VSRs interfere with siRNAs or miRNAs by targeting common mediators of these two pathways. In contrast, VSRs identified in insect viruses to date only interfere with the siRNA pathway whose effector Argonaute protein is Argonaute-2 (Ago-2). Although a majority of Drosophila miRNAs exerts their silencing activity through their loading into the Argonaute-1 protein, recent studies highlighted that a fraction of miRNAs can be loaded into Ago-2, thus acting as siRNAs. In light of these recent findings, we re-examined the role of insect VSRs on Ago-2-mediated miRNA silencing in Drosophila melanogaster. Using specific reporter systems in cultured Schneider-2 cells and transgenic flies, we showed here that the Cricket Paralysis virus VSR CrPV1-A but not the Flock House virus B2 VSR abolishes silencing by miRNAs loaded into the Ago-2 protein. Thus, our results provide the first evidence that insect VSR have the potential to directly interfere with the miRNA silencing pathway.
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Affiliation(s)
- Corinne Besnard-Guérin
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
| | - Caroline Jacquier
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
| | - Josette Pidoux
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
| | - Safia Deddouche
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
| | - Christophe Antoniewsk
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
- * E-mail:
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58
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Corduan A, Plé H, Laffont B, Wallon T, Plante I, Landry P, Provost P. Dissociation of SERPINE1 mRNA from the translational repressor proteins Ago2 and TIA-1 upon platelet activation. Thromb Haemost 2015; 113:1046-59. [PMID: 25673011 DOI: 10.1160/th14-07-0622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/26/2014] [Indexed: 11/05/2022]
Abstract
Platelets play an important role in haemostasis, as well as in thrombosis and coagulation processes. They harbour a wide variety of messenger RNAs (mRNAs), that can template de novo protein synthesis, and an abundant array of microRNAs, which are known to mediate mRNA translational repression through proteins of the Argonaute (Ago) family. The relationship between platelet microRNAs and proteins capable of mediating translational repression, however, remains unclear. Here, we report that half of platelet microRNAs is associated to mRNA-regulatory Ago2 protein complexes, in various proportions. Associated to these Ago2 complexes are platelet mRNAs known to support de novo protein synthesis. Reporter gene activity assays confirmed the capacity of the platelet microRNAs, found to be associated to Ago2 complexes, to regulate translation of these platelet mRNAs through their 3'UTR. Neither the microRNA repertoire nor the microRNA composition of Ago2 complexes of human platelets changed upon activation with thrombin. However, under conditions favoring de novo synthesis of Plasminogen Activator Inhibitor-1 (PAI-1) protein, we documented a rapid dissociation of the encoding platelet SERPINE1 mRNA from Ago2 protein complexes as well as from the translational repressor protein T-cell-restricted intracellular antigen-1 (TIA-1). These findings are consistent with a scenario by which lifting of the repressive effects of Ago2 and TIA-1 protein complexes, involving a rearrangement of proteinmRNA complexes rather than disassembly of Ago2microRNA complexes, would allow translation of SERPINE1 mRNA into PAI-1 in response to platelet activation.
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Affiliation(s)
| | | | | | | | | | | | - Patrick Provost
- Dr. Patrick Provost, CHUQ Research Center/CHUL, 2705 Blvd Laurier, Room T1-65, Quebec, QC G1V 4G2, Canada, Tel.: +1 418 525 4444 (ext. 48842), E-mail:
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59
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James V, Wong SCK, Sharp TV. MicroRNA-mediated gene silencing: are we close to a unifying model? Biomol Concepts 2014; 3:29-40. [PMID: 25436523 DOI: 10.1515/bmc.2011.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/11/2011] [Indexed: 01/21/2023] Open
Abstract
Abstract MicroRNAs (miRNAs) comprise a group of small non-coding RNA -21 nucleotides in length. They act as post-transcriptional regulators of gene expression by forming base pairing interactions with target messenger RNA (mRNA). At least 1000 miRNAs are predicted to be expressed in humans and are encoded for in the genome of almost all organisms. Functional studies indicate that every cellular process studied thus far is regulated at some level by miRNAs. Given this expansive role, it is not surprising that disruption of this crucial pathway underlies the initiation of, or in the least, contributes to the development and progression of numerous human diseases and physiological disorders. This review will focus on the latest developments in uncovering the mechanism(s) of miRNA-mediated silencing with specific reference to the function of terminal effector proteins, how translation of target mRNA is inhibited and whether we are moving towards understanding this fundamental gene silencing paradigm.
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60
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Xie Y, Zhang J, Lin Y, Gaeta X, Meng X, Wisidagama DRR, Cinkornpumin J, Koehler CM, Malone CS, Teitell MA, Lowry WE. Defining the role of oxygen tension in human neural progenitor fate. Stem Cell Reports 2014; 3:743-57. [PMID: 25418722 PMCID: PMC4235163 DOI: 10.1016/j.stemcr.2014.09.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 01/01/2023] Open
Abstract
Hypoxia augments human embryonic stem cell (hESC) self-renewal via hypoxia-inducible factor 2α-activated OCT4 transcription. Hypoxia also increases the efficiency of reprogramming differentiated cells to a pluripotent-like state. Combined, these findings suggest that low O2 tension would impair the purposeful differentiation of pluripotent stem cells. Here, we show that low O2 tension and hypoxia-inducible factor (HIF) activity instead promote appropriate hESC differentiation. Through gain- and loss-of-function studies, we implicate O2 tension as a modifier of a key cell fate decision, namely whether neural progenitors differentiate toward neurons or glia. Furthermore, our data show that even transient changes in O2 concentration can affect cell fate through HIF by regulating the activity of MYC, a regulator of LIN28/let-7 that is critical for fate decisions in the neural lineage. We also identify key small molecules that can take advantage of this pathway to quickly and efficiently promote the development of mature cell types. Low oxygen tension promotes gliogenesis of human neural progenitors HIF activation is required for gliogenic effect of lowered oxygen tension HIF acts through MYC to disrupt LIN28/let-7 in gliogenesis Small molecule stimulators of HIF or inhibitors of MYC can drive gliogenesis
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Affiliation(s)
- Yuan Xie
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jin Zhang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ying Lin
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xavier Gaeta
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiangzhi Meng
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dona R R Wisidagama
- Department of Biology, California State University, Northridge, Northridge, CA 91330, USA
| | - Jessica Cinkornpumin
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carla M Koehler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cindy S Malone
- Department of Biology, California State University, Northridge, Northridge, CA 91330, USA
| | - Michael A Teitell
- Eli and Edythe Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - William E Lowry
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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61
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Wilczynska A, Bushell M. The complexity of miRNA-mediated repression. Cell Death Differ 2014; 22:22-33. [PMID: 25190144 DOI: 10.1038/cdd.2014.112] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/10/2014] [Accepted: 06/25/2014] [Indexed: 01/01/2023] Open
Abstract
Since their discovery 20 years ago, miRNAs have attracted much attention from all areas of biology. These short (∼22 nt) non-coding RNA molecules are highly conserved in evolution and are present in nearly all eukaryotes. They have critical roles in virtually every cellular process, particularly determination of cell fate in development and regulation of the cell cycle. Although it has long been known that miRNAs bind to mRNAs to trigger translational repression and degradation, there had been much debate regarding their precise mode of action. It is now believed that translational control is the primary event, only later followed by mRNA destabilisation. This review will discuss the most recent advances in our understanding of the molecular underpinnings of miRNA-mediated repression. Moreover, we highlight the multitude of regulatory mechanisms that modulate miRNA function.
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Affiliation(s)
- A Wilczynska
- MRC Toxicology Unit, University of Leicester, Leicester, UK
| | - M Bushell
- MRC Toxicology Unit, University of Leicester, Leicester, UK
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62
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Rouya C, Siddiqui N, Morita M, Duchaine TF, Fabian MR, Sonenberg N. Human DDX6 effects miRNA-mediated gene silencing via direct binding to CNOT1. RNA (NEW YORK, N.Y.) 2014; 20:1398-409. [PMID: 25035296 PMCID: PMC4138323 DOI: 10.1261/rna.045302.114] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/20/2014] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) play critical roles in a variety of biological processes through widespread effects on protein synthesis. Upon association with the miRNA-induced silencing complex (miRISC), miRNAs repress target mRNA translation and accelerate mRNA decay. Degradation of the mRNA is initiated by shortening of the poly(A) tail by the CCR4-NOT deadenylase complex followed by the removal of the 5' cap structure and exonucleolytic decay of the mRNA. Here, we report a direct interaction between the large scaffolding subunit of CCR4-NOT, CNOT1, with the translational repressor and decapping activator protein, DDX6. DDX6 binds to a conserved CNOT1 subdomain in a manner resembling the interaction of the translation initiation factor eIF4A with eIF4G. Importantly, mutations that disrupt the DDX6-CNOT1 interaction impair miRISC-mediated gene silencing in human cells. Thus, CNOT1 facilitates recruitment of DDX6 to miRNA-targeted mRNAs, placing DDX6 as a downstream effector in the miRNA silencing pathway.
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Affiliation(s)
- Christopher Rouya
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Nadeem Siddiqui
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Masahiro Morita
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Thomas F Duchaine
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Marc R Fabian
- Lady Davis Institute for Medical Research, SMBD-Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
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63
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Wu X, Bhayani MK, Dodge CT, Nicoloso MS, Chen Y, Yan X, Adachi M, Thomas L, Galer CE, Jiffar T, Pickering CR, Kupferman ME, Myers JN, Calin GA, Lai SY. Coordinated targeting of the EGFR signaling axis by microRNA-27a*. Oncotarget 2014; 4:1388-98. [PMID: 23963114 PMCID: PMC3824521 DOI: 10.18632/oncotarget.1239] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) has been characterized as a critical factor in the development and progression of multiple solid tumors, including head and neck squamous cell carcinoma (HNSCC). However, monotherapy with EGFR-specific agents has not been as dramatic as preclinical studies have suggested. Since complex regulation of the EGFR signaling axis might confound current attempts to inhibit EGFR directly, we searched for microRNAs (miRNAs) that may target the EGFR signaling axis. We identified miR-27a (miR-27a-3p) and its complementary or star (*) strand, miR-27a* (miR-27a-5p), as novel miRNAs targeting EGFR, which were significantly downregulated in multiple HNSCC cell lines. Analysis of human specimens demonstrated that miR-27a* is significantly underexpressed in HNSCC as compared to normal mucosa. Increased expression of miR-27a* in HNSCC produced a profound cytotoxic effect not seen with miR-27a. Analysis for potential targets of miR-27a* led to the identification of AKT1 (protein kinase B) and mTOR (mammalian target of rapamycin) within the EGFR signaling axis. Treatment with miR-27a* led to coordinated downregulation of EGFR, AKT1 and mTOR. Overexpression of EGFR signaling pathway components decreased the overall effect of miR-27a* on HNSCC cell viability. Constitutive and inducible expression of miR-27a* in a murine orthotopic xenograft model of oral cavity cancer led to decreased tumor growth. Direct intratumoral injection of miR-27a* inhibited tumor growth in vivo. These findings identify miR-27a* as a functional star sequence that exhibits novel coordinated regulation of the EGFR pathway in solid tumors and potentially represents a novel therapeutic option.
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Affiliation(s)
- Xiaoli Wu
- Department of Head and Neck Surgery, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
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64
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Temme C, Simonelig M, Wahle E. Deadenylation of mRNA by the CCR4-NOT complex in Drosophila: molecular and developmental aspects. Front Genet 2014; 5:143. [PMID: 24904643 PMCID: PMC4033318 DOI: 10.3389/fgene.2014.00143] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/02/2014] [Indexed: 11/13/2022] Open
Abstract
Controlled shortening of the poly(A) tail of mRNAs is the first step in eukaryotic mRNA decay and can also be used for translational inactivation of mRNAs. The CCR4-NOT complex is the most important among a small number of deadenylases, enzymes catalyzing poly(A) tail shortening. Rates of poly(A) shortening differ between mRNAs as the CCR4-NOT complex is recruited to specific mRNAs by means of either sequence-specific RNA binding proteins or miRNAs. This review summarizes our current knowledge concerning the subunit composition and deadenylation activity of the Drosophila CCR4-NOT complex and the mechanisms by which the complex is recruited to particular mRNAs. We discuss genetic data implicating the complex in the regulation of specific mRNAs, in particular in the context of development.
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Affiliation(s)
- Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg Halle, Germany
| | - Martine Simonelig
- Genetics and Development, Institute of Human Genetics - CNRS UPR1142 Montpellier, France
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg Halle, Germany
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65
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Chen Y, Boland A, Kuzuoğlu-Öztürk D, Bawankar P, Loh B, Chang CT, Weichenrieder O, Izaurralde E. A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing. Mol Cell 2014; 54:737-50. [PMID: 24768540 DOI: 10.1016/j.molcel.2014.03.034] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 02/13/2014] [Accepted: 03/18/2014] [Indexed: 12/14/2022]
Abstract
CCR4-NOT is a major effector complex in miRNA-mediated gene silencing. It is recruited to miRNA targets through interactions with tryptophan (W)-containing motifs in TNRC6/GW182 proteins and is required for both translational repression and degradation of miRNA targets. Here, we elucidate the structural basis for the repressive activity of CCR4-NOT and its interaction with TNRC6/GW182s. We show that the conserved CNOT9 subunit attaches to a domain of unknown function (DUF3819) in the CNOT1 scaffold. The resulting complex provides binding sites for TNRC6/GW182, and its crystal structure reveals tandem W-binding pockets located in CNOT9. We further show that the CNOT1 MIF4G domain interacts with the C-terminal RecA domain of DDX6, a translational repressor and decapping activator. The crystal structure of this complex demonstrates striking similarity to the eIF4G-eIF4A complex. Together, our data provide the missing physical links in a molecular pathway that connects miRNA target recognition with translational repression, deadenylation, and decapping.
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Affiliation(s)
- Ying Chen
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Andreas Boland
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Duygu Kuzuoğlu-Öztürk
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Praveen Bawankar
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Belinda Loh
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Chung-Te Chang
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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66
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Abstract
MicroRNAs regulate the expression of protein-coding genes in animals and plants. They function by binding to mRNA transcripts with complementary sequences and inhibit their expression. The level of sequence complementarity between the microRNA and mRNA transcript varies between animal and plant systems. Owing to this subtle difference, it was initially believed that animal and plant microRNAs act in different ways. Recent developments revealed that, although differences still remain in the two kingdoms, the differences are smaller than first thought. It is now clear that both animal and plant microRNAs mediate both translational repression of intact mRNAs and also cause mRNA degradation.
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67
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Abe M, Naqvi A, Hendriks GJ, Feltzin V, Zhu Y, Grigoriev A, Bonini NM. Impact of age-associated increase in 2'-O-methylation of miRNAs on aging and neurodegeneration in Drosophila. Genes Dev 2014; 28:44-57. [PMID: 24395246 PMCID: PMC3894412 DOI: 10.1101/gad.226654.113] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
miRNAs exhibit heterogeneity in length and sequence in different biological contexts. Abe et al. found that Drosophila miRNAs undergo isoform pattern changes with age, and an increase of some miRNAs reflects increased 2′-O-methylation of select isoforms. Loading of miRNAs into Ago2, but not Ago1, increased with age. Hen1 and Ago2 mutations caused accelerated neurodegeneration and shorter life span, suggesting that the age-associated increase of 2′-O-methylation of miRNAs affects age-associated processes. MicroRNAs (miRNAs) are 20- to ∼24-nucleotide (nt) small RNAs that impact a variety of biological processes, from development to age-associated events. To study the role of miRNAs in aging, studies have profiled the levels of miRNAs with time. However, evidence suggests that miRNAs show heterogeneity in length and sequence in different biological contexts. Here, by examining the expression pattern of miRNAs by Northern blot analysis, we found that Drosophila miRNAs show distinct isoform pattern changes with age. Surprisingly, an increase of some miRNAs reflects increased 2′-O-methylation of select isoforms. Small RNA deep sequencing revealed a global increase of miRNAs loaded into Ago2, but not into Ago1, with age. Our data suggest increased loading of miRNAs into Ago2, but not Ago1, with age, indicating a mechanism for differential loading of miRNAs with age between Ago1 and Ago2. Mutations in Hen1 and Ago2, which lack 2′-O-methylation of miRNAs, result in accelerated neurodegeneration and shorter life span, suggesting a potential impact of the age-associated increase of 2′-O-methylation of small RNAs on age-associated processes. Our study highlights that miRNA 2′-O-methylation at the 3′ end is modulated by differential partitioning of miRNAs between Ago1 and Ago2 with age and that this process, along with other functions of Ago2, might impact age-associated events in Drosophila.
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Affiliation(s)
- Masashi Abe
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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68
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Elramah S, Landry M, Favereaux A. MicroRNAs regulate neuronal plasticity and are involved in pain mechanisms. Front Cell Neurosci 2014; 8:31. [PMID: 24574967 PMCID: PMC3920573 DOI: 10.3389/fncel.2014.00031] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/22/2014] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are emerging as master regulators of gene expression in the nervous system where they contribute not only to brain development but also to neuronal network homeostasis and plasticity. Their function is the result of a cascade of events including miRNA biogenesis, target recognition, and translation inhibition. It has been suggested that miRNAs are major switches of the genome owing to their ability to regulate multiple genes at the same time. This regulation is essential for normal neuronal activity and, when affected, can lead to drastic pathological conditions. As an example, we illustrate how deregulation of miRNAs can affect neuronal plasticity leading to chronic pain. The origin of pain and its dual role as a key physiological function and a debilitating disease has been highly debated until now. The incidence of chronic pain is estimated to be 20-25% worldwide, thus making it a public health problem. Chronic pain can be considered as a form of maladaptive plasticity. Long-lasting modifications develop as a result of global changes in gene expression, and are thus likely to be controlled by miRNAs. Here, we review the literature on miRNAs and their targets responsible for maladaptive plasticity in chronic pain conditions. In addition, we conduct a retrospective analysis of miRNA expression data published for different pain models, taking into account recent progress in our understanding of the role of miRNAs in neuronal plasticity.
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Affiliation(s)
- Sara Elramah
- Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux Bordeaux, France ; Interdisciplinary Institute for Neuroscience, UMR 5297, Centre National de la Recherche Scientifique Bordeaux, France
| | - Marc Landry
- Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux Bordeaux, France ; Interdisciplinary Institute for Neuroscience, UMR 5297, Centre National de la Recherche Scientifique Bordeaux, France
| | - Alexandre Favereaux
- Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux Bordeaux, France ; Interdisciplinary Institute for Neuroscience, UMR 5297, Centre National de la Recherche Scientifique Bordeaux, France
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69
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Liu Q, Wang F, Axtell MJ. Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay. THE PLANT CELL 2014; 26:741-53. [PMID: 24510721 PMCID: PMC3967037 DOI: 10.1105/tpc.113.120972] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/16/2014] [Accepted: 01/21/2014] [Indexed: 05/17/2023]
Abstract
MicroRNAs (miRNAs) guide RNA-induced silencing complexes to target RNAs based on miRNA-target complementarity. Using a dual-luciferase based sensor system in Nicotiana benthamiana, we quantitatively assessed the relationship between miRNA-target complementarity and silencing efficacy measured at both the RNA and protein levels, using several conserved miRNAs and their known target sites from Arabidopsis thaliana. We found that naturally occurring sites have variable efficacies attributable to their complementarity patterns. We also observed that sites with a few mismatches to the miRNA 3' regions, which are common in plants, are often equally effective and sometimes more effective than perfectly matched sites. By contrast, mismatches to the miRNA 5' regions strongly reduce or eliminate repression efficacy but are nonetheless present in several natural sites, suggesting that in some cases, suboptimal miRNA efficacies are either tolerated or perhaps selected for. Central mismatches fully abolished repression efficacy in our system, but such sites then became effective miRNA target mimics. Complementarity patterns that are functional in animals (seed sites, 3'-supplementary sites, and centered sites) did not reliably confer repression, regardless of context (3'-untranslated region or open reading frame) or measurement type (RNA or protein levels). Overall, these data provide a robust and empirical foundation for understanding, predicting, and designing functional miRNA target sites in plants.
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Affiliation(s)
- Qikun Liu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Plant Biology PhD Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Feng Wang
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Plant Biology PhD Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michael J. Axtell
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Plant Biology PhD Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
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70
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Anbazhagan AN, Priyamvada S, Kumar A, Maher DB, Borthakur A, Alrefai WA, Malakooti J, Kwon JH, Dudeja PK. Translational repression of SLC26A3 by miR-494 in intestinal epithelial cells. Am J Physiol Gastrointest Liver Physiol 2014; 306:G123-31. [PMID: 24177028 PMCID: PMC3920076 DOI: 10.1152/ajpgi.00222.2013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
SLC26A3 [downregulated in adenoma (DRA)] is a Cl(-)/HCO3(-) exchanger involved in electroneutral NaCl absorption in the mammalian intestine. Altered DRA expression levels are associated with infectious and inflammatory diarrheal diseases. Therefore, it is critical to understand the regulation of DRA expression. MicroRNAs (miRNAs) are endogenous, small RNAs that regulate protein expression via blocking the translation and/or promoting mRNA degradation. To investigate potential modulation of DRA expression by miRNA, five different in silico algorithms were used to predict the miRNAs that target DRA. Of these miRNAs, miR-494 was shown to have a highly conserved putative binding site in the DRA 3'-untranslated region (3'-UTR) compared with other DRA-targeting miRNAs in vertebrates. Transfection with pmirGLO dual luciferase vector containing DRA 3'-UTR (pmirGLO-3'-UTR DRA) resulted in a significant decrease in relative luciferase activity compared with empty vector. Cotransfection of the DRA 3'-UTR luciferase vector with a miR-494 mimic further decreased luciferase activity compared with cells transfected with negative control. The transfection of a miR-494 mimic into Caco-2 and T-84 cells significantly increased the expression of miR-494 and concomitantly decreased the DRA protein expression. Mutation of the seed sequences for miR-494 in 3'-UTR of DRA abrogated the effect of miR-494 on 3'-UTR. These data demonstrate a novel regulatory mechanism of DRA expression via miR-494 and indicate that targeting this microRNA may serve to be a potential therapeutic strategy for diarrheal diseases.
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Affiliation(s)
- Arivarasu N. Anbazhagan
- 1Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois;
| | - Shubha Priyamvada
- 1Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois;
| | - Anoop Kumar
- 1Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois;
| | - Daniel B. Maher
- 1Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois;
| | - Alip Borthakur
- 1Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois;
| | - Waddah A. Alrefai
- 1Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois; ,2Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and
| | - Jaleh Malakooti
- 1Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois;
| | - John H. Kwon
- 3Department of Medicine, University of Chicago, Chicago, Illinois
| | - Pradeep K. Dudeja
- 1Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois; ,2Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and
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71
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Abstract
MicroRNAs (miRNAs) are 21-22 nucleotide small noncoding RNAs that regulate gene expression posttranscriptionally. The miRNA is incorporated into the miRNP effector complex. The miRNP complex binds to the mRNA containing the target sites, which are partially homologous to the miRNA sequence, and represses protein synthesis. One of the critical functions of miRNP is the recruitment of deadenylase complexes to the target mRNAs. Deadenylation causes translational inhibition as well as mRNA destabilization. In this chapter, we describe our method to recapitulate miRNA-mediated deadenylation in a mammalian cell-free system.
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Affiliation(s)
- Motoaki Wakiyama
- Post-transcriptional Control Research Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan,
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72
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Wynant N, Santos D, Vanden Broeck J. Biological mechanisms determining the success of RNA interference in insects. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 312:139-67. [PMID: 25262241 DOI: 10.1016/b978-0-12-800178-3.00005-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Insects constitute the largest group of animals on this planet, having a huge impact on our environment, as well as on our quality of life. RNA interference (RNAi) is a posttranscriptional gene silencing mechanism triggered by double-stranded (ds)RNA fragments. This process not only forms the basis of a widely used reverse genetics research method in many different eukaryotes but also holds great promise to contribute to the species-specific control of agricultural pests and to combat viral infections in beneficial and disease vectoring insects. However, in many economically important insect species, such as flies, mosquitoes, and caterpillars, systemic delivery of naked dsRNA does not trigger effective gene silencing. Although many components of the RNAi pathway have initially been deciphered in the fruit fly, Drosophila melanogaster, it will be of major importance to investigate this process in a wider variety of species, including dsRNA-sensitive insects such as locusts and beetles, to elucidate the factors responsible for the remarkable variability in RNAi efficiency, as observed in different insects. In this chapter, we review the current knowledge on the RNAi pathway, as well as the most recent insights into the mechanisms that might determine successful RNAi in insects.
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Affiliation(s)
- Niels Wynant
- Department of Animal Physiology and Neurobiology, KU Leuven, Naamsestraat, Leuven, Belgium.
| | - Dulce Santos
- Department of Animal Physiology and Neurobiology, KU Leuven, Naamsestraat, Leuven, Belgium
| | - Jozef Vanden Broeck
- Department of Animal Physiology and Neurobiology, KU Leuven, Naamsestraat, Leuven, Belgium
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73
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Yamasaki T, Voshall A, Kim EJ, Moriyama E, Cerutti H, Ohama T. Complementarity to an miRNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green alga Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:1045-56. [PMID: 24127635 DOI: 10.1111/tpj.12354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 10/02/2013] [Accepted: 10/09/2013] [Indexed: 05/12/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nt non-coding RNAs that play important regulatory roles in a broad range of eukaryotes by pairing with mRNAs to direct post-transcriptional repression. The mechanistic details of miRNA-mediated post-transcriptional regulation have been well documented in multicellular model organisms. However, this process remains poorly studied in algae such as Chlamydomonas reinhardtii, and specific features of miRNA biogenesis, target mRNA recognition and subsequent silencing are not well understood. In this study, we report on the characterization of a Chlamydomonas miRNA, cre-miR1174.2, which is processed from a near-perfect hairpin RNA. Using Gaussia luciferase (gluc) reporter genes, we have demonstrated that cre-miR1174.2 is functional in Chlamydomonas and capable of triggering site-specific cleavage at the center of a perfectly complementary target sequence. A mismatch tolerance test assay, based on pools of transgenic strains, revealed that target hybridization to nucleotides of the seed region, at the 5' end of an miRNA, was sufficient to induce moderate repression of expression. In contrast, pairing to the 3' region of the miRNA was not critical for silencing. Our results suggest that the base-pairing requirements for small RNA-mediated repression in C. reinhardtii are more similar to those of metazoans compared with the extensive complementarity that is typical of land plants. Individual Chlamydomonas miRNAs may potentially modulate the expression of numerous endogenous targets as a result of these relaxed base-pairing requirements.
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Affiliation(s)
- Tomohito Yamasaki
- Department of Environmental Systems Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami, Kochi, 782-8502, Japan
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74
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Wu PH, Isaji M, Carthew RW. Functionally diverse microRNA effector complexes are regulated by extracellular signaling. Mol Cell 2013; 52:113-23. [PMID: 24055343 DOI: 10.1016/j.molcel.2013.08.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 07/08/2013] [Accepted: 08/13/2013] [Indexed: 01/08/2023]
Abstract
Because microRNAs (miRNAs) influence the expression of many genes in cells, discovering how the miRNA pathway is regulated is an important area of investigation. We found that the Drosophila miRNA-induced silencing complex (miRISC) exists in multiple forms. A constitutive form, called G-miRISC, is comprised of Ago1, miRNA, and GW182. Two distinct miRISC complexes that lack GW182 are regulated by mitogenic signaling. Exposure of cells to serum, lipids, or the tumor promoter PMA suppressed formation of these complexes. P-miRISC is comprised of Ago1, miRNA, and Loqs-PB, and it associates with mRNAs assembled into polysomes. The other regulated Ago1 complex associates with membranous organelles and is likely an intermediate in miRISC recycling. The formation of these complexes is correlated with a 5- to 10-fold stronger repression of target gene expression inside cells. Taken together, these results indicate that mitogenic signaling regulates the miRNA effector machinery to attenuate its repressive activities.
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Affiliation(s)
- Pei-Hsuan Wu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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75
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Kallen AN, Zhou XB, Xu J, Qiao C, Ma J, Yan L, Lu L, Liu C, Yi JS, Zhang H, Min W, Bennett AM, Gregory RI, Ding Y, Huang Y. The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell 2013; 52:101-12. [PMID: 24055342 DOI: 10.1016/j.molcel.2013.08.027] [Citation(s) in RCA: 888] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 05/22/2013] [Accepted: 08/06/2013] [Indexed: 12/22/2022]
Abstract
Abundantly expressed in fetal tissues and adult muscle, the developmentally regulated H19 long noncoding RNA (lncRNA) has been implicated in human genetic disorders and cancer. However, how H19 acts to regulate gene function has remained enigmatic, despite the recent implication of its encoded miR-675 in limiting placental growth. We noted that vertebrate H19 harbors both canonical and noncanonical binding sites for the let-7 family of microRNAs, which plays important roles in development, cancer, and metabolism. Using H19 knockdown and overexpression, combined with in vivo crosslinking and genome-wide transcriptome analysis, we demonstrate that H19 modulates let-7 availability by acting as a molecular sponge. The physiological significance of this interaction is highlighted in cultures in which H19 depletion causes precocious muscle differentiation, a phenotype recapitulated by let-7 overexpression. Our results reveal an unexpected mode of action of H19 and identify this lncRNA as an important regulator of the major let-7 family of microRNAs.
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Affiliation(s)
- Amanda N Kallen
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA
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76
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Ma X, Cao X, Mo B, Chen X. Trip to ER: MicroRNA-mediated translational repression in plants. RNA Biol 2013; 10:1586-92. [PMID: 24100209 DOI: 10.4161/rna.26313] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
miRNAs elicit gene silencing at the post-transcriptional level by several modes of action: translational repression, mRNA decay, and mRNA cleavage. Studies in animals have suggested that translational repression occurs at early steps of translation initiation, which can be followed by deadenylation and mRNA decay. Plant miRNAs were originally thought to solely participate in mRNA cleavage, but increasing evidence has indicated that they are also commonly involved in translational inhibition. Here we discuss recent findings on miRNA-mediated translational repression in plants. The identification of AMP1 in Arabidopsis as a protein required for the translational repression but not the mRNA cleavage activity of miRNAs links miRNA-based translational repression to the endoplasmic reticulum (ER). Future work is required to further elucidate the miRNA machinery on the ER.
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Affiliation(s)
- Xuan Ma
- Shenzhen Key Laboratory of Microbial Genetic Engineering; College of Life Sciences; Shenzhen University; Shenzhen, P.R. China; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing, P.R. China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing, P.R. China
| | - Beixin Mo
- Shenzhen Key Laboratory of Microbial Genetic Engineering; College of Life Sciences; Shenzhen University; Shenzhen, P.R. China
| | - Xuemei Chen
- Department of Botany and Plant Sciences; Institute of Integrative Genome Biology; University of California; Riverside, CA USA; Howard Hughes Medical Institute; University of California; Riverside, CA USA
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77
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Barišić-Jäger E, Kręcioch I, Hosiner S, Antic S, Dorner S. HPat a decapping activator interacting with the miRNA effector complex. PLoS One 2013; 8:e71860. [PMID: 23977167 PMCID: PMC3747071 DOI: 10.1371/journal.pone.0071860] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/04/2013] [Indexed: 01/01/2023] Open
Abstract
Animal miRNAs commonly mediate mRNA degradation and/or translational repression by binding to their target mRNAs. Key factors for miRNA-mediated mRNA degradation are the components of the miRNA effector complex (AGO1 and GW182) and the general mRNA degradation machinery (deadenylation and decapping enzymes). The CCR4-NOT1 complex required for the deadenylation of target mRNAs is directly recruited to the miRNA effector complex. However, it is unclear whether the following decapping step is only a consequence of deadenylation occurring independent of the miRNA effector complex or e.g. decapping activators can get recruited to the miRNA effector complex. In this study we performed split-affinity purifications in Drosophila cells and provide evidence for the interaction of the decapping activator HPat with the miRNA effector complex. Furthermore, in knockdown analysis of various mRNA degradation factors we demonstrate the importance of NOT1 for this interaction. This suggests that deadenylation and/or the recruitment of NOT1 protein precedes the association of HPat with the miRNA effector complex. Since HPat couples deadenylation and decapping, the recruitment of HPat to the miRNA effector complex provides a mechanism to commit the mRNA target for degradation.
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Affiliation(s)
- Elisabeth Barišić-Jäger
- Max F. Perutz Laboratories, University of Vienna, Department of Microbiology, Immunbiology and Genetics, Vienna, Austria
| | - Izabela Kręcioch
- Max F. Perutz Laboratories, University of Vienna, Department of Microbiology, Immunbiology and Genetics, Vienna, Austria
| | - Stefanie Hosiner
- Max F. Perutz Laboratories, University of Vienna, Department of Microbiology, Immunbiology and Genetics, Vienna, Austria
| | - Sanja Antic
- Max F. Perutz Laboratories, University of Vienna, Department of Microbiology, Immunbiology and Genetics, Vienna, Austria
| | - Silke Dorner
- Max F. Perutz Laboratories, University of Vienna, Department of Microbiology, Immunbiology and Genetics, Vienna, Austria
- * E-mail:
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78
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Olson CM, Donovan MR, Spellberg MJ, Marr MT. The insulin receptor cellular IRES confers resistance to eIF4A inhibition. eLife 2013; 2:e00542. [PMID: 23878722 PMCID: PMC3713452 DOI: 10.7554/elife.00542] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/11/2013] [Indexed: 11/17/2022] Open
Abstract
Under conditions of stress, such as limited growth factor signaling, translation is inhibited by the action of 4E-BP and PDCD4. These proteins, through inhibition of eIF4E and eIF4A, respectively, impair cap-dependent translation. Under stress conditions FOXO transcription factors activate 4E-BP expression amplifying the repression. Here we show that Drosophila FOXO binds the PDCD4 promoter and stimulates the transcription of PDCD4 in response to stress. We have shown previously that the 5′ UTR of the Drosophila insulin-like receptor (dINR) supports cap-independent translation that is resistant to 4E-BP. Using hippuristanol, an eIF4A inhibitor, we find that translation of dINR UTR containing transcripts are also resistant to eIF4A inhibition. In addition, the murine insulin receptor and insulin-like growth factor receptor 5′ UTRs support cap-independent translation and have a similar resistance to hippuristanol. This resistance to inhibition of eIF4E and eIF4A indicates a conserved strategy to allow translation of growth factor receptors under stress conditions. DOI:http://dx.doi.org/10.7554/eLife.00542.001 Protein synthesis in eukaryotes occurs in two stages: transcription of DNA into messenger RNA (mRNA) in the nucleus, and then translation of that mRNA into a protein by ribosomes in the cytoplasm. These processes are regulated by a complex network of signaling pathways that enables cells to tailor protein synthesis to match current conditions. This involves regulating the expression of the genes that code for these proteins. When cells experience stressful events, such as a shortage of oxygen or nutrients, they reduce the synthesis of most proteins. This response is regulated, in part, by a signaling pathway known as the insulin and insulin-like receptor pathway. In particular, stressful events inhibit a protein complex called eIF4F, which normally initiates the translation of mRNA molecules by binding to a structure on one end of the mRNA called the 5′ cap. Despite this general inhibition, the production of certain other proteins—including the insulin receptor itself—is actually increased in response to stress. Olson et al. have carried out a series of experiments to explore how inhibition of the eIF4F protein complex influences the translation of the mRNA for the insulin receptor. The eIF4F complex is made up of three proteins, including one that binds to the 5′ cap and a helicase that unwinds the RNA. Previous work in the fruit fly Drosophila showed that translation of this mRNA can continue even if formation of the eIF4F complex is inhibited by targeting the cap binding protein. Olsen et al. now show that translation of this mRNA is also independent of the helicase. Instead, translation is maintained under these conditions because the insulin receptor mRNA contains a sequence called an internal ribosome entry site, which allows ribosomes to bind to the mRNA without the influence of the 5′ cap. Olson et al. reveal the details of this regulatory pathway in Drosophila and show that similar mechanisms are at work in mammalian cells, suggesting this pathway represents a crucial regulatory process that has been conserved during evolution. A key question for future research is whether other genes within the insulin and insulin-receptor like signaling pathway use this same trick to evade translational inhibitors. DOI:http://dx.doi.org/10.7554/eLife.00542.002
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Affiliation(s)
- Calla M Olson
- Department of Biology and the Rosenstiel Basic Medical Sciences Research Center , Brandeis University , Waltham , United States
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79
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Up-regulation of microRNA* strands by their target transcripts. Int J Mol Sci 2013; 14:13231-40. [PMID: 23803656 PMCID: PMC3742184 DOI: 10.3390/ijms140713231] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 05/29/2013] [Accepted: 06/17/2013] [Indexed: 11/24/2022] Open
Abstract
During microRNA (miRNA) biogenesis, one strand of a 21–23 nucleotide RNA duplex is preferentially selected for entry into an RNA-induced silencing complex (RISC). The other strand, known as the miRNA* species, is typically thought to be degraded. Previous studies have provided miRNA* selection models, but it remains unclear how the dominance of one arm arises during the biogenesis of miRNA. Using miRNA sponge-like methods, we cloned four tandem target sequences (artificial target) of miR-7b* and then measured miR-7b* expression levels after transfection of the artificial target. miR-7b* levels were found to significantly increase after transfection of the artificial target. We postulate that the abundance of target transcripts drives miRNA arm selection.
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80
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Abstract
MicroRNAs (miRNAs) regulate the expression of most genes in animals, but we are only now beginning to understand how they are generated, assembled into functional complexes and destroyed. Various mechanisms have now been identified that regulate miRNA stability and that diversify miRNA sequences to create distinct isoforms. The production of different isoforms of individual miRNAs in specific cells and tissues may have broader implications for miRNA-mediated gene expression control. Rigorously testing the many discrepant models for how miRNAs function using quantitative biochemical measurements made in vivo and in vitro remains a major challenge for the future.
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81
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Sergeeva AM, Pinzón Restrepo N, Seitz H. Quantitative aspects of RNA silencing in metazoans. BIOCHEMISTRY. BIOKHIMIIA 2013; 78:613-626. [PMID: 23980888 DOI: 10.1134/s0006297913060072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Small regulatory RNAs (microRNAs, siRNAs, and piRNAs) exhibit several unique features that clearly distinguish them from other known gene regulators. Their genomic organization, mode of action, and proposed biological functions raise specific questions. In this review, we focus on the quantitative aspect of small regulatory RNA biology. The original nature of these small RNAs accelerated the development of novel detection techniques and improved statistical methods and promoted new concepts that may unexpectedly generalize to other gene regulators. Quantification of natural phenomena is at the core of scientific practice, and the unique challenges raised by small regulatory RNAs have prompted many creative innovations by the scientific community.
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Affiliation(s)
- A M Sergeeva
- IGH du CNRS UPR 1142, 34396 Montpellier, France.
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82
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Lucas KJ, Myles KM, Raikhel AS. Small RNAs: a new frontier in mosquito biology. Trends Parasitol 2013; 29:295-303. [PMID: 23680188 DOI: 10.1016/j.pt.2013.04.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/06/2013] [Accepted: 04/08/2013] [Indexed: 12/23/2022]
Abstract
The discovery of small non-coding RNAs has revolutionized our understanding of regulatory networks governing multiple functions in animals and plants. However, our knowledge of mosquito small RNAs is limited. We discuss here the state of current knowledge regarding the roles of small RNAs and their targets in mosquitoes, and describe the ongoing efforts to understand the role of the RNA interference (RNAi) pathway in mosquito antiviral immunity and transposon silencing. Providing a clear picture into the role of small RNAs in mosquito vectors will pave the way to the utilization of these small molecules in developing novel control approaches that target mosquito immunity and/or reproductive events. Elucidation of the functions of small RNAs represents a new frontier in mosquito biology.
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Affiliation(s)
- Keira J Lucas
- Department of Entomology, University of California Riverside, Riverside, CA 92521, USA
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83
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Abstract
RNA interference (RNAi) is an ancient process by which non-coding RNAs regulate gene expression in a sequence-specific manner. The core components of RNAi are small regulatory RNAs, approximately 21-30 nucleotides in length, including small interfering RNAs (siRNAs) and microRNAs (miRNAs). The past two decades have seen considerable progress in our understanding of the molecular mechanisms underlying the biogenesis of siRNAs and miRNAs. Recent advances have also revealed the crucial regulatory roles played by small RNAs in such diverse processes as development, homeostasis, innate immunity, and oncogenesis. Accumulating evidence indicates that RNAi initially evolved as a host defense mechanism against viruses and transposons. The ability of the host small RNA biogenesis machinery to recognize viral double-stranded RNA replication intermediates and transposon transcripts is critical to this process, as is small RNA-guided targeting of RNAs via complementary base pairing. Collectively, these properties confer unparalleled specificity and precision to RNAi-mediated gene silencing as an effective antiviral mechanism.
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Affiliation(s)
- Rui Zhou
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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84
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Khoshgoo N, Kholdebarin R, Iwasiow BM, Keijzer R. MicroRNAs and lung development. Pediatr Pulmonol 2013; 48:317-23. [PMID: 23281163 DOI: 10.1002/ppul.22739] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 08/12/2012] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) constitute a large group of small (∼22 nucleotides), non-coding RNA sequences that are highly conserved among animals, plants and microorganisms, suggesting that microRNAs represent a highly conserved and important regulatory mechanism. They have been demonstrated to play an important role in gene regulation. Recently, miRNAs have become a major focus of interest for research in organ development. Research focusing on the potential role of microRNAs during lung development is slowly starting to emerge. A number of miRNAs have been demonstrated to play important roles during early and late lung development. Several studies have begun to profile miRNA expression at various stages of lung development and this article provides an overview of the various miRNAs that have been implicated in lung organogenesis.
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Affiliation(s)
- Naghmeh Khoshgoo
- Department of Surgery, University of Manitoba, Winnipeg, Manitoba, Canada
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85
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Pinder BD, Smibert CA. Smaug: an unexpected journey into the mechanisms of post-transcriptional regulation. Fly (Austin) 2013; 7:142-5. [PMID: 23519205 DOI: 10.4161/fly.24336] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Drosophila Smaug is a sequence-specific RNA-binding protein that can repress the translation and induce the degradation of target mRNAs in the early Drosophila embryo. Our recent work has uncovered a new mechanism of Smaug-mediated translational repression whereby it interacts with and recruits the Argonaute 1 (Ago1) protein to an mRNA. Argonaute proteins are typically recruited to mRNAs through an associated small RNA, such as a microRNA (miRNA). Surprisingly, we found that Smaug is able to recruit Ago1 to an mRNA in a miRNA-independent manner. This work suggests that other RNA-binding proteins are likely to employ a similar mechanism of miRNA-independent Ago recruitment to control mRNA expression. Our work also adds yet another mechanism to the list that Smaug can use to regulate its targets and here we discuss some of the issues that are raised by Smaug's multi-functional nature.
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Affiliation(s)
- Benjamin D Pinder
- Department of Biochemistry; University of Toronto; Toronto, ON Canada
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86
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Ma X, Kim EJ, Kook I, Ma F, Voshall A, Moriyama E, Cerutti H. Small interfering RNA-mediated translation repression alters ribosome sensitivity to inhibition by cycloheximide in Chlamydomonas reinhardtii. THE PLANT CELL 2013; 25:985-98. [PMID: 23512853 PMCID: PMC3634701 DOI: 10.1105/tpc.113.109256] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Small RNAs (sRNAs; ∼20 to 30 nucleotides in length) play important roles in gene regulation as well as in defense responses against transposons and viruses in eukaryotes. Their biogenesis and modes of action have attracted great attention in recent years. However, many aspects of sRNA function, such as the mechanism(s) of translation repression at postinitiation steps, remain poorly characterized. In the unicellular green alga Chlamydomonas reinhardtii, sRNAs derived from genome-integrated inverted repeat transgenes, perfectly complementary to the 3' untranslated region of a target transcript, can inhibit protein synthesis without or with only minimal mRNA destabilization. Here, we report that the sRNA-repressed transcripts are not altered in their polyadenylation status and they remain associated with polyribosomes, indicating inhibition at a postinitiation step of translation. Interestingly, ribosomes associated with sRNA-repressed transcripts show reduced sensitivity to translation inhibition by some antibiotics, such as cycloheximide, both in ribosome run-off assays and in in vivo experiments. Our results suggest that sRNA-mediated repression of protein synthesis in C. reinhardtii may involve alterations to the function/structural conformation of translating ribosomes. Additionally, sRNA-mediated translation inhibition is now known to occur in a number of phylogenetically diverse eukaryotes, suggesting that this mechanism may have been a feature of an ancestral RNA interference machinery.
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87
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Ryu I, Park JH, An S, Kwon OS, Jang SK. eIF4GI facilitates the MicroRNA-mediated gene silencing. PLoS One 2013; 8:e55725. [PMID: 23409027 PMCID: PMC3567085 DOI: 10.1371/journal.pone.0055725] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 12/29/2012] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene silencing by binding to complementary target mRNAs and recruiting the miRNA-containing ribonucleoprotein complexes to the mRNAs. However, the molecular basis of this silencing is unclear. Here, we show that human Ago2 associates with the cap-binding protein complex and this association is mediated by human eIF4GI, a scaffold protein required for the translation initiation. Using a cap photo-crosslinking method, we show that Ago2 closely associates with the cap structure. Taken together, these data suggest that eIF4GI participates in the miRNA-mediated post-transcriptional gene silencing by promoting the association of Ago2 with the cap-binding complex.
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Affiliation(s)
- Incheol Ryu
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Ji Hoon Park
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Sihyeon An
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Oh Sung Kwon
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Sung Key Jang
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
- Biotechnology Research Center, Pohang University of Science and Technology, Pohang, Korea
- * E-mail:
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88
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Li J, Hobman TC, Simmonds AJ. Gawky (GW) is the Drosophila melanogaster GW182 homologue. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:127-45. [PMID: 23224968 DOI: 10.1007/978-1-4614-5107-5_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jing Li
- Department of Cell Biology, University of Alberta, Edmonton, Canada.
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89
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Chen CYA, Shyu AB. Deadenylation and P-bodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:183-95. [PMID: 23224971 DOI: 10.1007/978-1-4614-5107-5_11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deadenylation is the major step in triggering mRNA decay and results in mRNA translation inhibition in eukaryotic cells. Therefore, it is plausible that deadenylation also induces the mRNP remodeling required for formation of GW bodies or RNA processing bodies (P-bodies), which harbor translationally silenced mRNPs. In this chapter, we discuss several examples to illustrate the roles of deadenylation in regulating gene expression. We highlight several lines of evidence indicating that even though non-translatable mRNPs may be prepared and/or assembled into P-bodies in different ways, deadenylation is always a necessary, and perhaps the earliest, step in mRNA decay pathways that enable mRNP remodeling required for P-body formation. Thus, deadenylation and the participating deadenylases are not simply required for preparing mRNA substrates; they play an indispensable role both structurally and functionally in P-body formation and regulation.
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Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, TX 77030, USA
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90
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Braun JE, Huntzinger E, Izaurralde E. The role of GW182 proteins in miRNA-mediated gene silencing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:147-63. [PMID: 23224969 DOI: 10.1007/978-1-4614-5107-5_9] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
GW182 family proteins are essential for microRNA-mediated gene silencing in animal cells. They are recruited to miRNA targets through direct interactions with Argonaute proteins and promote target silencing. They do so by repressing translation and enhancing mRNA turnover. Although the precise mechanism of action of GW182 proteins is not fully understood, these proteins have been shown to interact with the cytoplasmic poly(A)-binding protein (PABP) and with the PAN2-PAN3 and CCR4-NOT deadenylase complexes. These findings suggest that GW182 proteins function as scaffold proteins for the assembly of the multiprotein complex that silences miRNA targets.
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Affiliation(s)
- Joerg E Braun
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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91
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Lee S, Vasudevan S. Post-transcriptional stimulation of gene expression by microRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:97-126. [PMID: 23224967 DOI: 10.1007/978-1-4614-5107-5_7] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs are small noncoding RNA regulatory molecules that control gene expression by guiding associated effector complexes to other RNAs via sequence-specific recognition of target sites. Misregulation of microRNAs leads to a wide range of diseases including cancers, inflammatory and developmental disorders. MicroRNAs were found to mediate deadenylation-dependent decay and translational repression of messages through partially complementary microRNA target sites in the 3'-UTR (untranslated region). A growing series of studies has demonstrated that microRNAs and their associated complexes (microRNPs) elicit alternate functions that enable stimulation of gene expression in addition to their assigned repressive roles. These reports, discussed in this chapter, indicate that microRNA-mediated effects via natural 3' and 5'-UTRs can be selective and controlled, dictated by the RNA sequence context, associated complex, and cellular conditions. Similar to the effects of repression, upregulated gene expression by microRNAs varies from small refinements to significant amplifications in expression. An emerging theme from this literature is that microRNAs have a versatile range of abilities to manipulate post-transcriptional control mechanisms leading to controlled gene expression. These studies reveal new potentials for microRNPs in gene expression control that develop as responses to specific cellular conditions.
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92
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Braun JE, Huntzinger E, Izaurralde E. A molecular link between miRISCs and deadenylases provides new insight into the mechanism of gene silencing by microRNAs. Cold Spring Harb Perspect Biol 2012; 4:4/12/a012328. [PMID: 23209154 DOI: 10.1101/cshperspect.a012328] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
MicroRNAs (miRNAs) are a large family of endogenous noncoding RNAs that, together with the Argonaute family of proteins (AGOs), silence the expression of complementary mRNA targets posttranscriptionally. Perfectly complementary targets are cleaved within the base-paired region by catalytically active AGOs. In the case of partially complementary targets, however, AGOs are insufficient for silencing and need to recruit a protein of the GW182 family. GW182 proteins induce translational repression, mRNA deadenylation and exonucleolytic target degradation. Recent work has revealed a direct molecular link between GW182 proteins and cellular deadenylase complexes. These findings shed light on how miRNAs bring about target mRNA degradation and promise to further our understanding of the mechanism of miRNA-mediated repression.
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Affiliation(s)
- Joerg E Braun
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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93
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microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein. EMBO Rep 2012. [PMID: 23184089 DOI: 10.1038/embor.2012.192] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Argonaute (Ago) proteins are typically recruited to target messenger RNAs via an associated small RNA such as a microRNA (miRNA). Here, we describe a new mechanism of Ago recruitment through the Drosophila Smaug RNA-binding protein. We show that Smaug interacts with the Ago1 protein, and that Ago1 interacts with and is required for the translational repression of the Smaug target, nanos mRNA. The Ago1/nanos mRNA interaction does not require a miRNA, but it does require Smaug. Taken together, our data suggest a model whereby Smaug directly recruits Ago1 to nanos mRNA in a miRNA-independent manner, thereby repressing translation.
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94
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Ricci EP, Limousin T, Soto-Rifo R, Rubilar PS, Decimo D, Ohlmann T. miRNA repression of translation in vitro takes place during 43S ribosomal scanning. Nucleic Acids Res 2012; 41:586-98. [PMID: 23161679 PMCID: PMC3592420 DOI: 10.1093/nar/gks1076] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
microRNAs (miRNAs) regulate gene expression at multiple levels by repressing translation, stimulating deadenylation and inducing the premature decay of target messenger RNAs (mRNAs). Although the mechanism by which miRNAs repress translation has been widely studied, the precise step targeted and the molecular insights of such repression are still evasive. Here, we have used our newly designed in vitro system, which allows to study miRNA effect on translation independently of deadenylation. By using specific inhibitors of various stages of protein synthesis, we first show that miRNAs target exclusively the early steps of translation with no effect on 60S ribosomal subunit joining, elongation or termination. Then, by using viral proteases and IRES-driven mRNA constructs, we found that translational inhibition takes place during 43S ribosomal scanning and requires both the poly(A) binding protein and eIF4G independently from their physical interaction.
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Affiliation(s)
- Emiliano P Ricci
- Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, Inserm U758, Lyon F-69364, France
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95
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Fukaya T, Tomari Y. MicroRNAs mediate gene silencing via multiple different pathways in drosophila. Mol Cell 2012; 48:825-36. [PMID: 23123195 DOI: 10.1016/j.molcel.2012.09.024] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/15/2012] [Accepted: 09/27/2012] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) guide RNA-induced silencing complex (RISC) that contains an Argonaute family protein to complementary target messenger RNAs (mRNAs). Via RISC, miRNAs silence the expression of target mRNAs by shortening the poly(A) tail-which leads to mRNA decay-and by repressing translation. It has been suggested that GW182, an Argonaute-associating protein, plays the central role in such microRNA actions. Here we show that, although GW182 is obligatory for poly(A) shortening, translational repression by microRNAs occurs even in the absence of GW182. Yet, GW182 is also capable of inducing translational repression independently. Both of these translational repression mechanisms block formation of 48S and 80S ribosomal complexes. Thus microRNAs utilize at least three distinct silencing pathways: GW182-mediated deadenylation and GW182-dependent and -independent repression of early translation initiation. Differential contribution from these multiple pathways may explain previous, apparently contradictory observations of how microRNAs inhibit protein synthesis.
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Affiliation(s)
- Takashi Fukaya
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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96
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Abstract
Shortening of the poly(A) tail is the first and often rate-limiting step in mRNA degradation. Three poly(A)-specific 3' exonucleases have been described that can carry out this reaction: PAN, composed of two subunits; PARN, a homodimer; and the CCR4-NOT complex, a heterooligomer that contains two catalytic subunits and may have additional functions in the cell. Current evidence indicates that all three enzymes use a two-metal ion mechanism to release nucleoside monophosphates in a hydrolytic reaction. The CCR4-NOT is the main deadenylase in all organisms examined, and mutations affecting the complex can be lethal. The contribution of PAN, apparently an initial deadenylation preceding the activity of CCR4-NOT, is less important, whereas the activity of PARN seems to be restricted to specific substrates or circumstances, for example, stress conditions. Rapid deadenylation and decay of specific mRNAs can be caused by recruitment of both PAN and the CCR4-NOT complex. This function can be carried out by RNA-binding proteins, for example, members of the PUF family. Alternatively, miRNAs can recruit the deadenylase complexes with the help of their associated GW182 proteins.
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Affiliation(s)
- Christiane Harnisch
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Bodo Moritz
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Christiane Rammelt
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Claudia Temme
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany
| | - Elmar Wahle
- Martin-Luther-University of Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, Halle, Germany.
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97
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Djuranovic S, Nahvi A, Green R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 2012; 336:237-40. [PMID: 22499947 DOI: 10.1126/science.1215691] [Citation(s) in RCA: 659] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
microRNAs (miRNAs) regulate gene expression through translational repression and/or messenger RNA (mRNA) deadenylation and decay. Because translation, deadenylation, and decay are closely linked processes, it is important to establish their ordering and thus to define the molecular mechanism of silencing. We have investigated the kinetics of these events in miRNA-mediated gene silencing by using a Drosophila S2 cell-based controllable expression system and show that mRNAs with both natural and engineered 3' untranslated regions with miRNA target sites are first subject to translational inhibition, followed by effects on deadenylation and decay. We next used a natural translational elongation stall to show that miRNA-mediated silencing inhibits translation at an early step, potentially translation initiation.
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Affiliation(s)
- Sergej Djuranovic
- Howard Hughes Medical Institute (HHMI) and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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98
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Morozova N, Zinovyev A, Nonne N, Pritchard LL, Gorban AN, Harel-Bellan A. Kinetic signatures of microRNA modes of action. RNA (NEW YORK, N.Y.) 2012; 18:1635-55. [PMID: 22850425 PMCID: PMC3425779 DOI: 10.1261/rna.032284.112] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of all important biological processes, including development, differentiation, and cancer. Although remarkable progress has been made in deciphering the mechanisms used by miRNAs to regulate translation, many contradictory findings have been published that stimulate active debate in this field. Here we contribute to this discussion in three ways. First, based on a comprehensive analysis of the existing literature, we hypothesize a model in which all proposed mechanisms of microRNA action coexist, and where the apparent mechanism that is detected in a given experiment is determined by the relative values of the intrinsic characteristics of the target mRNAs and associated biological processes. Among several coexisting miRNA mechanisms, the one that will effectively be measurable is that which acts on or changes the sensitive parameters of the translation process. Second, we have created a mathematical model that combines nine known mechanisms of miRNA action and estimated the model parameters from the literature. Third, based on the mathematical modeling, we have developed a computational tool for discriminating among different possible individual mechanisms of miRNA action based on translation kinetics data that can be experimentally measured (kinetic signatures). To confirm the discriminatory power of these kinetic signatures and to test our hypothesis, we have performed several computational experiments with the model in which we simulated the coexistence of several miRNA action mechanisms in the context of variable parameter values of the translation.
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Affiliation(s)
- Nadya Morozova
- CNRS FRE 3377, CEA Saclay, and
- Université Paris-Sud, F-91191, Gif-sur-Yvette, France
| | - Andrei Zinovyev
- Institut Curie, Service Bioinformatique, F-75248 Paris, France
- Ecole des Mines ParisTech, F-77300 Fontainebleau, France
- INSERM, U900, Paris, F-75248, France
| | - Nora Nonne
- CNRS FRE 3377, CEA Saclay, and
- Université Paris-Sud, F-91191, Gif-sur-Yvette, France
| | | | - Alexander N. Gorban
- University of Leicester, Centre for Mathematical Modelling, Leicester, LE1 7RH, United Kingdom
| | - Annick Harel-Bellan
- CNRS FRE 3377, CEA Saclay, and
- Université Paris-Sud, F-91191, Gif-sur-Yvette, France
- Corresponding authorE-mail
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99
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Tettweiler G, Kowanda M, Lasko P, Sonenberg N, Hernández G. The Distribution of eIF4E-Family Members across Insecta. Comp Funct Genomics 2012; 2012:960420. [PMID: 22745595 PMCID: PMC3382400 DOI: 10.1155/2012/960420] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 03/14/2012] [Indexed: 11/20/2022] Open
Abstract
Insects are part of the earliest faunas that invaded terrestrial environments and are the first organisms that evolved controlled flight. Nowadays, insects are the most diverse animal group on the planet and comprise the majority of extant animal species described. Moreover, they have a huge impact in the biosphere as well as in all aspects of human life and economy; therefore understanding all aspects of insect biology is of great importance. In insects, as in all cells, translation is a fundamental process for gene expression. However, translation in insects has been mostly studied only in the model organism Drosophila melanogaster. We used all publicly available genomic sequences to investigate in insects the distribution of the genes encoding the cap-binding protein eIF4E, a protein that plays a crucial role in eukaryotic translation. We found that there is a diversity of multiple ortholog genes encoding eIF4E isoforms within the genus Drosophila. In striking contrast, insects outside this genus contain only a single eIF4E gene, related to D. melanogaster eIF4E-1. We also found that all insect species here analyzed contain only one Class II gene, termed 4E-HP. We discuss the possible evolutionary causes originating the multiplicity of eIF4E genes within the genus Drosophila.
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Affiliation(s)
- Gritta Tettweiler
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada H3A 1A3
| | - Michelle Kowanda
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
| | - Paul Lasko
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada H3A 1A3
| | - Greco Hernández
- Division of Basic Research, National Institute for Cancer (INCan), Avenida San Fernando No. 22, Tlalpan, 14080 Mexico City, DF, Mexico
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100
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Donald CL, Kohl A, Schnettler E. New Insights into Control of Arbovirus Replication and Spread by Insect RNA Interference Pathways. INSECTS 2012; 3:511-31. [PMID: 26466541 PMCID: PMC4553608 DOI: 10.3390/insects3020511] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 12/17/2022]
Abstract
Arthropod-borne (arbo) viruses are transmitted by vectors, such as mosquitoes, to susceptible vertebrates. Recent research has shown that arbovirus replication and spread in mosquitoes is not passively tolerated but induces host responses to control these pathogens. Small RNA-mediated host responses are key players among these antiviral immune strategies. Studies into one such small RNA-mediated antiviral response, the exogenous RNA interference (RNAi) pathway, have generated a wealth of information on the functions of this mechanism and the enzymes which mediate antiviral activities. However, other small RNA-mediated host responses may also be involved in modulating antiviral activity. The aim of this review is to summarize recent research into the nature of small RNA-mediated antiviral responses in mosquitoes and to discuss future directions for this relatively new area of research.
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Affiliation(s)
- Claire L Donald
- MRC-University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow G11 5JR, Scotland, UK.
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow G11 5JR, Scotland, UK.
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow G11 5JR, Scotland, UK.
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