1
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Sekar V, Mármol-Sánchez E, Kalogeropoulos P, Stanicek L, Sagredo EA, Widmark A, Doukoumopoulos E, Bonath F, Biryukova I, Friedländer MR. Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE. Nat Biotechnol 2024; 42:1296-1302. [PMID: 37735263 PMCID: PMC11324520 DOI: 10.1038/s41587-023-01951-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions of cells. Here we have overcome these limitations by fusing the miRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing the detection of miRNA targets transcriptome-wide in single cells. miRNAs guide the fusion protein to their natural target transcripts, causing them to undergo A>I editing, which can be detected by sensitive single-cell RNA sequencing. We show that agoTRIBE identifies functional miRNA targets, which are supported by evolutionary sequence conservation. In one application of the method we study microRNA interactions in single cells and identify substantial differential targeting across the cell cycle. AgoTRIBE also provides transcriptome-wide measurements of RNA abundance and allows the deconvolution of miRNA targeting in complex tissues at the single-cell level.
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Affiliation(s)
- Vaishnovi Sekar
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Laura Stanicek
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eduardo A Sagredo
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Albin Widmark
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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2
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Arora R, Bodak M, Penouty L, Hackman C, Ciaudo C. Sequestration of
LINE
‐1 in cytosolic aggregates by
MOV10
restricts retrotransposition. EMBO Rep 2022; 23:e54458. [PMID: 35856394 PMCID: PMC9442310 DOI: 10.15252/embr.202154458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Rajika Arora
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Maxime Bodak
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Laura Penouty
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Cindy Hackman
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
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3
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Liu Y, Gao W, Wu S, Lu L, Chen Y, Guo J, Men S, Zhang X. AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis. PLANTS 2020; 9:plants9030362. [PMID: 32182993 PMCID: PMC7154835 DOI: 10.3390/plants9030362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/27/2020] [Accepted: 03/11/2020] [Indexed: 12/20/2022]
Abstract
Small RNA (sRNA) turnover is a key but poorly understood mechanism that determines the homeostasis of sRNAs. Animal XRN genes contribute the degradation of sRNAs, AtXRN2 and AtXRN3 also contribute the pri-miRNA processing and miRNA loop degradation in plants. However, the possible functions of the plant XRN genes in sRNA degradation are far from known. Here, we find that AtXRN4 contributes the turnover of plant sRNAs in Arabidopsis thaliana mainly by sRNA-seq, qRT-PCR and Northern blot. The mutation of AtXRN4 alters the sRNA profile and the accumulation of 21 nt sRNAs was increased. Some miRNA*s levels are significantly increased in xrn4 mutant plants. However, the accumulation of the primary miRNAs (pri-miRNAs) and miRNA precursors (pre-miRNAs) were generally unchanged in xrn4 mutant plants which indicates that AtXRN4 contributes the degradation of some miRNA*s. Moreover, AtXRN4 interacts with Arabidopsis Argonaute 2 (AtAGO2). This interaction takes place in Processing bodies (P-bodies). Taken together, our observations identified the interaction between XRN4 with AtAGO2 and suggested that plant XRN4 also contributes the turnover of sRNAs.
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Affiliation(s)
- Yan Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (W.G.); (S.W.); (L.L.); (Y.C.); (J.G.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenrui Gao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (W.G.); (S.W.); (L.L.); (Y.C.); (J.G.)
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University and Tianjin Key Laboratory of Protein Science, Tianjin 300071, China;
| | - Shuangyang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (W.G.); (S.W.); (L.L.); (Y.C.); (J.G.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (W.G.); (S.W.); (L.L.); (Y.C.); (J.G.)
| | - Yaqiu Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (W.G.); (S.W.); (L.L.); (Y.C.); (J.G.)
- Henan Normal University, Department of Life Sciences, Xinxiang, Henan 453007, China
| | - Junliang Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (W.G.); (S.W.); (L.L.); (Y.C.); (J.G.)
- Institute of Physical Science and Information Technology, Anhui University, He fei, Anhui 230601, China
| | - Shuzhen Men
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University and Tianjin Key Laboratory of Protein Science, Tianjin 300071, China;
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (W.G.); (S.W.); (L.L.); (Y.C.); (J.G.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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4
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Xu M, Mazur MJ, Tao X, Kormelink R. Cellular RNA Hubs: Friends and Foes of Plant Viruses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:40-54. [PMID: 31415225 DOI: 10.1094/mpmi-06-19-0161-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA granules are dynamic cellular foci that are widely spread in eukaryotic cells and play essential roles in cell growth and development, and immune and stress responses. Different types of granules can be distinguished, each with a specific function and playing a role in, for example, RNA transcription, modification, processing, decay, translation, and arrest. By means of communication and exchange of (shared) components, they form a large regulatory network in cells. Viruses have been reported to interact with one or more of these either cytoplasmic or nuclear granules, and act either proviral, to enable and support viral infection and facilitate viral movement, or antiviral, protecting or clearing hosts from viral infection. This review describes an overview and recent progress on cytoplasmic and nuclear RNA granules and their interplay with virus infection, first in animal systems and as a prelude to the status and current developments on plant viruses, which have been less well studied on this thus far.
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Affiliation(s)
- Min Xu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Magdalena J Mazur
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Xiaorong Tao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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5
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Wang Y, Shen W, Liang XH, Crooke ST. Phosphorothioate Antisense Oligonucleotides Bind P-Body Proteins and Mediate P-Body Assembly. Nucleic Acid Ther 2019; 29:343-358. [PMID: 31429620 DOI: 10.1089/nat.2019.0806] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Antisense oligonucleotides (ASOs) regulate gene expression by binding to complementary target RNA, and ASOs can be designed to take advantage of a growing array of post RNA binding molecular mechanisms. Intracellular trafficking of ASOs influences their efficacy. We have identified a number of membrane-less structures in the nucleus, nucleolus, and cytoplasm where phosphorothioate-modified ASOs (PS-ASOs) accumulate and have shown that PS-ASOs can induce the formation of new nuclear structures such as PS-bodies and paraspeckle-like structures. In this study, we report that PS-ASOs can localize to cytoplasmic processing bodies (P-bodies) and increase the number of P-bodies in cells. The antisense activity of PS-ASOs was not affected by the absence of essential P-body assembly proteins DDX6 and LSm14A. Moreover, the effects of PS-ASOs on P-body assembly were independent of their antisense activities. The phosphorothioate modification stabilizes the association between ASOs and cellular proteins and is essential for the P-body localization of ASOs. Since PS-ASOs bind to major P-body components, PS-ASOs may serve as scaffolds for P-body formation. Taken together, these results indicate that interactions of PS-ASO with proteins, rather than antisense activities, are essential for the dynamic interplay between PS-ASOs and P-bodies.
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Affiliation(s)
- Ying Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
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6
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Standart N, Weil D. P-Bodies: Cytosolic Droplets for Coordinated mRNA Storage. Trends Genet 2018; 34:612-626. [PMID: 29908710 DOI: 10.1016/j.tig.2018.05.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/21/2022]
Abstract
P-bodies (PBs) are cytosolic RNP granules that are conserved among eukaryotic organisms. In the past few years, major progress has been made in understanding the biochemical and biophysical mechanisms that lead to their formation. However, whether they play a role in mRNA storage or decay remains actively debated. P-bodies were recently isolated from human cells by a novel fluorescence-activated particle sorting (FAPS) approach that enabled the characterization of their protein and RNA content, providing new insights into their function. Together with recent innovative imaging studies, these new data show that mammalian PBs are primarily involved not in RNA decay but rather in the coordinated storage of mRNAs encoding regulatory functions. These small cytoplasmic droplets could thus be important for cell adaptation to the environment.
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Affiliation(s)
- Nancy Standart
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, F-75005 Paris, France.
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7
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Wang X, Chang L, Wang H, Su A, Wu Z. Dcp1a and GW182 Induce Distinct Cellular Aggregates and Have Different Effects on microRNA Pathway. DNA Cell Biol 2017; 36:565-570. [DOI: 10.1089/dna.2017.3633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Xiaohui Wang
- Department of Hematology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, People's Republic of China
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Liang Chang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Huanru Wang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Airong Su
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
- State Key Lab of Analytical Chemistry for Life Science, Nanjing University, Nanjing, People's Republic of China
- Jiangsu Laboratory for Molecular Medicines, Nanjing University, Nanjing, People's Republic of China
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8
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Alves LR, Goldenberg S. RNA-binding proteins related to stress response and differentiation in protozoa. World J Biol Chem 2016; 7:78-87. [PMID: 26981197 PMCID: PMC4768126 DOI: 10.4331/wjbc.v7.i1.78] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 09/23/2015] [Accepted: 11/17/2015] [Indexed: 02/05/2023] Open
Abstract
RNA-binding proteins (RBPs) are key regulators of gene expression. There are several distinct families of RBPs and they are involved in the cellular response to environmental changes, cell differentiation and cell death. The RBPs can differentially combine with RNA molecules and form ribonucleoprotein (RNP) complexes, defining the function and fate of RNA molecules in the cell. RBPs display diverse domains that allow them to be categorized into distinct families. They play important roles in the cellular response to physiological stress, in cell differentiation, and, it is believed, in the cellular localization of certain mRNAs. In several protozoa, a physiological stress (nutritional, temperature or pH) triggers differentiation to a distinct developmental stage. Most of the RBPs characterized in protozoa arise from trypanosomatids. In these protozoa gene expression regulation is mostly post-transcriptional, which suggests that some RBPs might display regulatory functions distinct from those described for other eukaryotes. mRNA stability can be altered as a response to stress. Transcripts are sequestered to RNA granules that ultimately modulate their availability to the translation machinery, storage or degradation, depending on the associated proteins. These aggregates of mRNPs containing mRNAs that are not being translated colocalize in cytoplasmic foci, and their numbers and size vary according to cell conditions such as oxidative stress, nutritional status and treatment with drugs that inhibit translation.
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9
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Buemo CP, Gambini A, Moro LN, Hiriart MI, Fernández-Martín R, Collas P, Salamone DF. Embryo Aggregation in Pig Improves Cloning Efficiency and Embryo Quality. PLoS One 2016; 11:e0146390. [PMID: 26894831 PMCID: PMC4760708 DOI: 10.1371/journal.pone.0146390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/16/2015] [Indexed: 11/19/2022] Open
Abstract
In this study, we analyzed the effects of the cloned embryo aggregation on in vitro embryo development and embryo quality by measuring blastocyst diameter and cell number, DNA fragmentation levels and the expression of genes associated with pluripotency, apoptosis, trophoblast and DNA methylation in the porcine. Zona-free reconstructed cloned embryos were cultured in the well of the well system, placing one (1x non aggregated group) or three (3x group) embryos per microwell. Our results showed that aggregation of three embryos increased blastocyst formation rate and blastocyst diameter of cloned pig embryos. DNA fragmentation levels in 3x aggregated cloned blastocysts were significantly decreased compared to 1x blastocysts. Levels of Oct4, Klf4, Igf2, Bax and Dnmt 1 transcripts were significantly higher in aggregated embryos, whereas Nanog levels were not affected. Transcripts of Cdx2 and Bcl-xl were essentially non-detectable. Our study suggests that embryo aggregation in the porcine may be beneficial for cloned embryo development and embryo quality, through a reduction in apoptotic levels and an improvement in cell reprogramming.
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Affiliation(s)
- Carla Paola Buemo
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - Andrés Gambini
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - Lucia Natalia Moro
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - María Inés Hiriart
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - Rafael Fernández-Martín
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, Oslo, Norway
| | - Daniel Felipe Salamone
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
- * E-mail:
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10
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Matsui M, Li L, Janowski BA, Corey DR. Reduced Expression of Argonaute 1, Argonaute 2, and TRBP Changes Levels and Intracellular Distribution of RNAi Factors. Sci Rep 2015; 5:12855. [PMID: 26242502 PMCID: PMC4525381 DOI: 10.1038/srep12855] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022] Open
Abstract
Until recently, Argonaute 2 (AGO2) and other RNA factors were believed to be restricted to the cytoplasm of mammalian somatic cells. It is now becoming appreciated that RNAi factors can also be found in cell nuclei, but much remains to be learned about their transport, molecular recognition, and function. We find that siRNA-mediated reduction of AGO1 or AGO2 increases the proportion of AGO1 or AGO2 in cell nuclei. Inhibition of AGO1 expression led to increased AGO2 levels, while knockdown of AGO2 led to increased levels of AGO1. Blocking AGO1, AGO2, or TRBP expression changed expression levels and nuclear distribution of RNAi factors Dicer, TNRC6A (GW182), and TRBP. These data reveal the expression of RNAi proteins is mutually dependent and that perturbation can affect subcellular distribution of those factors inside cells.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Liande Li
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Bethany A Janowski
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - David R Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
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11
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Dysregulated RNA-Induced Silencing Complex (RISC) Assembly within CNS Corresponds with Abnormal miRNA Expression during Autoimmune Demyelination. J Neurosci 2015; 35:7521-37. [PMID: 25972178 DOI: 10.1523/jneurosci.4794-14.2015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) associate with Argonaute (Ago), GW182, and FXR1 proteins to form RNA-induced silencing complexes (RISCs). RISCs represent a critical checkpoint in the regulation and bioavailability of miRNAs. Recent studies have revealed dysregulation of miRNAs in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE); however, the function of RISCs in EAE and MS is largely unknown. Here, we examined the expression of Ago, GW182, and FXR1 in CNS tissue, oligodendrocytes (OLs), brain-infiltrating T lymphocytes, and CD3(+)splenocytes (SCs) of EAE mic, and found that global RISC protein levels were significantly dysregulated. Specifically, Ago2 and FXR1 levels were decreased in OLs and brain-infiltrating T cells in EAE mice. Accordingly, assembly of Ago2/GW182/FXR1 complexes in EAE brain tissues was disrupted, as confirmed by immunoprecipitation experiments. In parallel with alterations in RISC complex content in OLs, we found downregulation of miRNAs essential for differentiation and survival of OLs and myelin synthesis. In brain-infiltrating T lymphocytes, aberrant RISC formation contributed to miRNA-dependent proinflammatory helper T-cell polarization. In CD3(+) SCs, we found increased expression of both Ago2 and FXR1 in EAE compared with nonimmunized mice. Therefore, our results demonstrate a gradient in expression of miRNA between primary activated T cells in the periphery and polarized CNS-infiltrating T cells. These results suggest that, in polarized autoreactive effector T cells, miRNA synthesis is inhibited in response to dysregulated RISC assembly, allowing these cells to maintain a highly specific proinflammatory program. Therefore, our findings may provide a mechanism that leads to miRNA dysregulation in EAE/MS.
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12
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Biggar KK, Storey KB. Insight into post-transcriptional gene regulation: stress-responsive microRNAs and their role in the environmental stress survival of tolerant animals. J Exp Biol 2015; 218:1281-9. [DOI: 10.1242/jeb.104828] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
ABSTRACT
Living animals are constantly faced with various environmental stresses that challenge normal life, including: oxygen limitation, very low or high temperature, as well as restriction of water and food. It has been well established that in response to these stresses, tolerant organisms regularly respond with a distinct suite of cellular modifications that involve transcriptional, translational and post-translational modification. In recent years, a new mechanism of rapid and reversible transcriptome regulation, via the action of non-coding RNA molecules, has emerged into post-transcriptional regulation and has since been shown to be part of the survival response. However, these RNA-based mechanisms by which tolerant organisms respond to stressed conditions are not well understood. Recent studies have begun to show that non-coding RNAs control gene expression and translation of mRNA to protein, and can also have regulatory influence over major cellular processes. For example, select microRNAs have been shown to have regulatory influence over the cell cycle, apoptosis, signal transduction, muscle atrophy and fatty acid metabolism during periods of environmental stress. As we are on the verge of dissecting the roles of non-coding RNA in environmental stress adaptation, this Commentary summarizes the hallmark alterations in microRNA expression that facilitate stress survival.
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Affiliation(s)
- Kyle K. Biggar
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada N6A 5C1
| | - Kenneth B. Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
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13
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Aizer A, Kalo A, Kafri P, Shraga A, Ben-Yishay R, Jacob A, Kinor N, Shav-Tal Y. Quantifying mRNA targeting to P-bodies in living human cells reveals their dual role in mRNA decay and storage. J Cell Sci 2014; 127:4443-56. [PMID: 25128566 DOI: 10.1242/jcs.152975] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The 5'-to-3' mRNA degradation machinery localizes to cytoplasmic processing bodies (P-bodies), which are non-membranous structures found in all eukaryotes. Although P-body function has been intensively studied in yeast, less is known about their role in mammalian cells, such as whether P-body enzymes are actively engaged in mRNA degradation or whether P-bodies serve as mRNA storage depots, particularly during cellular stress. We examined the fate of mammalian mRNAs in P-bodies during translational stress, and show that mRNAs accumulate within P-bodies during amino acid starvation. The 5' and 3' ends of the transcripts residing in P-bodies could be identified, but poly(A) tails were not detected. Using the MS2 mRNA-tagging system for mRNA visualization in living cells, we found that a stationary mRNA population formed in P-bodies during translational stress, which cleared gradually after the stress was relieved. Dcp2-knockdown experiments showed that there is constant degradation of part of the P-body-associated mRNA population. This analysis demonstrates the dual role of P-bodies as decay sites and storage areas under regular and stress conditions.
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Affiliation(s)
- Adva Aizer
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Alon Kalo
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Pinhas Kafri
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Amit Shraga
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Rakefet Ben-Yishay
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Avi Jacob
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
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14
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Abstract
In eukaryotic cells, non-translating mRNAs can accumulate into cytoplasmic mRNP (messenger ribonucleoprotein) granules such as P-bodies (processing bodies) and SGs (stress granules). P-bodies contain the mRNA decay and translational repression machineries and are ubiquitously expressed in mammalian cells and lower eukaryote species including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans. In contrast, SGs are only detected during cellular stress when translation is inhibited and form from aggregates of stalled pre-initiation complexes. SGs and P-bodies are related to NGs (neuronal granules), which are essential in the localization and control of mRNAs in neurons. Importantly, RNA granules are linked to the cytoskeleton, which plays an important role in mediating many of their dynamic properties. In the present review, we discuss how P-bodies, SGs and NGs are linked to cytoskeletal networks and the importance of these linkages in maintaining localization of their RNA cargoes.
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15
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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: 59] [Impact Index Per Article: 5.4] [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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16
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Fritzler MJ, Chan EKL. The Discovery of GW Bodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:5-21. [DOI: 10.1007/978-1-4614-5107-5_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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17
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Reflections on ten years of history of, and future prospects for, GW182 and GW/P body research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:261-70. [PMID: 23224975 DOI: 10.1007/978-1-4614-5107-5_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Moser JJ, Fritzler MJ. Relationship of other cytoplasmic ribonucleoprotein bodies (cRNPB) to GW/P bodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:213-42. [PMID: 23224973 DOI: 10.1007/978-1-4614-5107-5_13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
GW/P body components are involved in the post-transcriptional -processing of messenger RNA (mRNA) through the RNA interference and 5' → 3' mRNA degradation pathways, as well as functioning in mRNA transport and stabilization. It is currently thought that the relevant mRNA silencing and degrading factors are partitioned to these cytoplasmic microdomains thus effecting post-transcriptional regulation and the prevention of accidental degradation of functional mRNA. Although much attention has focused on GW/P bodies, a variety of other cytoplasmic RNP bodies (cRNPB) also have highly specialized functions and have been shown to interact or co-localize with components of GW/P bodies. These cRNPB include neuronal transport RNP granules, stress granules, RNP-rich cytoplasmic germline granules or chromatoid bodies, sponge bodies, cytoplasmic prion protein-induced RNP granules, U bodies and TAM bodies. Of clinical relevance, autoantibodies directed against protein and miRNA components of GW/P bodies have been associated with autoimmune diseases, neurological diseases and cancer. Understanding the molecular function of GW/P bodies and their interactions with other cRNPB may provide clues to the etiology or pathogenesis of diseases associated with autoantibodies directed to these structures. This chapter will focus on the similarities and differences of the various cRNPB as an approach to understanding their functional relationships to GW/P bodies.
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Affiliation(s)
- Joanna J Moser
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
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19
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Mathematical Modeling of microRNA–Mediated Mechanisms of Translation Repression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 774:189-224. [DOI: 10.1007/978-94-007-5590-1_11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Leung AKL, Sharp PA. Quantifying Argonaute proteins in and out of GW/P-bodies: implications in microRNA activities. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:165-82. [PMID: 23224970 DOI: 10.1007/978-1-4614-5107-5_10] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
MicroRNAs (miRNAs) are a class of ∼22nt non-coding RNAs that regulate the translational potential and stability of mRNAs. Though constituting only 1-4% of human genes, miRNAs are predicted to regulate more than 60% of all mRNAs. The action of miRNAs is mediated through their associations with Argonaute proteins and mRNA targets. Previous studies indicated that though the majority of Argonaute proteins is diffusely distributed in the cytoplasm, a small fraction is consistently observed to be concentrated in a cytoplasmic compartment called GW/P-bodies. In this chapter, we will provide a quantitative and dynamic view of the subcellular localization of miRNA function, followed by a discussion on the possible roles of PBs in miRNA silencing.
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Affiliation(s)
- Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
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21
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Yao B, Li S, Chan EKL. Function of GW182 and GW bodies in siRNA and miRNA pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:71-96. [PMID: 23224966 DOI: 10.1007/978-1-4614-5107-5_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
GW182 is an 182 kDa protein with multiple glycine/tryptophan repeats (GW or WG) playing a central role in siRNA- and miRNA-mediated gene silencing. GW182 interacts with its functional partner Argonaute proteins (AGO) via multiple domains to exert its silencing activity in both pathways. In siRNA-mediated silencing, knockdown either GW182 or Ago2 causes loss of silencing activity correlating with the disassembly of GWBs. In contrast, GW182 and its longer isoform TNGW1 appear to be downstream repressors that function independent of Ago2, whereas the Ago2-GW182 interaction is critical for the localization of Ago2 in the cytoplasmic foci and its repression function. GW182 contains two non-overlapping repression domains that can trigger translational repression with mild effect on mRNA decay. Collectively, GW182 plays a critical role in miRNA-mediated gene silencing.
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Affiliation(s)
- Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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22
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Bukong TN, Hou W, Kodys K, Szabo G. Ethanol facilitates hepatitis C virus replication via up-regulation of GW182 and heat shock protein 90 in human hepatoma cells. Hepatology 2013; 57:70-80. [PMID: 22898980 PMCID: PMC3540130 DOI: 10.1002/hep.26010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 07/31/2012] [Indexed: 12/11/2022]
Abstract
UNLABELLED Alcohol use and hepatitis C virus (HCV) infection synergize to cause liver damage, and microRNA-122 (miR-122) appears to play a key role in this process. Argonaute 2 (Ago2), a key component of the RNA-induced silencing complex (RISC), has been shown to be important in modulating miR-122 function during HCV infection. However, GW182, a critical component of processing bodies (GW bodies) that is recruited by Ago2 to target messenger RNA (mRNA), has not been assessed in HCV infection. To characterize the role of GW182 in the pathogenesis of HCV infection, we determined its transcription and protein expression in an HCV J6/JFH1 culture system. Transcript and protein levels of GW182 as well as HCV RNA and protein expression increased with alcohol exposure. Specific silencing of mRNA expression by small interfering RNA against GW182 significantly decreased HCV RNA and protein expression. Overexpression of GW182 significantly increased HCV RNA and protein expression in HCV J6/JFH1 infected Huh7.5 cells. Furthermore, GW182 colocalized and coimmunoprecipitated with heat shock protein 90 (HSP90), which increased upon alcohol exposure with and without HCV infection and enhanced HCV gene expression. The use of an HSP90 inhibitor or knockdown of HSP90 decreased GW182 and miR-122 expression and significantly reduced HCV replication. CONCLUSION Overall, our results suggest that GW182 protein that is linked to miR-122 biogenesis and HSP90, which has been shown to stabilize the RISC, are novel host proteins that regulate HCV infection during alcohol abuse.
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Affiliation(s)
| | | | | | - Gyongyi Szabo
- Contact Information: Gyongyi Szabo, MD PhD, Department of Medicine, University of Massachusetts Medical School, LRB208, 364 Plantation Street, Worcester, MA 01605, USA; Tel: 00-1-508-856-5275; Fax: 00-1-508-856-4770;
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23
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Chan EKL, Ceribelli A, Satoh M. MicroRNA-146a in autoimmunity and innate immune responses. Ann Rheum Dis 2012; 72 Suppl 2:ii90-5. [PMID: 23253933 DOI: 10.1136/annrheumdis-2012-202203] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNA (miRNA) are approximately 22 nucleotide single-stranded RNA that regulate the stability of target messenger RNA by selective binding to specific sites at the 3'-untranslated regions (UTR). This triggers repression in translation and mRNA degradation. It has been estimated that approximately 60% of all mRNA are under the control of miRNA. Among the known hundreds of miRNA, some are considered master regulators controlling either a single or multiple cellular pathways. Some miRNA are known to affect development and cell differentiation, while others are implicated in immunity and autoimmune diseases. A very interesting example is miR-146a, which has been reported to be downregulated in systemic lupus erythematosus and upregulated in rheumatoid arthritis (RA). Several groups have recently focused their attention on miRNA in the pathogenesis of RA. Interestingly, the expression of miR-146a is upregulated in different cell types and tissues in RA patients. miRNA in RA could also be considered as possible future targets for new therapeutic approaches. This discussion will focus on the current understanding in the function of miR-146a in endotoxin tolerance and cross-tolerance, and how it may contribute to modulate the overproduction of known pathogenic cytokines, such as tumour necrosis factor α.
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Affiliation(s)
- Edward K L Chan
- Correspondence to Professor Edward K L Chan, Department of Oral Biology, University of Florida, Gainesville, FL 32610-0424, USA.
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24
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Bowen T, Jenkins RH, Fraser DJ. MicroRNAs, transforming growth factor beta-1, and tissue fibrosis. J Pathol 2012; 229:274-85. [DOI: 10.1002/path.4119] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 08/31/2012] [Accepted: 09/19/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Timothy Bowen
- Institute of Molecular and Experimental Medicine, School of Medicine; Cardiff University; UK
| | - Robert H Jenkins
- Institute of Molecular and Experimental Medicine, School of Medicine; Cardiff University; UK
| | - Donald J Fraser
- Institute of Molecular and Experimental Medicine, School of Medicine; Cardiff University; UK
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25
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Pager CT, Schütz S, Abraham TM, Luo G, Sarnow P. Modulation of hepatitis C virus RNA abundance and virus release by dispersion of processing bodies and enrichment of stress granules. Virology 2012; 435:472-84. [PMID: 23141719 DOI: 10.1016/j.virol.2012.10.027] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/11/2012] [Accepted: 10/16/2012] [Indexed: 12/12/2022]
Abstract
Components of cytoplasmic processing bodies (P-bodies) and stress granules can be subverted during viral infections to modulate viral gene expression. Because hepatitis C virus (HCV) RNA abundance is regulated by P-body components such as microRNA miR-122, Argonaute 2 and RNA helicase RCK/p54, we examined whether HCV infection modulates P-bodies and stress granules during viral infection. It was discovered that HCV infection decreased the number of P-bodies, but induced the formation of stress granules. Immunofluorescence studies revealed that a number of P-body and stress granule proteins co-localized with viral core protein at lipid droplets, the sites for viral RNA packaging. Depletion of selected P-body proteins decreased overall HCV RNA and virion abundance. Depletion of stress granule proteins also decreased overall HCV RNA abundance, but surprisingly enhanced the accumulation of infectious, extracellular virus. These data argue that HCV subverts P-body and stress granule components to aid in viral gene expression at particular sites in the cytoplasm.
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Affiliation(s)
- Cara T Pager
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5124, United States
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26
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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: 82] [Impact Index Per Article: 6.8] [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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27
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Ernoult-Lange M, Bénard M, Kress M, Weil D. P-bodies and mitochondria: which place in RNA interference? Biochimie 2012; 94:1572-7. [PMID: 22445682 DOI: 10.1016/j.biochi.2012.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 03/07/2012] [Indexed: 11/25/2022]
Abstract
Micro-RNAs (miRNAs) are major actors of RNA interference (RNAi), a regulation pathway which leads to translational repression and/or degradation of specific mRNAs. They provide target specificity by incorporating into the RISC complex and guiding its binding to mRNA. Since the discovery of RNAi, many progresses have been made on the mechanism of action of the RISC complex and on the identification of target mRNAs. However, the regulation of RNAi has been poorly investigated so far. Recently, various studies have revealed physical and functional relationships between RNAi, P-bodies and mitochondria. This review intends to recapitulate these data and discuss their potential importance in cell metabolism.
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28
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Pegtel DM, van de Garde MDB, Middeldorp JM. Viral miRNAs exploiting the endosomal-exosomal pathway for intercellular cross-talk and immune evasion. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:715-21. [PMID: 21855666 DOI: 10.1016/j.bbagrm.2011.08.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 08/02/2011] [Accepted: 08/03/2011] [Indexed: 12/21/2022]
Abstract
The class of persistent gamma-herpesviruses has developed a variety of strategies that exploit host-cell regulatory pathways to ensure a long-lasting, well-balanced infection of their host. However when these pathways are deregulated, an otherwise harmless infection can lead to disease including cancer. We recently demonstrated that the human herpes virus 4 (HHV4) also known as Epstein-Barr virus (EBV), encodes for small regulatory non-coding microRNAs (miRNAs) that can be transferred from an infected cell to uninfected neighboring cells. Upon arrival these miRNAs are functional in the recipient cell, in that they are able to down regulate specific target genes. These secreted miRNAs are transported to recipient cells via small nano-sized vesicles (known as exosomes) that are of endosomal origin, formed as intraluminal vesicles (ILV) inside multivesicular bodies (MVB). One question that needs to be addressed is how viral miRNAs are sorted into these exosomes. Mature miRNAs, including those of viral origin, are loaded into RNA-induced silencing complexes (RISC) for gene silencing via blocking mRNA translation and/or initiating mRNA decay. Recent insights indicate that cytoplasmic RNA granules rich in RISC complexes are closely associated with endosomes. In fact, selective components of RISC, including GW182 and Argonaut proteins, miRNAs and mRNAs are present in exosomes. Thus miRNA function, mRNA stability and exosome-mediated intercellular communication converge at the level of endosomes. Since endosomes can be considered as key intracellular cross-roads that regulate communication of cells with their exterior, including neighboring cells, it is perhaps not surprising that viruses have found means to exploit this pathway to their benefit. Little is known however, how and if (micro) RNA species are specifically sorted into ILVs and what (micro)RNA-binding proteins are involved. Here we discuss recent developments relating to intracellular trafficking and function of miRNA-containing protein complexes that EBV may exploit for promoting or restricting miRNAs sorting into exosomes for intercellular regulatory functions. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.
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Affiliation(s)
- D Michiel Pegtel
- VU University Medical Center, Department of Pathology, Amsterdam, the Netherlands.
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29
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Affiliation(s)
- Stacy L Erickson
- Division of Biology, University of California San Diego, La Jolla, CA 92093, USA
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30
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Macfarlane LA, Murphy PR. MicroRNA: Biogenesis, Function and Role in Cancer. Curr Genomics 2011; 11:537-61. [PMID: 21532838 PMCID: PMC3048316 DOI: 10.2174/138920210793175895] [Citation(s) in RCA: 1216] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 08/23/2010] [Accepted: 09/06/2010] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are small, highly conserved non-coding RNA molecules involved in the regulation of gene expression. MicroRNAs are transcribed by RNA polymerases II and III, generating precursors that undergo a series of cleavage events to form mature microRNA. The conventional biogenesis pathway consists of two cleavage events, one nuclear and one cytoplasmic. However, alternative biogenesis pathways exist that differ in the number of cleavage events and enzymes responsible. How microRNA precursors are sorted to the different pathways is unclear but appears to be determined by the site of origin of the microRNA, its sequence and thermodynamic stability. The regulatory functions of microRNAs are accomplished through the RNA-induced silencing complex (RISC). MicroRNA assembles into RISC, activating the complex to target messenger RNA (mRNA) specified by the microRNA. Various RISC assembly models have been proposed and research continues to explore the mechanism(s) of RISC loading and activation. The degree and nature of the complementarity between the microRNA and target determine the gene silencing mechanism, slicer-dependent mRNA degradation or slicer-independent translation inhibition. Recent evidence indicates that P-bodies are essential for microRNA-mediated gene silencing and that RISC assembly and silencing occurs primarily within P-bodies. The P-body model outlines microRNA sorting and shuttling between specialized P-body compartments that house enzymes required for slicer –dependent and –independent silencing, addressing the reversibility of these silencing mechanisms. Detailed knowledge of the microRNA pathways is essential for understanding their physiological role and the implications associated with dysfunction and dysregulation.
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Affiliation(s)
- Leigh-Ann Macfarlane
- Department of Physiology & Biophysics, Faculty of Medicine, Dalhousie University, 5850 College Street, Sir Charles Tupper Medical Building, Halifax, Nova Scotia, B3H 1X5, Canada
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31
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Wu D, Raafat M, Pak E, Hammond S, Murashov AK. MicroRNA machinery responds to peripheral nerve lesion in an injury-regulated pattern. Neuroscience 2011; 190:386-97. [PMID: 21689732 DOI: 10.1016/j.neuroscience.2011.06.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/02/2011] [Indexed: 12/20/2022]
Abstract
Recently, functional and potent RNA interference (RNAi) has been reported in peripheral nerve axons transfected with short-interfering RNA (siRNA). In addition, components of RNA-induced silencing complex (RISC) have been identified in axotomized sciatic nerve fibers as well as in regenerating dorsal root ganglia (DRG) neurons in vitro. Based on these observations, and on the fact that siRNA and microRNA (miRNA) share the same effector enzymes, we hypothesized that the endogenous miRNA biosynthetic pathway would respond to peripheral nerve injury. To answer this question, we investigated changes in the expression of miRNA biosynthetic enzymes following peripheral nerve crush injury in mice. Here, we show that several pivotal miRNA biosynthetic enzymes are expressed in an injury-regulated pattern in sciatic nerve in vivo, and in DRG axons in vitro. Moreover, the sciatic nerve lesion induced expression of mRNA-processing bodies (P-bodies), which are the local foci of mRNA degradation in DRG axons. In addition, a group of injury-regulated miRNAs was identified by miRNA microarray and validated by real-time quantitative PCR (qPCR) and in situ hybridization analyses. Taken together, our data support the hypothesis that the peripheral nerve regeneration processes may be regulated by miRNA pathway.
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Affiliation(s)
- D Wu
- Department of Physiology, East Carolina University, Greenville, NC 27834, USA
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32
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Ceribelli A, Nahid MA, Satoh M, Chan EKL. MicroRNAs in rheumatoid arthritis. FEBS Lett 2011; 585:3667-74. [PMID: 21600203 DOI: 10.1016/j.febslet.2011.05.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 05/03/2011] [Accepted: 05/04/2011] [Indexed: 12/11/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic and severe autoimmune disease that affects joint tissues, bone, and cartilage. However, the pathogenesis of RA is still unclear. Autoantibodies such as rheumatoid factor and anti-cyclic citrullinated peptide are useful tools for early diagnosis, monitoring disease activity, and predicting prognosis. Recently, many groups have focused their attention on the role of microRNAs in the pathogenesis of RA, as well as a potential biomarker to monitor RA. In fact, the expression of some microRNAs, such as miR-146a, is upregulated in different cell types and tissues in RA patients. MicroRNAs in RA could also be considered as possible future targets for new therapeutic approaches.
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Affiliation(s)
- Angela Ceribelli
- Department of Oral Biology, University of Florida, Gainesville, FL 32610-0424, USA.
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33
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Ricci EP, Limousin T, Soto-Rifo R, Allison R, Pöyry T, Decimo D, Jackson RJ, Ohlmann T. Activation of a microRNA response in trans reveals a new role for poly(A) in translational repression. Nucleic Acids Res 2011; 39:5215-31. [PMID: 21385827 PMCID: PMC3130266 DOI: 10.1093/nar/gkr086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Here, we report that the untreated rabbit reticulocyte lysate contains over 300 different endogenous microRNAs together with the major components of the RNA-induced silencing complex and thus can be used as a model in vitro system to study the effects of microRNAs on gene expression. By using this system, we were able to show that microRNA hybridization to its target resulted in a very rapid and strong inhibition of expression that was exerted exclusively at the level of translation initiation with no involvement of transcript degradation or deadenylation. Moreover, we demonstrate that the magnitude of microRNA-induced repression can only be recapitulated in the context of a competitive translating environment. By using a wide spectrum of competitor cellular and viral RNAs, we could further show that competition was not exerted at the level of general components of the translational machinery, but relied exclusively on the presence of the poly(A) tail with virtually no involvement of the cap structure.
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Affiliation(s)
- Emiliano P Ricci
- Ecole Normale Supérieure de Lyon, Unité de Virologie Humaine, IFR 128, Lyon, F-69364 France
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34
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Eulalio A, Fröhlich KS, Mano M, Giacca M, Vogel J. A candidate approach implicates the secreted Salmonella effector protein SpvB in P-body disassembly. PLoS One 2011; 6:e17296. [PMID: 21390246 PMCID: PMC3046968 DOI: 10.1371/journal.pone.0017296] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 01/28/2011] [Indexed: 01/11/2023] Open
Abstract
P-bodies are dynamic aggregates of RNA and proteins involved in several post-transcriptional regulation processes. P-bodies have been shown to play important roles in regulating viral infection, whereas their interplay with bacterial pathogens, specifically intracellular bacteria that extensively manipulate host cell pathways, remains unknown. Here, we report that Salmonella infection induces P-body disassembly in a cell type-specific manner, and independently of previously characterized pathways such as inhibition of host cell RNA synthesis or microRNA-mediated gene silencing. We show that the Salmonella-induced P-body disassembly depends on the activation of the SPI-2 encoded type 3 secretion system, and that the secreted effector protein SpvB plays a major role in this process. P-body disruption is also induced by the related pathogen, Shigella flexneri, arguing that this might be a new mechanism by which intracellular bacterial pathogens subvert host cell function.
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Affiliation(s)
- Ana Eulalio
- RNA Biology Group, Max Planck Institute for Infection Biology, Berlin, Germany
- * E-mail: (JV); (AE)
| | - Kathrin S. Fröhlich
- Institute of Molecular Infection Biology, Würzburg University, Würzburg, Germany
| | - Miguel Mano
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Jörg Vogel
- RNA Biology Group, Max Planck Institute for Infection Biology, Berlin, Germany
- Institute of Molecular Infection Biology, Würzburg University, Würzburg, Germany
- * E-mail: (JV); (AE)
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35
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Lindsay AJ, McCaffrey MW. Myosin Va is required for P body but not stress granule formation. J Biol Chem 2011; 286:11519-28. [PMID: 21245139 DOI: 10.1074/jbc.m110.182808] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the present study we demonstrate an association between mammalian myosin Va and cytoplasmic P bodies, microscopic ribonucleoprotein granules that contain components of the 5'-3' mRNA degradation machinery. Myosin Va colocalizes with several P body markers and its RNAi-mediated knockdown results in the disassembly of P bodies. Overexpression of a dominant-negative mutant of myosin Va reduced the motility of P bodies in living cells. Co-immunoprecipitation experiments demonstrate that myosin Va physically associates with eIF4E, an mRNA binding protein that localizes to P bodies. In contrast, we find that myosin Va does not play a role in stress granule formation. Stress granules are ribonucleoprotein structures that are involved in translational silencing and are spatially, functionally, and compositionally linked to P bodies. Myosin Va is found adjacent to stress granules in stressed cells but displays minimal localization within stress granules, and myosin Va knockdown has no effect on stress granule assembly or disassembly. Combined with recently published reports demonstrating a role for Drosophila and mammalian class V myosins in mRNA transport and the involvement of the yeast myosin V orthologue Myo2p in P body assembly, our results provide further evidence that the class V myosins serve an important role in the transport and turnover of mRNA.
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Affiliation(s)
- Andrew J Lindsay
- Department of Biochemistry, Biosciences Institute, University College Cork, Cork, Ireland.
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37
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Abstract
The central effector of mammalian RNA interference (RNAi) is the RNA-induced silencing complex (RISC). Proteins of the Argonaute family are the core components of RISC. Recent work from multiple laboratories has shown that Argonaute family members are associated with at least two types of cytoplasmic RNA granules: GW/Processing bodies and stress granules. These Argonaute-containing granules harbor proteins that function in mRNA degradation and translational repression in response to stress. The known role of Argonaute proteins in miRNA-mediated translational repression and siRNA-directed mRNA cleavage (i.e., Argonaute 2) has prompted speculation that the association of Argonautes with these granules may reflect the activity of RNAi in vivo. Accordingly, studying the dynamic association between Argonautes and RNA granules in living cells will undoubtedly provide insight into the regulatory mechanisms of RNA-based silencing. This chapter describes a method for imaging fluorescently tagged Argonaute proteins in living mammalian cells using spinning disk confocal microscopy.
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Abstract
MicroRNAs are short non-coding RNA molecules that are involved in diverse physiological and developmental processes by controlling the gene expression of target mRNAs. They play important roles in almost all kinds of cancer where they modulate key processes during tumorigenesis such as metastasis, apoptosis, proliferation, or angiogenesis. Depending on the mRNA targets they regulate, they can act as oncogenes or as tumor suppressor genes. Multiple links between microRNA biogenesis and cancer highlight its significance for tumor diseases. However, mechanisms of their own regulation on the transcriptional and posttranscriptional level in health and disease are only beginning to emerge. Here, we review the microRNA-processing pathway as well as recent insights into posttranscriptional regulation of microRNA expression.
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Yao B, Li S, Jung HM, Lian SL, Abadal GX, Han F, Fritzler MJ, Chan EKL. Divergent GW182 functional domains in the regulation of translational silencing. Nucleic Acids Res 2010; 39:2534-47. [PMID: 21131274 PMCID: PMC3074120 DOI: 10.1093/nar/gkq1099] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNA (miRNA)-mediated gene regulation has become a major focus in many biological processes. GW182 and its long isoform TNGW1 are marker proteins of GW/P bodies and bind to Argonaute proteins of the RNA induced silencing complex. The goal of this study is to further define and distinguish the repression domain(s) in human GW182/TNGW1. Two non-overlapping regions, Δ12 (amino acids 896–1219) containing the Ago hook and Δ5 (amino acids 1670–1962) containing the RRM, both induced comparable silencing in a tethering assay. Mapping data showed that the RRM and its flanking sequences in Δ5, but not the Ago hook in Δ12, were important for silencing. Repression mediated by Δ5 or Δ12 was not differentially affected when known endogenous repressors RCK/p54, GW182/TNGW1, TNRC6B were depleted. Transfected Δ5, but not Δ12, enhanced Ago2-mediated repression in a tethering assay. Transfected Δ12, but not Δ5, released endogenous miRNA reporter silencing without affecting siRNA function. Alanine substitution showed that GW/WG motifs in Δ12 (Δ12a, amino acids 896–1045) were important for silencing activity. Although Δ12 appeared to bind PABPC1 more efficiently than Δ5, neither Δ5 nor Δ12 significantly enhanced reporter mRNA degradation. These different functional characteristics of Δ5 and Δ12 suggest that their roles are distinct, and possibly dynamic, in human GW182-mediated silencing.
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Affiliation(s)
- Bing Yao
- Department of Oral Biology, University of Florida, Gainesville, FL 32610-0424, USA
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40
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Ding SL, Zhou LY, Li PF. MicroRNAs in cardiac hypertrophy: angels or devils. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:124-34. [PMID: 21956973 DOI: 10.1002/wrna.61] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are short noncoding RNA molecules that can regulate gene expression via affecting mRNA stability or translation efficiency. miRNAs mediate many important cellular processes and emerge as a newly discovered regulator of gene expression. In cardiac hypertrophy, miRNAs expression is aberrantly altered. Some of these miRNAs can promote cardiac hypertrophy, whereas others can inhibit the process. In this review, we summarize the up- and downregulated miRNAs during cardiac hypertrophy and discuss about their roles in cardiac hypertrophy. The studies on miRNAs shed new light on the mechanism of cardiac hypertrophy and suggest that they may be promising therapeutic targets in tackling cardiac hypertrophy.
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Affiliation(s)
- Su-Ling Ding
- Division of Cardiovascular Research, National Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Moser JJ, Fritzler MJ. The microRNA and messengerRNA profile of the RNA-induced silencing complex in human primary astrocyte and astrocytoma cells. PLoS One 2010; 5:e13445. [PMID: 20976148 PMCID: PMC2956662 DOI: 10.1371/journal.pone.0013445] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 09/14/2010] [Indexed: 12/18/2022] Open
Abstract
Background GW/P bodies are cytoplasmic ribonucleoprotein-rich foci involved in microRNA (miRNA)-mediated messenger RNA (mRNA) silencing and degradation. The mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 that bind miRNA in the RNA-induced silencing complex (RISC). To date there are no published reports of the profile of miRNA and mRNA targeted to the RISC or a comparison of the RISC-specific miRNA/mRNA profile differences in malignant and non-malignant cells. Methodology/Principal Findings RISC mRNA and miRNA components were profiled by microarray analysis of malignant human U-87 astrocytoma cells and its non-malignant counterpart, primary human astrocytes. Total cell RNA as well as RNA from immunoprecipitated RISC was analyzed. The novel findings were fourfold: (1) miRNAs were highly enriched in astrocyte RISC compared to U-87 astrocytoma RISC, (2) astrocytoma and primary astrocyte cells each contained unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3) miR-195, 10b, 29b, 19b, 34a and 455-3p levels were increased and the miR-181b level was decreased in U-87 astrocytoma RISC as compared to astrocyte RISC, and (4) the RISC contained decreased levels of mRNAs in primary astrocyte and U-87 astrocytoma cells. Conclusions/Significance The observation that miR-34a and miR-195 levels were increased in the RISC of U-87 astrocytoma cells suggests an oncogenic role for these miRNAs. Differential regulation of mRNAs by specific miRNAs is evidenced by the observation that three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated while one miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in malignancy and other conditions. This study points to the importance of the RISC and ultimately GW/P body composition and function in miRNA and mRNA deregulation in astrocytoma cells and possibly in other malignancies.
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Affiliation(s)
- Joanna J. Moser
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Marvin J. Fritzler
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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42
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Andes virus regulation of cellular microRNAs contributes to hantavirus-induced endothelial cell permeability. J Virol 2010; 84:11929-36. [PMID: 20844033 DOI: 10.1128/jvi.01658-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hantaviruses infect human endothelial cells (ECs) and cause two diseases marked by vascular permeability defects, hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). Vascular permeability occurs in the absence of EC lysis, suggesting that hantaviruses alter normal EC fluid barrier functions. ECs infected by pathogenic hantaviruses are hyperresponsive to vascular endothelial growth factor (VEGF), and this alters the fluid barrier function of EC adherens junctions, resulting in enhanced paracellular permeability. Vascular permeability and VEGF-directed responses are determined by EC-specific microRNAs (miRNAs), which regulate cellular mRNA transcriptional responses. miRNAs mature within cytoplasmic processing bodies (P bodies), and the hantavirus nucleocapsid (N) protein binds RNA and localizes to P bodies, suggesting that hantaviruses may modify miRNA functions within infected ECs. Here we assessed changes in EC miRNAs following infection by the HPS-causing Andes hantavirus (ANDV). We analyzed 352 human miRNAs within ANDV-infected ECs using quantitative real-time (RT)-PCR arrays. Fourteen miRNAs, including six miRNAs that are associated with regulating vascular integrity, were upregulated >4-fold following infection by ANDV. Nine miRNAs were downregulated 3- to 3,400-fold following ANDV infection; these included miR-410, involved in regulating secretion, and miR-218, which is linked to the regulation of EC migration and vascular permeability. We further analyzed changes in miR-126, an EC-specific miRNA that regulates vascular integrity by suppressing SPRED1 and PIK3R2 mRNAs. While miR-126 levels were only slightly altered, we found that SPRED1 and PIK3R2 mRNA levels were increased 10- and 7-fold, respectively, in ANDV-infected ECs but were unaltered in ECs infected by the nonpathogenic Tula hantavirus (TULV). Consistent with increased SPRED1 expression, we found that the level of phospho-cofilin was decreased within ANDV-infected ECs. Moreover, small interfering RNA (siRNA) knockdown of SPRED1 dramatically decreased the permeability of ANDV-infected ECs in response to VEGF, suggesting that increased SPRED1 contributes to EC permeability following ANDV infection. These findings suggest that interference with normal miRNA functions contributes to the enhanced paracellular permeability of ANDV-infected ECs and that hantavirus regulation of miRNA functions is an additional determinant of hantavirus pathogenesis.
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Mallick R, Patnaik SK, Yendamuri S. MicroRNAs and lung cancer: Biology and applications in diagnosis and prognosis. J Carcinog 2010; 9. [PMID: 20808843 PMCID: PMC2925280 DOI: 10.4103/1477-3163.67074] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 07/14/2010] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs are tiny non-coding RNA molecules which play important roles in the epigenetic control of cellular processes by preventing the translation of proteins from messenger RNAs (mRNAs). A single microRNA can target different mRNAs, and an mRNA can be targeted by multiple microRNAs. Such complex interplays underlie many molecular pathways in cells, and specific roles for many microRNAs in physiological as well as pathological phenomena have been identified. Changes in expression of microRNAs have been associated with a wide variety of disease conditions, and microRNA-based biomarkers are being developed for the identification and monitoring of such states. This review provides a general overview of the current state of knowledge about the biology of microRNAs, and specific information about microRNAs with regard to the diagnosis and prognosis of lung cancer.
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Affiliation(s)
- Reema Mallick
- Northeastern Ohio Universities College of Medicine, Rootstown, OH, USA
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44
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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: 3499] [Impact Index Per Article: 249.9] [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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45
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Jakymiw A, Patel RS, Deming N, Bhattacharyya I, Shah P, Lamont RJ, Stewart CM, Cohen DM, Chan EKL. Overexpression of dicer as a result of reduced let-7 MicroRNA levels contributes to increased cell proliferation of oral cancer cells. Genes Chromosomes Cancer 2010; 49:549-59. [PMID: 20232482 DOI: 10.1002/gcc.20765] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Recent reports have demonstrated that Dicer, an RNase III endonuclease required for microRNA (miRNA) maturation, is aberrantly expressed in different types of cancer. Furthermore, Dicer has been reported to be regulated by the let-7 family of miRNA genes. We hypothesize that Dicer is aberrantly expressed in oral cancer cells due to altered expressions of let-7 and that Dicer contributes to the development and progression of the disease. Western blot examination of Dicer protein levels in four head and neck squamous cell carcinoma (HNSCC) cell lines, including two oral cancer cell lines, demonstrated that Dicer had between 4- and 24-fold higher expression levels when compared to normal human primary gingival epithelial cells. Furthermore, five of six oral cancer tissues analyzed by indirect immunofluorescence had increased Dicer protein expression, compared to normal gingival epithelial tissue. The Dicer mRNA levels were not found to correlate well with protein expression in the HNSCC cell lines, suggesting that Dicer protein expression was post-transcriptionally regulated. Analysis of let-7a and let-7b levels in HNSCC cell lines by real-time PCR demonstrated that let-7b, but not let-7a, was significantly reduced in the HNSCC cell lines compared to control cells. Lastly, transfection of oral cancer cells with chemically synthesized let-7b and small interfering RNAs targeting Dicer significantly inhibited cell proliferation up to 83% and >100%, respectively, as early as 3 days post-transfection. Together, these data demonstrate that elevated expression levels of Dicer in oral cancer cells correlate with downregulation of let-7b and increased cell proliferation.
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Affiliation(s)
- Andrew Jakymiw
- Department of Oral Biology, University of Florida, 1600 SW Archer Road, Gainesville, FL 32610-0424, USA.
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Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA Translation and Stability by microRNAs. Annu Rev Biochem 2010; 79:351-79. [PMID: 20533884 DOI: 10.1146/annurev-biochem-060308-103103] [Citation(s) in RCA: 2319] [Impact Index Per Article: 165.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marc Robert Fabian
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland;
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Sobti M, Cubeddu L, Haynes PA, Mabbutt BC. Engineered rings of mixed yeast Lsm proteins show differential interactions with translation factors and U-rich RNA. Biochemistry 2010; 49:2335-45. [PMID: 20108977 DOI: 10.1021/bi901767w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The Lsm proteins organize as heteroheptameric ring assemblies capable of binding RNA substrates and ancillary protein factors. We have constructed simplified Lsm polyproteins that organize as multimeric ring structures as analogues of the functional Lsm complexes. Polyproteins Lsm[2+3], Lsm[4+1], and Lsm[5+6] incorporate natural sequence extensions as linker peptides between the core Lsm domains. In solution, the recombinant products organize as stable ring oligomers (75 A wide, 20 A pores) in discrete tetrameric and octameric forms. Following immobilization, the polyproteins successfully act as affinity pull-down ligands for proteins within yeast lysate, including native Lsm proteins. Interaction partners were consistent with current models of the mixed Lsm ring assembly in vivo but also suggest that dynamic rearrangements of Lsm protein complexes can occur. The Lsm polyprotein ring complexes were seen in gel shift assays to have a preference for U-rich RNA sequences, with tightest binding measured for Lsm[2+3] with U(10). Polyprotein rings containing truncated forms of Lsm1 and Lsm4 were found to associate with translation, initiation, and elongation protein factors in an RNA-dependent manner. Our findings suggest Lsm1 and/or Lsm4 can interact with translationally active mRNA.
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Affiliation(s)
- Meghna Sobti
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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Johnston M, Geoffroy MC, Sobala A, Hay R, Hutvagner G. HSP90 protein stabilizes unloaded argonaute complexes and microscopic P-bodies in human cells. Mol Biol Cell 2010; 21:1462-9. [PMID: 20237157 PMCID: PMC2861606 DOI: 10.1091/mbc.e09-10-0885] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The cancer drug geldanamycin, an HSP90 inhibitor, decreases the stability of key components of the miRNA regulatory pathway, the efficacy of siRNAs, and the formation of P-bodies without affecting endogenous miRNA function. Key components of the miRNA-mediated gene regulation pathway are localized in cytoplasmic processing bodies (P-bodies). Mounting evidence suggests that the presence of microscopic P-bodies are not always required for miRNA-mediated gene regulation. Here we have shown that geldanamycin, a well-characterized HSP90 inhibitor, abolishes P-bodies and significantly reduces Argonaute and GW182 protein levels but does not affect the miRNA level and the efficiency of miRNA-mediated gene repression; however, it significantly impairs siRNA loading and the efficacy of exogenous siRNA. Our data suggests that HSP90 protein chaperones Argonautes before binding RNA and may facilitate efficient loading of small RNA.
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Affiliation(s)
- Michael Johnston
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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49
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Abstract
P-bodies (processing bodies) are cytoplasmic foci visible by light microscopy in somatic cells of vertebrate and invertebrate origin as well as in yeast, plants and trypanosomes. At the molecular level, P-bodies are dynamic aggregates of specific mRNAs and proteins that serve a dual function: first, they harbour mRNAs that are translationally silenced, and such mRNA can exit again from P-bodies to re-engage in translation. Secondly, P-bodies recruit mRNAs that are targeted for deadenylation and degradation by the decapping/Xrn1 pathway. Whereas certain proteins are core constituents of P-bodies, others involved in recognizing short-lived mRNAs can only be trapped in P-bodies when mRNA decay is attenuated. This reflects the very transient interactions by which many proteins associate with P-bodies. In the present review, we summarize recent findings on the function, assembly and motility of P-bodies. An updated list of proteins and RNAs that localize to P-bodies will help in keeping track of this fast-growing field.
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Djuranovic S, Zinchenko MK, Hur JK, Nahvi A, Brunelle JL, Rogers EJ, Green R. Allosteric regulation of Argonaute proteins by miRNAs. Nat Struct Mol Biol 2010; 17:144-50. [PMID: 20062058 DOI: 10.1038/nsmb.1736] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 11/16/2009] [Indexed: 01/11/2023]
Abstract
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) bind to Argonaute (AGO) family proteins to form a related set of effector complexes that have diverse roles in post-transcriptional gene regulation throughout the eukaryotic lineage. Here sequence and structural analysis of the MID domain of the AGO proteins identified similarities with a family of allosterically regulated bacterial ligand-binding domains. We used in vitro and in vivo approaches to show that certain AGO proteins (those involved in translational repression) have conserved this functional allostery between two distinct sites, one involved in binding miRNA-target duplex and the other in binding the 5' cap feature (m(7)GpppG) of eukaryotic mRNAs. This allostery provides an explanation for how miRNA-bound effector complexes may avoid indiscriminate repressive action (mediated through binding interactions with the cap) before full target recognition.
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Affiliation(s)
- Sergej Djuranovic
- Howard Hughes Medical Institute and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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