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Riddihough G, Surridge C, Ladurner AG, Clyne RK, Hodges M, Heinrichs A, Marcinkiewicz K, Ullrich F, Perdigoto C, Osman S, Ciazynska K, Typas D. Looking back at 30 years of Nature Structural & Molecular Biology. Nat Struct Mol Biol 2024; 31:397-403. [PMID: 38499829 DOI: 10.1038/s41594-024-01248-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
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Pereiro P, Álvarez-Rodríguez M, Valenzuela-Muñoz V, Gallardo-Escárate C, Figueras A, Novoa B. RNA-Seq analysis reveals that spring viraemia of carp virus induces a broad spectrum of PIM kinases in zebrafish kidney that promote viral entry. FISH & SHELLFISH IMMUNOLOGY 2020; 99:86-98. [PMID: 32004617 DOI: 10.1016/j.fsi.2020.01.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
PIM kinases are a family of serine/threonine protein kinases that potentiate the progression of the cell cycle and inhibit apoptosis. Because of this, they are considered to be proto-oncogenes, and they represent an interesting target for the development of anticancer drugs. In mammals, three PIM kinases exist (PIM-1, PIM-2 and PIM-3), and different inhibitors have been developed to block their activity. In addition to their involvement in cancer, some publications have reported that the PIM kinases have pro-viral activity, and different mechanisms where PIM kinases favour viral infections have been proposed. Zebrafish possess more than 300 Pim kinase members in their genome, and by using RNA-Seq analysis, we found a high number of Pim kinase genes that were significantly induced after infection with spring viraemia of carp virus (SVCV). Moreover, analysis of the miRNAs modulated by this infection revealed that some of them could be involved in the post-transcriptional regulation of Pim kinase abundance. To elucidate the potential role of the 16 overexpressed Pim kinases in the infectivity of SVCV, we used three different pan-PIM kinase inhibitors (SGI-1776, INCB053914 and AZD1208), and different experiments were conducted both in vitro and in vivo. We observed that the PIM kinase inhibitors had a protective effect against SVCV, indicating that, similar to what is observed in mammals, PIM kinases are beneficial for the virus in zebrafish. Moreover, zebrafish Pim kinases seem to facilitate viral entry into the host cells because when ZF4 cells were pre-incubated with the virus and then were treated with the inhibitors, the protective effect of the inhibitors was abrogated. Although more investigation is necessary, these results show that pan-PIM kinase inhibitors could serve as a useful treatment for preventing the spread of viral diseases.
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Affiliation(s)
- Patricia Pereiro
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain; Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Margarita Álvarez-Rodríguez
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Valentina Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Antonio Figueras
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Beatriz Novoa
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.
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Baskara-Yhuellou I, Tost J. The impact of microRNAs on alterations of gene regulatory networks in allergic diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 120:237-312. [PMID: 32085883 DOI: 10.1016/bs.apcsb.2019.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Allergic diseases including asthma are worldwide on the rise and contribute significantly to health expenditures. Allergic diseases are prototypic diseases with a strong gene by environment interaction component and epigenetic mechanisms might mediate the effects of the environment on the disease phenotype. MicroRNAs, small non-coding RNAs (miRNAs), regulate gene expression post-transcriptionally. Functional single-stranded miRNAs are generated in multiple steps of enzymatic processing from their precursors and mature miRNAs are included into the RNA-induced silencing complex (RISC). They imperfectly base-pair with the 3'UTR region of targeted genes leading to translational repression or mRNA decay. The cellular context and microenvironment as well the isoform of the mRNA control the dynamics and complexity of the regulatory circuits induced by miRNAs that regulate cell fate decisions and function. MiR-21, miR-146a/b and miR-155 are among the best understood miRNAs of the immune system and implicated in different diseases including allergic diseases. MiRNAs are implicated in the induction of the allergy reinforcing the Th2 phenotype (miR-19a, miR-24, miR-27), while other miRNAs promote regulatory T cells associated with allergen tolerance or unresponsiveness. In the current chapter we describe in detail the biogenesis and regulatory function of miRNAs and summarize current knowledge on miRNAs in allergic diseases and allergy relevant cell fate decisions focusing mainly on immune cells. Furthermore, we evoke the principles of regulatory loops and feedback mechanisms involving miRNAs on examples with relevance for allergic diseases. Finally, we show the potential of miRNAs and exosomes containing miRNAs present in several biological fluids that can be exploited with non-invasive procedures for diagnostic and potentially therapeutic purposes.
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Affiliation(s)
- Indoumady Baskara-Yhuellou
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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Jin A, Bao R, Roth M, Liu L, Yang X, Tang X, Yang X, Sun Q, Lu S. microRNA-23a contributes to asthma by targeting BCL2 in airway epithelial cells and CXCL12 in fibroblasts. J Cell Physiol 2019; 234:21153-21165. [PMID: 31020662 DOI: 10.1002/jcp.28718] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/12/2022]
Abstract
The deregulated cross-talk between airway epithelial cells with subepithelial fibroblasts during inflammation drives the pathogenesis of asthma. Bioinformatics analysis and luciferase activity assay suggested that B cell lymphoma-2 (BCL2) and CXC ligand 12 (CXCL12) are potential targets of miR-23a. The aim of this study was to elucidate the effect of microRNA-23a (miR-23a) on BCL2, and CXCL12 in asthma. In E3 rats, miR-23a was upregulated in lung tissues after antigen-induced pulmonary inflammation during acute and chronic inflammation. Immunohistochemistry showed downregulation of BCL2 in the epithelium and of CXCL12 in subepithelial fibroblasts and smooth muscle cells. Treatment of isolated cells with miR-23a mimic or inhibitor modified the expression of BCL2 and of CXCL12 in the expected cell type-specific manner. Moreover, in epithelial cells, interleukin-4 upregulated miR-23a expression and thereby decreased the expression of BCL2, while increasing the caspase-3 expression, which was followed by apoptosis. In fibroblasts, the expression of miR-23a was increased by thymic stromal lymphopoietin (TSLP). Consequently, the CXCL12 expression was abrogated. The phosphorylation of CREB was also downregulated by TSLP through the action of miR-23a. This study describes a novel mechanism, where miR-23a is an important cell type-specific regulator for asthma-associated airway wall remodeling parameter. Thus, miR-23a may present a potential new target for the therapy of asthma.
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Affiliation(s)
- Ai Jin
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Rujuan Bao
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, People's Republic of China.,Department of Blood Transfusion, Tangdu Hospital, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shanxi, People's Republic of China
| | - Michael Roth
- Department of Biomedicine, Pneumology and Pulmonary Cell Research, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Li Liu
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Xudong Yang
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Xuemei Tang
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojun Yang
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingzhu Sun
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Department of Biomedicine, Pneumology and Pulmonary Cell Research, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Shemin Lu
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
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Zubeldía-Brenner L, De Winne C, Perrone S, Rodríguez-Seguí SA, Willems C, Ornstein AM, Lacau-Mengido I, Vankelecom H, Cristina C, Becu-Villalobos D. Inhibition of Notch signaling attenuates pituitary adenoma growth in Nude mice. Endocr Relat Cancer 2019; 26:13-29. [PMID: 30121620 DOI: 10.1530/erc-18-0337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/08/2018] [Indexed: 12/16/2022]
Abstract
Preclinical and clinical studies support that Notch signaling may play an important oncogenic role in cancer, but there is scarce information for pituitary tumors. We therefore undertook a functional study to evaluate Notch participation in pituitary adenoma growth. Tumors generated in Nude mice by subcutaneous GH3 somatolactotrope cell injection were treated in vivo with DAPT, a γ-secretase inhibitor, thus inactivating Notch signaling. This treatment led to pituitary tumor reduction, lower prolactin and GH tumor content and a decrease in angiogenesis. Furthermore, in silico transcriptomic and epigenomic analyses uncovered several tumor suppressor genes related to Notch signaling in pituitary tissue, namely Btg2, Nr4a1, Men1, Zfp36 and Cnot1. Gene evaluation suggested that Btg2, Nr4a1 and Cnot1 may be possible players in GH3 xenograft growth. Btg2 mRNA expression was lower in GH3 tumors compared to the parental line, and DAPT increased its expression levels in the tumor in parallel with the inhibition of its volume. Cnot1 mRNA levels were also increased in the pituitary xenografts by DAPT treatment. And the Nr4a1 gene was lower in tumors compared to the parental line, though not modified by DAPT. Finally, because DAPT in vivo may also be acting on tumor microenvironment, we determined the direct effect of DAPT on GH3 cells in vitro. We found that DAPT decreases the proliferative, secretory and migration potential of GH3 cells. These results position selective interruption of Notch signaling as a potential therapeutic tool in adjuvant treatments for aggressive or resistant pituitary tumors.
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Affiliation(s)
| | - Catalina De Winne
- Instituto de Biología y Medicina Experimental, IBYME-CONICET, Buenos Aires, Argentina
| | - Sofía Perrone
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires, CITNOBA (UNNOBA-CONICET), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Buenos Aires, Argentina
| | - Santiago A Rodríguez-Seguí
- Departamento de Fisiología y Biología Molecular y Celular, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Christophe Willems
- Department of Development and Regeneration, Cluster Stem Cell and Developmental Biology, Unit of Stem Cell Research, KU Leuven (University of Leuven), Leuven, Belgium
| | - Ana María Ornstein
- Instituto de Biología y Medicina Experimental, IBYME-CONICET, Buenos Aires, Argentina
| | - Isabel Lacau-Mengido
- Instituto de Biología y Medicina Experimental, IBYME-CONICET, Buenos Aires, Argentina
| | - Hugo Vankelecom
- Department of Development and Regeneration, Cluster Stem Cell and Developmental Biology, Unit of Stem Cell Research, KU Leuven (University of Leuven), Leuven, Belgium
| | - Carolina Cristina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires, CITNOBA (UNNOBA-CONICET), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Buenos Aires, Argentina
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Valenzuela-Miranda D, Valenzuela-Muñoz V, Farlora R, Gallardo-Escárate C. MicroRNA-based transcriptomic responses of Atlantic salmon during infection by the intracellular bacterium Piscirickettsia salmonis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:287-296. [PMID: 28870451 DOI: 10.1016/j.dci.2017.08.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that have emerged as key regulators in diverse biological processes across taxa. However, despite the importance of these transcripts, little is known about their role during the immune response in salmonids. Because of this, we use deep sequencing technologies to explore the microRNA-based transcriptomic response of the Atlantic salmon (Salmo salar) to the intracellular bacteria Piscirickettsia salmonis, one of the main threats to salmon aquaculture in Chile. Hence, 594 different miRNAs were identified from head kidney and spleen transcriptomic data. Among them, miRNA families mir-181, mir-143 and mir-21 were the most abundant in control groups, while after infection with P. salmonis, mir-21, mir-181 and mir-30 were the most predominant families. Furthermore, transcriptional analysis revealed 84 and 25 differentially expressed miRNAs in head kidney and spleen respectively, with an overlapping response of 10 miRNAs between the analyzed tissues. Target prediction, coupled with GO enrichment analysis, revealed that the possible targets of the most regulated miRNAs were genes involved in the immune response, such as cortisol metabolism, chemokine-mediated signaling pathway and neutrophil chemotaxis genes. Among these, predicted putative target genes such as C-C motif chemokine 19-like, stromal cell-derived factor 1-like, myxovirus resistance protein 2 and hepcidin-1 were identified. Overall, our results suggest that miRNA expression in co-modulation with transcription activity of target genes is related to putative roles of non-coding RNAs in the immune response of Atlantic salmon against intracellular bacterial pathogens.
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Affiliation(s)
- Diego Valenzuela-Miranda
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile
| | - Valentina Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile
| | - Rodolfo Farlora
- Laboratorio de Biotecnología Acuática y Genómica Reproductiva/Instituto de Biología, Facultad de Ciencias Universidad de Valparaíso, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile.
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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MicroRNA 665 Regulates Dentinogenesis through MicroRNA-Mediated Silencing and Epigenetic Mechanisms. Mol Cell Biol 2015; 35:3116-30. [PMID: 26124283 DOI: 10.1128/mcb.00093-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 06/18/2015] [Indexed: 12/26/2022] Open
Abstract
Studies of proteins involved in microRNA (miRNA) processing, maturation, and silencing have indicated the importance of miRNAs in skeletogenesis, but the specific miRNAs involved in this process are incompletely defined. Here, we identified miRNA 665 (miR-665) as a potential repressor of odontoblast maturation. Studies with cultured cell lines and primary embryonic cells showed that miR-665 represses the expression of early and late odontoblast marker genes and stage-specific proteases involved in dentin maturation. Notably, miR-665 directly targeted Dlx3 mRNA and decreased Dlx3 expression. Furthermore, RNA-induced silencing complex (RISC) immunoprecipitation and biotin-labeled miR-665 pulldown studies identified Kat6a as another potential target of miR-665. KAT6A interacted physically and functionally with RUNX2, activating tissue-specific promoter activity and prompting odontoblast differentiation. Overexpression of miR-665 reduced the recruitment of KAT6A to Dspp and Dmp1 promoters and prevented KAT6A-induced chromatin remodeling, repressing gene transcription. Taken together, our results provide novel molecular evidence that miR-665 functions in an miRNA-epigenetic regulatory network to control dentinogenesis.
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MicroRNA-9 regulates steroid-resistant airway hyperresponsiveness by reducing protein phosphatase 2A activity. J Allergy Clin Immunol 2015; 136:462-73. [PMID: 25772595 DOI: 10.1016/j.jaci.2014.11.044] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/16/2022]
Abstract
BACKGROUND Steroid-resistant asthma is a major clinical problem that is linked to activation of innate immune cells. Levels of IFN-γ and LPS are often increased in these patients. Cooperative signaling between IFN-γ/LPS induces macrophage-dependent steroid-resistant airway hyperresponsiveness (AHR) in mouse models. MicroRNAs (miRs) are small noncoding RNAs that regulate the function of innate immune cells by controlling mRNA stability and translation. Their role in regulating glucocorticoid responsiveness and AHR remains unexplored. OBJECTIVE IFN-γ and LPS synergistically increase the expression of miR-9 in macrophages and lung tissue, suggesting a role in the mechanisms of steroid resistance. Here we demonstrate the role of miR-9 in IFN-γ/LPS-induced inhibition of dexamethasone (DEX) signaling in macrophages and in induction of steroid-resistant AHR. METHODS MiRNA-9 expression was assessed by means of quantitative RT-PCR. Putative miR-9 targets were determined in silico and confirmed in luciferase reporter assays. miR-9 function was inhibited with sequence-specific antagomirs. The efficacy of DEX was assessed by quantifying glucocorticoid receptor (GR) cellular localization, protein phosphatase 2A (PP2A) activity, and AHR. RESULTS Exposure of pulmonary macrophages to IFN-γ/LPS synergistically induced miR-9 expression; reduced levels of its target transcript, protein phosphatase 2 regulatory subunit B (B56) δ isoform; attenuated PP2A activity; and inhibited DEX-induced GR nuclear translocation. Inhibition of miR-9 increased both PP2A activity and GR nuclear translocation in macrophages and restored steroid sensitivity in multiple models of steroid-resistant AHR. Pharmacologic activation of PP2A restored DEX efficacy and inhibited AHR. MiR-9 expression was increased in sputum of patients with neutrophilic but not those with eosinophilic asthma. CONCLUSION MiR-9 regulates GR signaling and steroid-resistant AHR. Targeting miR-9 function might be a novel approach for the treatment of steroid-resistant asthma.
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Valenzuela-Miranda D, Nuñez-Acuña G, Valenzuela-Muñoz V, Asgari S, Gallardo-Escárate C. MicroRNA biogenesis pathway from the salmon louse (Caligus rogercresseyi): Emerging role in delousing drug response. Gene 2015; 555:231-41. [DOI: 10.1016/j.gene.2014.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/24/2014] [Accepted: 11/06/2014] [Indexed: 12/20/2022]
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Stroynowska-Czerwinska A, Fiszer A, Krzyzosiak WJ. The panorama of miRNA-mediated mechanisms in mammalian cells. Cell Mol Life Sci 2014; 71:2253-70. [PMID: 24468964 PMCID: PMC4031385 DOI: 10.1007/s00018-013-1551-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/02/2013] [Accepted: 12/30/2013] [Indexed: 12/21/2022]
Abstract
MicroRNAs comprise a large family of short, non-coding RNAs that are present in most eukaryotic organisms and are typically involved in downregulating the expression of protein-coding genes. The detailed mechanisms of miRNA functioning in animals and plants have been under investigation for more than decade. In mammalian cells, miRNA guides the effector complex miRISC to bind with partially complementary sequences, usually within the 3′UTR of mRNAs, and inhibit protein synthesis with or without transcript degradation. In addition to these main mechanisms, several other modes of miRNA-mediated gene expression regulation have been described, but their scale and importance remain a matter of debate. In this review, we briefly summarize the pathway of miRNA precursor processing during miRNA biogenesis and continue with the description of the miRISC assembly process. Then, we present the miRNA-mediated mechanisms of gene expression regulation in detail, and we gather information concerning the proteins involved in these processes. In addition, we briefly refer to the current applications of miRNA mechanisms in therapeutic strategies. Finally, we highlight some of the remaining controversies surrounding the regulation of mammalian gene expression by miRNAs.
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Affiliation(s)
- Anna Stroynowska-Czerwinska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
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Rebane A, Akdis CA. MicroRNAs: Essential players in the regulation of inflammation. J Allergy Clin Immunol 2013; 132:15-26. [PMID: 23726263 DOI: 10.1016/j.jaci.2013.04.011] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 04/02/2013] [Accepted: 04/04/2013] [Indexed: 12/16/2022]
Abstract
Regulation of inflammatory responses is ensured by coordinated control of gene expression in participating immune system and tissue cells. One group of gene expression regulators, the functions of which have recently been started to be uncovered in relation to any type of inflammatory condition, is a class of short single-stranded RNA molecules termed microRNAs (miRNAs). miRNAs function together with partner proteins and mainly cause gene silencing through degradation of target mRNAs or inhibition of translation. A particular miRNA can have hundreds of target genes, and thereby miRNAs together influence the expression of a large proportion of proteins. The role of miRNAs in the immune system has been extensively studied since the discovery of miRNAs in mammalian cells approximately 10 years ago. The purpose of the current review is to provide an overview on the functions of miRNAs in the regulation of inflammation, with a specific focus on the mechanisms of allergic inflammation. Because recent studies clearly demonstrate the presence of extracellular miRNAs in body fluids and propose the involvement of miRNAs in cell-cell communication, we will also highlight findings about functions of extracellular miRNAs. The possible use of miRNAs as biomarkers, as well as miRNA-related novel treatment modalities, might open a new future for the diagnosis and treatment of many inflammatory conditions, including allergic diseases.
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Affiliation(s)
- Ana Rebane
- Swiss Institute of Allergy and Asthma Research, University of Zurich, Davos, Switzerland.
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RNA interference--a silent but an efficient therapeutic tool. Appl Biochem Biotechnol 2013; 169:1774-89. [PMID: 23340870 DOI: 10.1007/s12010-013-0098-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/10/2013] [Indexed: 12/12/2022]
Abstract
RNA interference (RNAi) is an evolutionary conserved gene regulation pathway that has emerged as an important discovery in the field of molecular biology. One of the important advantages of RNAi in therapy is that it brings about efficient downregulation of gene expression by targeting complementary transcripts in comparison with other antisense-based techniques. RNAi can be can be achieved by introducing chemically synthesized small interfering RNAs (siRNAs) into a cell system. A more stable knockdown effect can be brought about by the use of plasmid or viral vectors encoding the siRNA. RNAi has been used in reverse genetics to understand the function of specific genes and also as a therapeutic tool in treating human diseases. This review provides a brief insight into the therapeutic applications of RNAi against debilitating diseases.
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Gal-Ben-Ari S, Kenney JW, Ounalla-Saad H, Taha E, David O, Levitan D, Gildish I, Panja D, Pai B, Wibrand K, Simpson TI, Proud CG, Bramham CR, Armstrong JD, Rosenblum K. Consolidation and translation regulation. Learn Mem 2012; 19:410-22. [PMID: 22904372 PMCID: PMC3418764 DOI: 10.1101/lm.026849.112] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
mRNA translation, or protein synthesis, is a major component of the transformation of the genetic code into any cellular activity. This complicated, multistep process is divided into three phases: initiation, elongation, and termination. Initiation is the step at which the ribosome is recruited to the mRNA, and is regarded as the major rate-limiting step in translation, while elongation consists of the elongation of the polypeptide chain; both steps are frequent targets for regulation, which is defined as a change in the rate of translation of an mRNA per unit time. In the normal brain, control of translation is a key mechanism for regulation of memory and synaptic plasticity consolidation, i.e., the off-line processing of acquired information. These regulation processes may differ between different brain structures or neuronal populations. Moreover, dysregulation of translation leads to pathological brain function such as memory impairment. Both normal and abnormal function of the translation machinery is believed to lead to translational up-regulation or down-regulation of a subset of mRNAs. However, the identification of these newly synthesized proteins and determination of the rates of protein synthesis or degradation taking place in different neuronal types and compartments at different time points in the brain demand new proteomic methods and system biology approaches. Here, we discuss in detail the relationship between translation regulation and memory or synaptic plasticity consolidation while focusing on a model of cortical-dependent taste learning task and hippocampal-dependent plasticity. In addition, we describe a novel systems biology perspective to better describe consolidation.
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Affiliation(s)
- Shunit Gal-Ben-Ari
- Sagol Department of Neurobiology, University of Haifa, Haifa 31905, Israel
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15
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Tethering of proteins to RNAs using the bovine immunodeficiency virus–Tat peptide and BIV–TAR RNA. Anal Biochem 2012; 427:130-2. [DOI: 10.1016/j.ab.2012.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 11/19/2022]
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