1
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Galton R, Fejes-Toth K, Bronner ME. Co-option of the piRNA pathway to regulate neural crest specification. SCIENCE ADVANCES 2022; 8:eabn1441. [PMID: 35947657 PMCID: PMC9365273 DOI: 10.1126/sciadv.abn1441] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/24/2022] [Indexed: 05/26/2023]
Abstract
Across Metazoa, Piwi proteins play a critical role in protecting the germline genome through piRNA-mediated repression of transposable elements. In vertebrates, activity of Piwi proteins and the piRNA pathway was thought to be gonad specific. Our results reveal the expression of Piwil1 in a vertebrate somatic cell type, the neural crest. Piwil1 is expressed at low levels throughout the chicken neural tube, peaking in neural crest cells just before the specification event that enables epithelial-to-mesenchymal transition (EMT) and migration into the periphery. Loss of Piwil1 impedes neural crest specification and emigration. Small RNA sequencing reveals somatic piRNAs with sequence signatures of an active ping-pong loop. RNA-seq and functional experiments identify the transposon-derived gene ERNI as Piwil1's target in the neural crest. ERNI, in turn, suppresses Sox2 to precisely control the timing of neural crest specification and EMT. Our data provide mechanistic insight into a novel function of the piRNA pathway as a regulator of somatic development in a vertebrate species.
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Affiliation(s)
| | - Katalin Fejes-Toth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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2
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Hongdusit A, Fox JM. Optogenetic Analysis of Allosteric Control in Protein Tyrosine Phosphatases. Biochemistry 2021; 60:254-258. [PMID: 33450156 DOI: 10.1021/acs.biochem.0c00841] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric regulation enables dynamic adjustments to protein function that permit tight control over cellular biochemistry. Discrepancies in the allosteric systems of related proteins can thus reveal important differences in their susceptibilities to influential stimuli (e.g., allosteric ligands, mutations, or post-translational modifications). This study uses an optogenetic actuator as a tool to compare the allosteric systems of two structurally related regulatory proteins: protein tyrosine phosphatase 1B (PTP1B) and T-cell protein tyrosine phosphatase (TCPTP). It begins with an interesting observation: The fusion of a protein light switch to the allosterically influential α7 helix of PTP1B permits optical modulation of its catalytic activity, but a similar fusion to TCPTP does not. A subsequent analysis of different PTP chimeras shows that replacing regions of TCPTP with homologous regions from PTP1B can enhance photocontrol; as TCPTP becomes more "PTP1B-like", its photosensitivity increases. Interestingly, the structural changes required for photocontrol also enhance the sensitivity of TCPTP to other allosteric inputs, notably, an allosteric inhibitor and a newly reported activating mutation. Our findings indicate that the allosteric functionality of the α7 helix of PTP1B is not conserved across the PTP family and highlight residues necessary to transfer this functionality to other PTPs. More broadly, our results suggest that simple gene fusion events can strengthen allosteric communication within individual protein domains and describe an intriguing application for optogenetic actuators as structural probes-a sort of physically disruptive "ratchet"-for studying protein allostery.
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Affiliation(s)
- Akarawin Hongdusit
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
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3
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Gong M, Wang Y, Zhang J, Zhao Y, Wan J, Shang J, Yang R, Wu Y, Li Y, Tan Q, Bao D. Chilling Stress Triggers VvAgo1-Mediated miRNA-Like RNA Biogenesis in Volvariella volvacea. Front Microbiol 2020; 11:523593. [PMID: 33042047 PMCID: PMC7522536 DOI: 10.3389/fmicb.2020.523593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
In Volvariella volvacea, an important species of edible mushroom, cryogenic autolysis is a typical phenomenon that occurs during abnormal metabolism. Analysis of gene expression profiling and qPCR showed that chilling stress (CS) significantly and continuously upregulated only one type of Argonaute in V. volvacea, i.e., VvAgo1. Structural and evolutionary analysis revealed that VvAgo1 belongs to the Ago-like family, and its evolution has involved gene duplication, subsequent gene loss, and purifying selection. Analysis of its interaction network and expression suggested that CS triggers VvAgo1-mediated miRNA-like RNA (milRNA) biogenesis in V. volvacea V23 but not in VH3 (a composite mutant strain from V23 with improved CS resistance). Small RNA sequencing and qPCR analysis confirmed that CS triggered the increased milRNA expression in V23 and not in VH3. The predicted target genes of the increased milRNAs were enriched in several pathways, such as signal transduction and ubiquitination. Heatmap analysis showed that CS altered the expression profile of milRNAs with their target genes related to signal transduction and ubiquitination in V23. Combined analysis of transcriptome and proteome data confirmed that most of the target genes of the increased milRNAs were not translated into proteins. Our observations indicate that CS might trigger VvAgo1-mediated RNAi to facilitate the cryogenic autolysis of V. volvacea.
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Affiliation(s)
- Ming Gong
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, China
| | - Ying Wang
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinsong Zhang
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Zhao
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jianing Wan
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Junjun Shang
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ruiheng Yang
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yingying Wu
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qi Tan
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dapeng Bao
- Key Laboratory of Edible Fungi Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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4
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Abstract
The coordination of cell fate decisions within complex multicellular structures rests on intercellular communication. To generate ordered patterns, cells need to know their relative positions within the growing structure. This is commonly achieved via the production and perception of mobile signaling molecules. In animal systems, such positional signals often act as morphogens and subdivide a field of cells into domains of discrete cell identities using a threshold-based readout of their mobility gradient. Reflecting the independent origin of multicellularity, plants evolved distinct signaling mechanisms to drive cell fate decisions. Many of the basic principles underlying developmental patterning are, however, shared between animals and plants, including the use of signaling gradients to provide positional information. In plant development, small RNAs can act as mobile instructive signals, and similar to classical morphogens in animals, employ a threshold-based readout of their mobility gradient to generate precisely defined cell fate boundaries. Given the distinctive nature of peptide morphogens and small RNAs, how might mechanisms underlying the function of traditionally morphogens be adapted to create morphogen-like behavior using small RNAs? In this review, we highlight the contributions of mobile small RNAs to pattern formation in plants and summarize recent studies that have advanced our understanding regarding the formation, stability, and interpretation of small RNA gradients.
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Affiliation(s)
- Simon Klesen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Kristine Hill
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
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5
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Kiltschewskij D, Cairns MJ. Temporospatial guidance of activity-dependent gene expression by microRNA: mechanisms and functional implications for neural plasticity. Nucleic Acids Res 2019; 47:533-545. [PMID: 30535081 PMCID: PMC6344879 DOI: 10.1093/nar/gky1235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/30/2018] [Indexed: 01/08/2023] Open
Abstract
MicroRNA are major regulators of neuronal gene expression at the post-transcriptional and translational levels. This layer of control is critical for spatially and temporally restricted gene expression, facilitating highly dynamic changes to cellular structure and function associated with neural plasticity. Investigation of microRNA function in the neural system, however, is at an early stage, and many aspects of the mechanisms employing these small non-coding RNAs remain unclear. In this article, we critically review current knowledge pertaining to microRNA function in neural activity, with emphasis on mechanisms of microRNA repression, their subcellular remodelling and functional impacts on neural plasticity and behavioural phenotypes.
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Affiliation(s)
- Dylan Kiltschewskij
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2323, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton, NSW, 2323, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2323, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton, NSW, 2323, Australia
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6
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Skopelitis DS, Benkovics AH, Husbands AY, Timmermans MCP. Boundary Formation through a Direct Threshold-Based Readout of Mobile Small RNA Gradients. Dev Cell 2017; 43:265-273.e6. [PMID: 29107557 DOI: 10.1016/j.devcel.2017.10.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/28/2017] [Accepted: 10/03/2017] [Indexed: 11/17/2022]
Abstract
Small RNAs have emerged as a new class of mobile signals. Here, we investigate their mechanism of action and show that mobile small RNAs generate sharply defined domains of target gene expression through an intrinsic and direct threshold-based readout of their mobility gradients. This readout is highly sensitive to small RNA levels at the source, allowing plasticity in the positioning of a target gene expression boundary. Besides patterning their immediate targets, the readouts of opposing small RNA gradients enable specification of robust, uniformly positioned developmental boundaries. These patterning properties of small RNAs are reminiscent of those of animal morphogens. However, their mode of action and the intrinsic nature of their gradients distinguish mobile small RNAs from classical morphogens and present a unique direct mechanism through which to relay positional information. Mobile small RNAs and their targets thus emerge as highly portable, evolutionarily tractable regulatory modules through which to create pattern.
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Affiliation(s)
| | - Anna H Benkovics
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Aman Y Husbands
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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7
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Chen S, Gao G. MicroRNAs recruit eIF4E2 to repress translation of target mRNAs. Protein Cell 2017; 8:750-761. [PMID: 28755203 PMCID: PMC5636748 DOI: 10.1007/s13238-017-0444-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/06/2017] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) recruit the RNA-induced silencing complex (RISC) to repress the translation of target mRNAs. While the 5′ 7-methylguanosine cap of target mRNAs has been well known to be important for miRNA repression, the underlying mechanism is not clear. Here we show that TNRC6A interacts with eIF4E2, a homologue of eIF4E that can bind to the cap but cannot interact with eIF4G to initiate translation, to inhibit the translation of target mRNAs. Downregulation of eIF4E2 relieved miRNA repression of reporter expression. Moreover, eIF4E2 downregulation increased the protein levels of endogenous IMP1, PTEN and PDCD4, whose expression are repressed by endogenous miRNAs. We further provide evidence showing that miRNA enhances eIF4E2 association with the target mRNA. We propose that miRNAs recruit eIF4E2 to compete with eIF4E to repress mRNA translation.
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Affiliation(s)
- Shaohong Chen
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangxia Gao
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100101, China.
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8
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Webster A, Li S, Hur JK, Wachsmuth M, Bois JS, Perkins EM, Patel DJ, Aravin AA. Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper. Mol Cell 2016; 59:564-75. [PMID: 26295961 DOI: 10.1016/j.molcel.2015.07.017] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/26/2015] [Accepted: 07/20/2015] [Indexed: 02/08/2023]
Abstract
In Drosophila, two Piwi proteins, Aubergine (Aub) and Argonaute-3 (Ago3), localize to perinuclear "nuage" granules and use guide piRNAs to target and destroy transposable element transcripts. We find that Aub and Ago3 are recruited to nuage by two different mechanisms. Aub requires a piRNA guide for nuage recruitment, indicating that its localization depends on recognition of RNA targets. Ago3 is recruited to nuage independently of a piRNA cargo and relies on interaction with Krimper, a stable component of nuage that is able to aggregate in the absence of other nuage proteins. We show that Krimper interacts directly with Aub and Ago3 to coordinate the assembly of the ping-pong piRNA processing (4P) complex. Symmetrical dimethylated arginines are required for Aub to interact with Krimper, but they are dispensable for Ago3 to bind Krimper. Our study reveals a multi-step process responsible for the assembly and function of nuage complexes in piRNA-guided transposon repression.
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Affiliation(s)
- Alexandre Webster
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sisi Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10021 USA
| | - Junho K Hur
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Malte Wachsmuth
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Justin S Bois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Edward M Perkins
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10021 USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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9
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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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10
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Post C, Clark JP, Sytnikova YA, Chirn GW, Lau NC. The capacity of target silencing by Drosophila PIWI and piRNAs. RNA (NEW YORK, N.Y.) 2014; 20:1977-86. [PMID: 25336588 PMCID: PMC4238361 DOI: 10.1261/rna.046300.114] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Although Piwi proteins and Piwi-interacting RNAs (piRNAs) genetically repress transposable elements (TEs), it is unclear how the highly diverse piRNA populations direct Piwi proteins to silence TE targets without silencing the entire transcriptome. To determine the capacity of piRNA-mediated silencing, we introduced reporter genes into Drosophila OSS cells, which express microRNAs (miRNAs) and piRNAs, and compared the Piwi pathway to the Argonaute pathway in gene regulation. Reporter constructs containing several target sites that were robustly silenced by miRNAs were not silenced to the same degrees by piRNAs. However, another set of reporters we designed to enable a large number of both TE-directed and genic piRNAs to bind were robustly silenced by the PIWI/piRNA complex in OSS cells. These reporters show that a bulk of piRNAs are required to pair to the reporter's transcripts and not the reporter's DNA sequence to engage PIWI-mediated silencing. Following our genome-wide study of PIWI-regulated targets in OSS cells, we assessed candidate gene elements with our reporter platform. These results suggest TE sequences are the most direct of PIWI regulatory targets while coding genes are less directly affected by PIWI targeting. Finally, our study suggests that the PIWI transcriptional silencing mechanism triggers robust chromatin changes on targets with sufficient piRNA binding, and preferentially regulates TE transcripts because protein-coding transcripts lack a threshold of targeting by piRNA populations. This reporter platform will facilitate future dissections of the PIWI-targeting mechanism.
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Affiliation(s)
- Christina Post
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Josef P Clark
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Yuliya A Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Gung-Wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Nelson C Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02453, USA
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11
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Li Y, Tang W, Zhang LR, Zhang CY. FMRP regulates miR196a-mediated repression of HOXB8 via interaction with the AGO2 MID domain. MOLECULAR BIOSYSTEMS 2014; 10:1757-64. [DOI: 10.1039/c4mb00066h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Oh SS, Plakos K, Xiao Y, Eisenstein M, Soh HT. In vitro selection of shape-changing DNA nanostructures capable of binding-induced cargo release. ACS NANO 2013; 7:9675-9683. [PMID: 24168267 PMCID: PMC3919467 DOI: 10.1021/nn404079v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Many biological systems employ allosteric regulatory mechanisms, which offer a powerful means of directly linking a specific binding event to a wide spectrum of molecular functionalities. There is considerable interest in generating synthetic allosteric regulators that can perform useful molecular functions for applications in diagnostics, imaging and targeted therapies, but generating such molecules through either rational design or directed evolution has proven exceptionally challenging. To address this need, we present an in vitro selection strategy for generating conformation-switching DNA nanostructures that selectively release a small-molecule payload in response to binding of a specific trigger molecule. As an exemplar, we have generated a DNA nanostructure that hybridizes with a separate 'cargo strand' containing an abasic site. This abasic site stably sequesters a fluorescent cargo molecule in an inactive state until the DNA nanostructure encounters an ATP trigger molecule. This ATP trigger causes the nanostructure to release the cargo strand, thereby liberating the fluorescent payload and generating a detectable fluorescent readout. Our DNA nanostructure is highly sensitive, with an EC50 of 30 μM, and highly specific, releasing its payload in response to ATP but not to other chemically similar nucleotide triphosphates. We believe that this selection approach could be generalized to generate synthetic nanostructures capable of selective and controlled release of other small-molecule cargos in response to a variety of triggers, for both research and clinical applications.
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Affiliation(s)
- Seung Soo Oh
- Materials Department, University of California, Santa Barbara, CA 93106
| | - Kory Plakos
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Yi Xiao
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Michael Eisenstein
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Hyongsok Tom Soh
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
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13
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Wei K, Wu L, Chen Y, Lin Y, Wang Y, Liu X, Xie D. Argonaute protein as a linker to command center of physiological processes. Chin J Cancer Res 2013; 25:430-41. [PMID: 23997530 DOI: 10.3978/j.issn.1000-9604.2013.08.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 12/17/2012] [Indexed: 01/10/2023] Open
Abstract
MicroRNAs (miRNAs) post-transcriptionally regulate gene expression by binding to target mRNAs with perfect or imperfect complementarity, recruiting an Argonaute (AGO) protein complex that usually results in degradation or translational repression of the target mRNA. AGO proteins function as the Slicer enzyme in miRNA and small interfering RNA (siRNA) pathways involved in human physiological and pathophysiological processes, such as antiviral responses and disease formation. Although the past decade has witnessed rapid advancement in studies of AGO protein functions, to further elucidate the molecular mechanism of AGO proteins in cellular function and biochemical process is really a challenging area for researchers. In order to understand the molecular causes underlying the pathological processes, we mainly focus on five fundamental problems of AGO proteins, including evolution, functional domain, subcellular location, post-translational modification and protein-protein interactions. Our discussion highlight their roles in early diagnosis, disease prevention, drug target identification, drug response, etc.
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Affiliation(s)
- Kaifa Wei
- Department of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
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14
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Nishihara T, Zekri L, Braun JE, Izaurralde E. miRISC recruits decapping factors to miRNA targets to enhance their degradation. Nucleic Acids Res 2013; 41:8692-705. [PMID: 23863838 PMCID: PMC3794582 DOI: 10.1093/nar/gkt619] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MicroRNA (miRNA)-induced silencing complexes (miRISCs) repress translation and promote degradation of miRNA targets. Target degradation occurs through the 5′-to-3′ messenger RNA (mRNA) decay pathway, wherein, after shortening of the mRNA poly(A) tail, the removal of the 5′ cap structure by decapping triggers irreversible decay of the mRNA body. Here, we demonstrate that miRISC enhances the association of the decapping activators DCP1, Me31B and HPat with deadenylated miRNA targets that accumulate when decapping is blocked. DCP1 and Me31B recruitment by miRISC occurs before the completion of deadenylation. Remarkably, miRISC recruits DCP1, Me31B and HPat to engineered miRNA targets transcribed by RNA polymerase III, which lack a cap structure, a protein-coding region and a poly(A) tail. Furthermore, miRISC can trigger decapping and the subsequent degradation of mRNA targets independently of ongoing deadenylation. Thus, miRISC increases the local concentration of the decapping machinery on miRNA targets to facilitate decapping and irreversibly shut down their translation.
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Affiliation(s)
- Tadashi Nishihara
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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15
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Molecular dissection of human Argonaute proteins by DNA shuffling. Nat Struct Mol Biol 2013; 20:818-26. [PMID: 23748378 DOI: 10.1038/nsmb.2607] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 05/13/2013] [Indexed: 01/01/2023]
Abstract
A paramount task in RNA interference research is to decipher the complex biology of cellular effectors, exemplified in humans by four pleiotropic Argonaute proteins (Ago1-Ago4). Here, we exploited DNA family shuffling, a molecular evolution technology, to generate chimeric Ago protein libraries for dissection of intricate phenotypes independently of prior structural knowledge. Through shuffling of human Ago2 and Ago3, we discovered two N-terminal motifs that govern RNA cleavage in concert with the PIWI domain. Structural modeling predicts an impact on protein rigidity and/or RNA-PIWI alignment, suggesting new mechanistic explanations for Ago3's slicing deficiency. Characterization of hybrids including Ago1 and Ago4 solidifies that slicing requires the juxtaposition and combined action of multiple disseminated modules. We also present a Gateway library of codon-optimized chimeras of human Ago1-Ago4 and molecular evolution analysis software as resources for future investigations into RNA interference sequence-structure-function relationships.
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16
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Zhu L, Masaki Y, Tatsuke T, Li Z, Mon H, Xu J, Lee JM, Kusakabe T. A MC motif in silkworm Argonaute 1 is indispensible for translation repression. INSECT MOLECULAR BIOLOGY 2013; 22:320-330. [PMID: 23521747 DOI: 10.1111/imb.12023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Small RNA-mediated gene silencing is a fundamental gene regulatory mechanism, which is conserved in many organisms. Argonaute (Ago) family proteins in the RNA-induced silencing complex (RISC) play crucial roles in RNA interference (RNAi) pathways. In the silkworm Bombyx mori, four Ago proteins have been identified, named as Ago1, Ago2, Ago3 and Siwi. Ago2 participates in double-stranded RNA (dsRNA)-induced RNAi, whereas Ago3 and Siwi are involved in the Piwi-interacting RNA (piRNA) pathway. However, there is no experimental evidence concerning silkworm Ago1 (BmAgo1) in the RNAi mechanism. In the present study, we analysed the function of BmAgo1 in the microRNA (miRNA)-mediated RNAi pathway using tethering and miRNA sensor reporter assays. These results clearly demonstrate that BmAgo1 plays an indispensable role in translation repression in silkworm. Moreover, coimmunoprecipitation data indicated that BmAgo1 interacts with BmDcp2, an orthologue of mRNA-decapping enzyme 2 (Dcp2) protein in the Drosophila processing-bodies (P-bodies). Substitutions of two conserved phenylalanines (F522 and F557) by valines in the MC motif strongly impaired the function of BmAgo1 in translation repression and its localization in P-bodies, suggesting that these two amino acid residues in the MC motif of BmAgo1 are prerequisites for mRNA translation repression in B. mori.
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Affiliation(s)
- L Zhu
- Laboratory of Silkworm Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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17
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Hur JK, Zinchenko MK, Djuranovic S, Green R. Regulation of Argonaute slicer activity by guide RNA 3' end interactions with the N-terminal lobe. J Biol Chem 2013; 288:7829-7840. [PMID: 23329841 PMCID: PMC3597821 DOI: 10.1074/jbc.m112.441030] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/16/2013] [Indexed: 12/18/2022] Open
Abstract
Structural studies indicate that binding of both the guide RNA (siRNA and miRNA) and the target mRNA trigger substantial conformational changes in the Argonaute proteins. Here we explore the role of the N-terminal lobe (and its PAZ domain) in these conformational changes using biochemical and cell culture-based approaches. In vitro, whereas deletion (or mutation) of the N-terminal lobe of DmAgo1 and DmAgo2 had no effect on binding affinity to guide RNAs, we observed a loss of protection of the 3' end of the guide RNA and decreased target RNA binding; consistent with this, in cells, loss of function DmAgo1 PAZ variant proteins (PAZ6 and ΔN-PAZ) still bind RNA, although the RNAs are shorter than normal. We also find that deletion of the N-terminal lobe results in constitutive activation of endogenous PIWI domain-based cleavage activity in vitro, providing insights into how cleavage activity may be regulated in vivo in response to different types of pairing interactions with the target mRNAs.
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Affiliation(s)
- Junho K Hur
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Michelle K Zinchenko
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Sergej Djuranovic
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.
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18
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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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19
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Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, Hur JK, Aravin AA, Tóth KF. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev 2013; 27:390-9. [PMID: 23392610 DOI: 10.1101/gad.209841.112] [Citation(s) in RCA: 374] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the metazoan germline, piwi proteins and associated piwi-interacting RNAs (piRNAs) provide a defense system against the expression of transposable elements. In the cytoplasm, piRNA sequences guide piwi complexes to destroy complementary transposon transcripts by endonucleolytic cleavage. However, some piwi family members are nuclear, raising the possibility of alternative pathways for piRNA-mediated regulation of gene expression. We found that Drosophila Piwi is recruited to chromatin, colocalizing with RNA polymerase II (Pol II) on polytene chromosomes. Knockdown of Piwi in the germline increases expression of transposable elements that are targeted by piRNAs, whereas protein-coding genes remain largely unaffected. Derepression of transposons upon Piwi depletion correlates with increased occupancy of Pol II on their promoters. Expression of piRNAs that target a reporter construct results in a decrease in Pol II occupancy and an increase in repressive H3K9me3 marks and heterochromatin protein 1 (HP1) on the reporter locus. Our results indicate that Piwi identifies targets complementary to the associated piRNA and induces transcriptional repression by establishing a repressive chromatin state when correct targets are found.
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Affiliation(s)
- Adrien Le Thomas
- California Institute of Technology, Pasadena, California 91125, USA
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20
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Thangavel C, Boopathi E, Ertel A, Lim M, Addya S, Fortina P, Witkiewicz AK, Knudsen ES. Regulation of miR106b cluster through the RB pathway: mechanism and functional targets. Cell Cycle 2012; 12:98-111. [PMID: 23255112 DOI: 10.4161/cc.23029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The RB pathway plays a critical role in proliferation control that is commonly subverted in tumor development. However, restoration of RB pathway function can be elicited in many tumor cells by the inhibition of CDK4/6 activity that leads to dephosphorylation of RB and subsequent repression of E2F-mediated transcription. In this context, active RB/E2F complexes inhibit the expression of a critical program of coding genes that promote cell cycle progression. However, the non-coding RNA target genes downstream from RB that could be relevant for tumor biology remain obscure. Here, miRNA gene expression profiling identified the miR106b cluster as being efficiently repressed with CDK4/6 inhibition in an E2F and RB-dependent manner. Importantly, the miR106B-cluster is intragenic of MCM7, and through a series of functional studies, the basis of MCM7 regulation and concordant expression of the miRNA species within the 106b cluster was determined. Importantly, RB-mediated repression of the 106b cluster enhances the transcript levels of p21Cip1 and PTEN. These data provide a mechanistic basis for cross-talk between the RB pathway and p21 and PTEN through the regulation of the MCM7/miR106b locus.
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21
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Yamayoshi A, Yamada Y, Kobori A, Murakami A. Structural Insights for Design of Inhibitors against RISC Function. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Asako Yamayoshi
- Department of Biomolecular Engineering, Kyoto Institute of Technology
| | - Yukiko Yamada
- Department of Biomolecular Engineering, Kyoto Institute of Technology
| | - Akio Kobori
- Department of Biomolecular Engineering, Kyoto Institute of Technology
| | - Akira Murakami
- Department of Biomolecular Engineering, Kyoto Institute of Technology
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22
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Bouasker S, Simard MJ. The slicing activity of miRNA-specific Argonautes is essential for the miRNA pathway in C. elegans. Nucleic Acids Res 2012; 40:10452-62. [PMID: 22904066 PMCID: PMC3488219 DOI: 10.1093/nar/gks748] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Among the set of Argonautes proteins encoded by metazoan genomes, some have conserved amino acids important for catalytic or slicing activity. The functional significance of these residues in microRNA (miRNA)-specific Argonautes in animals is still unclear since miRNAs do not induce site-specific cleavage of targeted messenger RNAs (mRNAs), unlike small interfering RNAs (siRNAs). Here, we report that miRNA-specific ALG-1 and ALG-2 Argonautes from Caenorhabditis elegans possess the slicing activity normally implicated in the siRNA-silencing pathway. We also find that ALG-1/2 can bind and use a Dicer-processed miRNA duplex to target mRNAs, suggesting an ability to displace RNA strands. Importantly, the slicing activity of ALG-1 or ALG-2 is essential for the miRNA pathway in vivo, as shown by the accumulation of truncated miRNA precursors and altered miRNA-induced silencing complex (miRISC) formation. Taken together, our data demonstrate that the slicing activity of Argonautes contributes to a new and unexpected step in the canonical miRNA pathway that occurs prior to miRISC loading in animals.
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Affiliation(s)
- Samir Bouasker
- Laval University Cancer Research Centre, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
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23
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24
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Structural insights into small RNA sorting and mRNA target binding by Arabidopsis Argonaute Mid domains. FEBS Lett 2012; 586:3200-7. [DOI: 10.1016/j.febslet.2012.06.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/22/2012] [Indexed: 12/21/2022]
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25
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Wei KF, Wu LJ, Chen J, Chen YF, Xie DX. Structural evolution and functional diversification analyses of argonaute protein. J Cell Biochem 2012; 113:2576-85. [DOI: 10.1002/jcb.24133] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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26
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Fabian MR, Sonenberg N. The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat Struct Mol Biol 2012; 19:586-93. [PMID: 22664986 DOI: 10.1038/nsmb.2296] [Citation(s) in RCA: 775] [Impact Index Per Article: 59.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Since their discovery almost two decades ago, microRNAs (miRNAs) have been shown to function by post-transcriptionally regulating protein accumulation. Understanding how miRNAs silence targeted mRNAs has been the focus of intensive research. Multiple models have been proposed, with few mechanistic details having been worked out. However, the past few years have witnessed a quantum leap forward in our understanding of the molecular mechanics of miRNA-mediated gene silencing. In this review we describe recent discoveries, with an emphasis on how miRISC post-transcriptionally controls gene expression by inhibiting translation and/or initiating mRNA decay, and how trans-acting factors control miRNA action.
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Affiliation(s)
- Marc R Fabian
- Department of Biochemistry, Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada.
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27
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Lages E, Ipas H, Guttin A, Nesr H, Berger F, Issartel JP. MicroRNAs: molecular features and role in cancer. Front Biosci (Landmark Ed) 2012; 17:2508-40. [PMID: 22652795 DOI: 10.2741/4068] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
microRNAs (miRNAs) are small noncoding endogenously produced RNAs that play key roles in controlling the expression of many cellular proteins. Once they are recruited and incorporated into a ribonucleoprotein complex miRISC, they can target specific mRNAs in a miRNA sequence-dependent process and interfere in the translation into proteins of the targeted mRNAs via several mechanisms. Consequently, miRNAs can regulate many cellular pathways and processes. Dysregulation of their physiological roles may largely contribute to disease. In particular, in cancer, miRNAs can be involved in the deregulation of the expression of important genes that play key roles in tumorigenesis, tumor development, and angiogenesis and have oncogenic or tumor suppressor roles. This review focuses on the biogenesis and maturation of miRNAs, their mechanisms of gene regulation, and the way their expression is deregulated in cancer. The involvement of miRNAs in several oncogenic pathways such as angiogenesis and apoptosis, and in the inter-cellular dialog mediated by miRNA-loaded exosomes as well as the development of new therapeutical strategies based on miRNAs will be discussed.
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Affiliation(s)
- Elodie Lages
- INSERM, U836, Team7 Nanomedicine and Brain, BP 170, Grenoble, France
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28
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Azzam G, Smibert P, Lai EC, Liu JL. Drosophila Argonaute 1 and its miRNA biogenesis partners are required for oocyte formation and germline cell division. Dev Biol 2012; 365:384-94. [PMID: 22445511 DOI: 10.1016/j.ydbio.2012.03.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 03/05/2012] [Accepted: 03/07/2012] [Indexed: 11/16/2022]
Abstract
Argonaute 1 (Ago1) is a member of the Argonaute/PIWI protein family involved in small RNA-mediated gene regulation. In Drosophila, Ago1 plays a specific role in microRNA (miRNA) biogenesis and function. Previous studies have demonstrated that Ago1 regulates the fate of germline stem cells. However, the function of Ago1 in other aspects of oogenesis is still elusive. Here we report the function of Ago1 in developing egg chambers. We find that Ago1 protein is enriched in the oocytes and is also highly expressed in the cytoplasm of follicle cells. Clonal analysis of multiple ago1 mutant alleles shows that many mutant egg chambers contain only 8 nurse cells without an oocyte which is phenocopied in dicer-1, pasha and drosha mutants. Our results suggest that Ago1 and its miRNA biogenesis partners play a role in oocyte determination and germline cell division in Drosophila.
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Affiliation(s)
- Ghows Azzam
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, South Parks Road, University of Oxford, Oxford, UK
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29
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Kenski DM, Willingham AT, Haringsma HJ, Li JJ, Flanagan WM. In vivo activity and duration of short interfering RNAs containing a synthetic 5'-phosphate. Nucleic Acid Ther 2012; 22:90-5. [PMID: 22400991 DOI: 10.1089/nat.2011.0333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Endogenous and exogenous short interfering RNAs (siRNAs) require a 5'-phosphate for loading into Ago2 and cleavage of the target mRNA. We applied a synthetic 5'-phosphate to siRNA guide strands to evaluate if phosphorylation in vivo is rate limiting for maximal siRNA knockdown and duration. We report, for the first time, an in vivo evaluation of siRNAs with a synthetic 5'-phosphate compared to their unphosphorylated versions. siRNAs that contained a 5'-phosphate had the same activity in vivo compared with unphosphorylated siRNAs, indicating phosphorylation of an siRNA is not a rate limiting step in vivo.
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30
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Tan GS, Chiu CH, Garchow BG, Metzler D, Diamond SL, Kiriakidou M. Small molecule inhibition of RISC loading. ACS Chem Biol 2012; 7:403-10. [PMID: 22026461 PMCID: PMC3282558 DOI: 10.1021/cb200253h] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Argonaute proteins are the core components of the microRNP/RISC.
The biogenesis and function of microRNAs and endo- and exo- siRNAs
are regulated by Ago2, an Argonaute protein with RNA binding and nuclease
activities. Currently, there are no in vitro assays
suitable for large-scale screening of microRNP/RISC loading modulators.
We describe a novel in vitro assay that is based
on fluorescence polarization of TAMRA-labeled RNAs loaded to human
Ago2. Using this assay, we identified potent small-molecule inhibitors
of RISC loading, including aurintricarboxylic acid (IC50 = 0.47 μM), suramin (IC50 = 0.69 μM), and
oxidopamine HCL (IC50 = 1.61 μM). Small molecules
identified by this biochemical screening assay also inhibited siRNA
loading to endogenous Ago2 in cultured cells.
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Affiliation(s)
- Grace S. Tan
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Chun-Hao Chiu
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Barry G. Garchow
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - David Metzler
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Scott L. Diamond
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Marianthi Kiriakidou
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
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31
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MicroRNA-binding is required for recruitment of human Argonaute 2 to stress granules and P-bodies. Biochem Biophys Res Commun 2011; 414:259-64. [DOI: 10.1016/j.bbrc.2011.09.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 09/14/2011] [Indexed: 12/13/2022]
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32
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Choe J, Cho H, Chi SG, Kim YK. Ago2/miRISC-mediated inhibition of CBP80/20-dependent translation and thereby abrogation of nonsense-mediated mRNA decay require the cap-associating activity of Ago2. FEBS Lett 2011; 585:2682-7. [DOI: 10.1016/j.febslet.2011.07.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 07/19/2011] [Accepted: 07/28/2011] [Indexed: 02/04/2023]
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Abstract
The tenth annual Keystone Symposium on the Mechanism and Biology of Silencing convened in Monterey, California, in March 2011. Those seeking some West Coast sunshine were, unfortunately, met with incessant precipitation throughout the meeting. Nevertheless, attendees were brightened by enlightening and vigorous scientific discussions. Here, we summarize the results presented at the meeting, which inspire and push this expanding field into new territories.
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Affiliation(s)
- Olivia S. Rissland
- Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Eric C. Lai
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
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34
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Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute protein. Proc Natl Acad Sci U S A 2011; 108:10466-71. [PMID: 21646546 DOI: 10.1073/pnas.1103946108] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Argonaute proteins (AGOs) are essential effectors in RNA-mediated gene silencing pathways. They are characterized by a bilobal architecture, in which one lobe contains the N-terminal and PAZ domains and the other contains the MID and PIWI domains. Here, we present the first crystal structure of the MID-PIWI lobe from a eukaryotic AGO, the Neurospora crassa QDE-2 protein. Compared to prokaryotic AGOs, the domain orientation is conserved, indicating a conserved mode of nucleic acid binding. The PIWI domain shows an adaptable surface loop next to a eukaryote-specific α-helical insertion, which are both likely to contact the PAZ domain in a conformation-dependent manner to sense the functional state of the protein. The MID-PIWI interface is hydrophilic and buries residues that were previously thought to participate directly in the allosteric regulation of guide RNA binding. The interface includes the binding pocket for the guide RNA 5' end, and residues from both domains contribute to binding. Accordingly, micro-RNA (miRNA) binding is particularly sensitive to alteration in the MID-PIWI interface in Drosophila melanogaster AGO1 in vivo. The structure of the QDE-2 MID-PIWI lobe provides molecular and mechanistic insight into eukaryotic AGOs and has significant implications for understanding the role of these proteins in silencing.
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35
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Frank F, Fabian MR, Stepinski J, Jemielity J, Darzynkiewicz E, Sonenberg N, Nagar B. Structural analysis of 5'-mRNA-cap interactions with the human AGO2 MID domain. EMBO Rep 2011; 12:415-20. [PMID: 21475248 DOI: 10.1038/embor.2011.48] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Revised: 02/25/2011] [Accepted: 03/01/2011] [Indexed: 12/15/2022] Open
Abstract
In RNA silencing, microRNA (miRNA)-mediated translational repression occurs through mechanisms that do not invoke messenger-RNA (mRNA) target cleavage by Argonaute proteins. The nature of these mechanisms is unclear, but several recent studies have proposed that a direct interaction between the mRNA-cap and the middle (MID) domain of Argonautes is involved. Here, we present crystallographic and NMR data demonstrating that cap analogues do not bind significantly to the isolated MID domain of human Argonaute 2 (hAGO2) and are found in the miRNA 5'-nucleotide binding site in an implausible binding mode. Additionally, in vitro pull-down experiments with full-length hAGO2 indicate that the interaction with cap analogues is nonspecific.
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Affiliation(s)
- Filipp Frank
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
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36
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Pandey SP, Minesinger BK, Kumar J, Walker GC. A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq. Nucleic Acids Res 2011; 39:4691-708. [PMID: 21325267 PMCID: PMC3113577 DOI: 10.1093/nar/gkr060] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The SMc01113/YbeY protein, belonging to the UPF0054 family, is highly conserved in nearly every bacterium. However, the function of these proteins still remains elusive. Our results show that SMc01113/YbeY proteins share structural similarities with the MID domain of the Argonaute (AGO) proteins, and might similarly bind to a small-RNA (sRNA) seed, making a special interaction with the phosphate on the 5′-side of the seed, suggesting they may form a component of the bacterial sRNA pathway. Indeed, eliminating SMc01113/YbeY expression in Sinorhizobium meliloti produces symbiotic and physiological phenotypes strikingly similar to those of the hfq mutant. Hfq, an RNA chaperone, is central to bacterial sRNA-pathway. We evaluated the expression of 13 target genes in the smc01113 and hfq mutants. Further, we predicted the sRNAs that may potentially target these genes, and evaluated the accumulation of nine sRNAs in WT and smc01113 and hfq mutants. Similar to hfq, smc01113 regulates the accumulation of sRNAs as well as the target mRNAs. AGOs are central components of the eukaryotic sRNA machinery and conceptual parallels between the prokaryotic and eukaryotic sRNA pathways have long been drawn. Our study provides the first line of evidence for such conceptual parallels. Furthermore, our investigation gives insights into the sRNA-mediated regulation of stress adaptation in S. meliloti.
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Affiliation(s)
- Shree P Pandey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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37
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Abstract
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) act with the Argonaute family of proteins to regulate target messenger RNAs (mRNAs) posttranscriptionally. SiRNAs typically induce endonucleolytic cleavage of mRNA with near-perfect complementarity. For targets with less complementarity, both translational repression and mRNA destabilization mechanisms have been implicated in miRNA-mediated gene repression, although the timing, coupling, and relative importance of these events have not been determined. Here, we review gene-specific and global approaches that probe miRNA function and mechanism, looking for a unifying model. More systematic analyses of the molecular specificities of the core components coupled with analysis of the relative timing of the different events will ultimately shed light on the mechanism of miRNA-mediated repression.
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Affiliation(s)
- Sergej Djuranovic
- Howard Hughes Medical Institute (HHMI), Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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38
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Leung AKL, Young AG, Bhutkar A, Zheng GX, Bosson AD, Nielsen CB, Sharp PA. Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat Struct Mol Biol 2011; 18:237-44. [PMID: 21258322 PMCID: PMC3078052 DOI: 10.1038/nsmb.1991] [Citation(s) in RCA: 212] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 11/29/2010] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) are 19-22-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking immunoprecipitation using antibodies to Argonaute (Ago2) followed by deep sequencing of RNAs (CLIP-seq). We also performed CLIP-seq in Dicer⁻/⁻ mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was miRNA dependent. A significantly enriched motif, GCACUU, was identified only in wild-type mESCs in 3' untranslated and coding regions. This motif matches the seed of a miRNA family that constitutes ~68% of the mESC miRNA population. Unexpectedly, a G-rich motif was enriched in sequences cross-linked to Ago2 in both the presence and absence of miRNAs. Expression analysis and reporter assays confirmed that the seed-related motif confers miRNA-directed regulation on host mRNAs and that the G-rich motif can modulate this regulation.
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Affiliation(s)
- Anthony K L Leung
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010; 11:597-610. [PMID: 20661255 DOI: 10.1038/nrg2843] [Citation(s) in RCA: 3647] [Impact Index Per Article: 243.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are a large family of post-transcriptional regulators of gene expression that are approximately 21 nucleotides in length and control many developmental and cellular processes in eukaryotic organisms. Research during the past decade has identified major factors participating in miRNA biogenesis and has established basic principles of miRNA function. More recently, it has become apparent that miRNA regulators themselves are subject to sophisticated control. Many reports over the past few years have reported the regulation of miRNA metabolism and function by a range of mechanisms involving numerous protein-protein and protein-RNA interactions. Such regulation has an important role in the context-specific functions of miRNAs.
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Affiliation(s)
- Jacek Krol
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
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Crystal structure and ligand binding of the MID domain of a eukaryotic Argonaute protein. EMBO Rep 2010; 11:522-7. [PMID: 20539312 PMCID: PMC2897117 DOI: 10.1038/embor.2010.81] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 05/10/2010] [Accepted: 05/12/2010] [Indexed: 11/08/2022] Open
Abstract
Argonaute (AGO) proteins are core components of RNA-induced silencing complexes and have essential roles in RNA-mediated gene silencing. They are characterized by a bilobal architecture, consisting of one lobe containing the amino-terminal and PAZ domains and another containing the MID and PIWI domains. Except for the PAZ domain, structural information on eukaryotic AGO domains is not yet available. In this study, we report the crystal structure of the MID domain of the eukaryotic AGO protein QDE-2 from Neurospora crassa. This domain adopts a Rossmann-like fold and recognizes the 5'-terminal nucleotide of a guide RNA in a manner similar to its prokaryotic counterparts. The 5'-nucleotide-binding site shares common residues with a second, adjacent ligand-binding site, suggesting a mechanism for the cooperative binding of ligands to the MID domain of eukaryotic AGOs.
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Gu S, Kay MA. How do miRNAs mediate translational repression? SILENCE 2010; 1:11. [PMID: 20459656 PMCID: PMC2881910 DOI: 10.1186/1758-907x-1-11] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 05/07/2010] [Indexed: 01/12/2023]
Abstract
Micro(mi)RNAs regulate gene expression by what are believed to be related but separate mechanistic processes. The relative contribution that each process plays, their mechanistic overlap, and the degree by which they regulate complex genetic networks is still being unraveled. One process by which miRNAs inhibit gene expression occurs through translational repression. In recent years, there has been a plethora of studies published, which have resulted in various molecular models of how miRNAs impair translation. At first evaluation, it appears that these models are quite different and incompatible with one another. In this paper, we focus on possible explanations for the various interpretations of these data sets, and provide a model that we believe is consistent with many of the observations published to date.
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Affiliation(s)
- Shuo Gu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA.
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Minshall N, Allison R, Marnef A, Wilczynska A, Standart N. Translational control assessed using the tethered function assay in Xenopus oocytes. Methods 2010; 51:165-9. [PMID: 20188836 DOI: 10.1016/j.ymeth.2010.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 02/18/2010] [Accepted: 02/20/2010] [Indexed: 10/19/2022] Open
Abstract
The tethered function assay is a method designed to address the role of an RNA-binding protein upon the metabolism of a reporter RNA. The basis of this assay is to artificially tether a test protein to a reporter mRNA by employing an unrelated bacteriophage MS2 or lambda N RNA-protein interaction, and to assess the effects of the test protein on the reporter RNA. In this chapter, we first discuss the principles and validity of the tethered function approach, drawing on appropriate examples from several cell types and of many proteins that regulate RNA in a variety of processes, including RNA processing (splicing, polyadenylation/deadenylation, decay), localisation and protein synthesis. Secondly, we will focus on the use of this approach to monitor translational activation and repression in Xenopus oocytes, giving a detailed protocol, and discussing possible optimizations we have explored.
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Affiliation(s)
- Nicola Minshall
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
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