1
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Pandey M, Luhur A, Sokol NS, Chawla G. Molecular Dissection of a Conserved Cluster of miRNAs Identifies Critical Structural Determinants That Mediate Differential Processing. Front Cell Dev Biol 2022; 10:909212. [PMID: 35784477 PMCID: PMC9247461 DOI: 10.3389/fcell.2022.909212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Differential processing is a hallmark of clustered microRNAs (miRNAs) and the role of position and order of miRNAs in a cluster together with the contribution of stem-base and terminal loops has not been explored extensively within the context of a polycistronic transcript. To elucidate the structural attributes of a polycistronic transcript that contribute towards the differences in efficiencies of processing of the co-transcribed miRNAs, we constructed a series of chimeric variants of Drosophila let-7-Complex that encodes three evolutionary conserved and differentially expressed miRNAs (miR-100, let-7 and miR-125) and examined the expression and biological activity of the encoded miRNAs. The kinetic effects of Drosha and Dicer processing on the chimeric precursors were examined by in vitro processing assays. Our results highlight the importance of stem-base and terminal loop sequences in differential expression of polycistronic miRNAs and provide evidence that processing of a particular miRNA in a polycistronic transcript is in part determined by the kinetics of processing of adjacent miRNAs in the same cluster. Overall, this analysis provides specific guidelines for achieving differential expression of a particular miRNA in a cluster by structurally induced changes in primary miRNA (pri-miRNA) sequences.
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Affiliation(s)
- Manish Pandey
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, India
| | - Arthur Luhur
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Nicholas S. Sokol
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Geetanjali Chawla
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, India
- *Correspondence: Geetanjali Chawla,
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2
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Dell’Orco M, Elyaderani A, Vannan A, Sekar S, Powell G, Liang WS, Neisewander JL, Perrone-Bizzozero NI. HuD Regulates mRNA-circRNA-miRNA Networks in the Mouse Striatum Linked to Neuronal Development and Drug Addiction. BIOLOGY 2021; 10:biology10090939. [PMID: 34571817 PMCID: PMC8468275 DOI: 10.3390/biology10090939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 11/26/2022]
Abstract
Simple Summary Gene expression controls all aspects of life, including that of humans. Genes are expressed by copying the information stored in the DNA into RNA molecules, and this process is regulated in part by multiple RNA-binding proteins (RBPs). One such protein, HuD, plays a critical role in the development of neurons and has been implicated in childhood brain tumors, neurodegenerative disorders (Parkinson’s, Alzheimer’s, and ALS), and drug abuse. In addition, HuD participates in neuronal remodeling mechanisms in the mature brain and promotes regeneration of peripheral nerves. HuD primarily binds to transcribed messenger RNAs, which are then stabilized for translation into proteins. However, recent studies demonstrate that HuD also regulates the expression of non-coding RNAs, such as circular RNAs (circRNAs) and microRNAs (miRNAs). In this study, we examined the role of HuD in the control of non-coding RNA expression in the mouse striatum, a brain region associated both with normal behaviors and pathological conditions such as drug abuse. Our results show that HuD regulates mRNA-circRNA-miRNA networks involved in the expression of genes associated with brain development and remodeling of neuronal connections. These findings suggest the possibility of new mechanisms controlling brain development, neurodegenerative diseases, and substance use disorders. Abstract The RNA-binding protein HuD (a.k.a., ELAVL4) is involved in neuronal development and synaptic plasticity mechanisms, including addiction-related processes such as cocaine conditioned-place preference (CPP) and food reward. The most studied function of this protein is mRNA stabilization; however, we have recently shown that HuD also regulates the levels of circular RNAs (circRNAs) in neurons. To examine the role of HuD in the control of coding and non-coding RNA networks associated with substance use, we identified sets of differentially expressed mRNAs, circRNAs and miRNAs in the striatum of HuD knockout (KO) mice. Our findings indicate that significantly downregulated mRNAs are enriched in biological pathways related to cell morphology and behavior. Furthermore, deletion of HuD altered the levels of 15 miRNAs associated with drug seeking. Using these sets of data, we predicted that a large number of upregulated miRNAs form competing endogenous RNA (ceRNA) networks with circRNAs and mRNAs associated with the neuronal development and synaptic plasticity proteins LSAMP and MARK3. Additionally, several downregulated miRNAs form ceRNA networks with mRNAs and circRNAs from MEF2D, PIK3R3, PTRPM and other neuronal proteins. Together, our results indicate that HuD regulates ceRNA networks controlling the levels of mRNAs associated with neuronal differentiation and synaptic physiology.
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Affiliation(s)
- Michela Dell’Orco
- Department of Neurosciences, University of New Mexico Health Science Center, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Amir Elyaderani
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ 85004, USA; (A.E.); (S.S.); (W.S.L.)
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.V.); (G.P.); (J.L.N.)
| | - Shobana Sekar
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ 85004, USA; (A.E.); (S.S.); (W.S.L.)
| | - Gregory Powell
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.V.); (G.P.); (J.L.N.)
| | - Winnie S. Liang
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ 85004, USA; (A.E.); (S.S.); (W.S.L.)
| | - Janet L. Neisewander
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.V.); (G.P.); (J.L.N.)
| | - Nora I. Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico Health Science Center, University of New Mexico, Albuquerque, NM 87131, USA;
- Correspondence:
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3
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Translational control of enzyme scavenger expression with toxin-induced micro RNA switches. Sci Rep 2021; 11:2462. [PMID: 33510250 PMCID: PMC7844233 DOI: 10.1038/s41598-021-81679-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
Biological computation requires in vivo control of molecular behavior to progress development of autonomous devices. miRNA switches represent excellent, easily engineerable synthetic biology tools to achieve user-defined gene regulation. Here we present the construction of a synthetic network to implement detoxification functionality. We employed a modular design strategy by engineering toxin-induced control of an enzyme scavenger. Our miRNA switch results show moderate synthetic expression control over a biologically active detoxification enzyme molecule, using an established design protocol. However, following a new design approach, we demonstrated an evolutionarily designed miRNA switch to more effectively activate enzyme activity than synthetically designed versions, allowing markedly improved extrinsic user-defined control with a toxin as inducer. Our straightforward new design approach is simple to implement and uses easily accessible web-based databases and prediction tools. The ability to exert control of toxicity demonstrates potential for modular detoxification systems that provide a pathway to new therapeutic and biocomputing applications.
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4
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Dexheimer PJ, Cochella L. MicroRNAs: From Mechanism to Organism. Front Cell Dev Biol 2020; 8:409. [PMID: 32582699 PMCID: PMC7283388 DOI: 10.3389/fcell.2020.00409] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
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5
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Chen WC, Wei CK, Lee JC. MicroRNA-let-7c suppresses hepatitis C virus replication by targeting Bach1 for induction of haem oxygenase-1 expression. J Viral Hepat 2019; 26:655-665. [PMID: 30706605 DOI: 10.1111/jvh.13072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/17/2018] [Accepted: 01/05/2019] [Indexed: 12/26/2022]
Abstract
MicroRNAs are small noncoding RNAs that are central factors between hepatitis C virus (HCV) and host cellular factors for viral replication and liver disease progression, including liver fibrosis, cirrhosis and hepatocellular carcinoma. In the present study, we found that overexpressing miR-let-7c markedly reduced HCV replication because it induced haem oxygenase-1 (HO-1) expression by targeting HO-1 transcriptional repressor Bach1, ultimately leading to stimulating an antiviral interferon response and blockade of HCV viral protease activity. In contrast, the antiviral actions of miR-let-7c were attenuated by miR-let-7c inhibitor treatment, exogenously expressing Bach1 or suppressing HO-1 activity and expression. A proposed model indicates a key role for miR-let-7c targeting Bach1 to transactivate HO-1-mediated antiviral actions against HCV. miR-let-7c may serve as an attractive target for antiviral development.
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Affiliation(s)
- Wei-Chun Chen
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Ku Wei
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jin-Ching Lee
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.,PhD Program in Life Sciences, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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6
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression. Precursor miRNA molecules undergo nuclear and cytoplasmic processing events, carried out by the endoribonucleases DROSHA and DICER, respectively, to produce mature miRNAs that are loaded onto the RISC (RNA-induced silencing complex) to exert their biological function. Regulation of mature miRNA levels is critical in development, differentiation, and disease, as demonstrated by multiple levels of control during their biogenesis cascade. Here, we will focus on post-transcriptional mechanisms and will discuss the impact of cis-acting sequences in precursor miRNAs, as well as trans-acting factors that bind to these precursors and influence their processing. In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and function.
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Affiliation(s)
- Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Zhejiang 314400, P.R. China
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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7
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Boudouresque F, Siret C, Dobric A, Silvy F, Soubeyran P, Iovanna J, Lombardo D, Berthois Y. Ribonuclease MCPiP1 contributes to the loss of micro-RNA-200 family members in pancreatic cancer cells. Oncotarget 2018; 9:35941-35961. [PMID: 30542509 PMCID: PMC6267598 DOI: 10.18632/oncotarget.26310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/25/2018] [Indexed: 02/07/2023] Open
Abstract
The microRNA-200 (miR-200) family is frequently down-regulated in tumors, including pancreatic adenocarcinomas (PDACs). In this study we have examined the mechanisms involved in the loss of miR-200s in tumoral pancreatic cells. Whereas miR-200 gene promoters appear methylated in mature miR-200 deficient cell lines, miR-200 precursors are detected in nuclear but not cytoplasmic compartment of these cells, indicating that promoter hypermethylation is not sufficient to explain the deficit of mature miR-200s. The ribonuclease Monocyte Chemotactic Protein-induced Protein-1 (MCPiP1) may counteract Dicer1 in miRNA maturation process. MCPiP1/Dicer1 mRNA and protein ratios appear higher in miR-200 deficient compared to miR-200 proficient cells, suggesting that MCPiP1 may compete with Dicer1 in mature miR-200 deficient cells. Inhibition of MCPiP1 allows the detection of miR-200 precursors in cytoplasm of miR-200 deficient cells, confirming its involvement in the loss of miR-200s. Also, reversion of MCPiP1/Dicer1 ratio by over-expression of Dicer1 in miR-200 deficient cells leads to the recovery of mature miR-200s. Finally, whereas human malignant pancreatic tissues (PDACs) express lower miR-200 levels than non malignant tissues (non-MPDs), MCPiP1/Dicer1 ratio appears higher in PDACs, when compared to non-MPDs, supporting the hypothesis that MCPiP1/Dicer1 ratio is determinant in regulating miR-200 maturation process in a subset of tumoral pancreatic cells.
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Affiliation(s)
| | - Carole Siret
- Aix-Marseille Univ, INSERM UMR 911, CRO2, Marseille, France.,Aix-Marseille Univ, CNRS, INSERM, CIML Marseille, France
| | - Aurélie Dobric
- Aix-Marseille Univ, INSERM UMR 911, CRO2, Marseille, France.,Present address: Aix-Marseille University, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Pancreatic Cancer Team, Marseille, France
| | - Françoise Silvy
- Aix-Marseille Univ, INSERM UMR 911, CRO2, Marseille, France.,Present address: Aix-Marseille University, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Pancreatic Cancer Team, Marseille, France
| | - Philippe Soubeyran
- Present address: Aix-Marseille University, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Pancreatic Cancer Team, Marseille, France
| | - Juan Iovanna
- Present address: Aix-Marseille University, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Pancreatic Cancer Team, Marseille, France
| | | | - Yolande Berthois
- Aix-Marseille Univ, INSERM UMR 911, CRO2, Marseille, France.,Present address: Aix-Marseille University, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Pancreatic Cancer Team, Marseille, France
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8
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Atanasov J, Groher F, Weigand JE, Suess B. Design and implementation of a synthetic pre-miR switch for controlling miRNA biogenesis in mammals. Nucleic Acids Res 2017; 45:e181. [PMID: 29036355 PMCID: PMC5727447 DOI: 10.1093/nar/gkx858] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/22/2017] [Accepted: 09/20/2017] [Indexed: 01/07/2023] Open
Abstract
Synthetic RNA-based systems have increasingly been used for the regulation of eukaryotic gene expression. Due to their structural properties, riboregulators provide a convenient basis for the development of ligand-dependent controllable systems. Here, we demonstrate reversible conditional control of miRNA biogenesis with an aptamer domain as a sensing unit connected to a natural miRNA precursor for the first time. For the design of the pre-miR switch, we replaced the natural terminal loop with the TetR aptamer. Thus, the TetR aptamer was positioned close to the Dicer cleavage sites, which allowed sterical control over pre-miR processing by Dicer. Our design proved to be highly versatile, allowing us to regulate the biogenesis of three structurally different miRNAs: miR-126, -34a and -199a. Dicer cleavage was inhibited up to 143-fold via co-expression of the TetR protein, yet could be completely restored upon addition of doxycycline. Moreover, we showed the functionality of the pre-miR switches for gene regulation through the interaction of the respective miRNA with its specific target sequence. Our designed device is capable of robust and reversible control of miRNA abundance. Thus, we offer a novel investigational tool for functional miRNA analysis.
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Affiliation(s)
- Janina Atanasov
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Florian Groher
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Julia E. Weigand
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
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9
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Treiber T, Treiber N, Plessmann U, Harlander S, Daiß JL, Eichner N, Lehmann G, Schall K, Urlaub H, Meister G. A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Mol Cell 2017; 66:270-284.e13. [PMID: 28431233 DOI: 10.1016/j.molcel.2017.03.014] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/22/2016] [Accepted: 03/20/2017] [Indexed: 12/19/2022]
Abstract
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels. Indeed, a large number of the investigated candidates, including splicing factors and other mRNA processing proteins, have effects on miRNA processing. As an example, we show that TRIM71/LIN41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. We provide an extended database of RBPs that interact with pre-miRNAs in extracts of different cell types, highlighting a widespread layer of co- and posttranscriptional regulation of miRNA biogenesis.
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Affiliation(s)
- Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - Simone Harlander
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Julia-Lisa Daiß
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Norbert Eichner
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gerhard Lehmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Schall
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany.
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10
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Beusch I, Barraud P, Moursy A, Cléry A, Allain FHT. Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7. eLife 2017. [PMID: 28650318 PMCID: PMC5503513 DOI: 10.7554/elife.25736] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
HnRNP A1 regulates many alternative splicing events by the recognition of splicing silencer elements. Here, we provide the solution structures of its two RNA recognition motifs (RRMs) in complex with short RNA. In addition, we show by NMR that both RRMs of hnRNP A1 can bind simultaneously to a single bipartite motif of the human intronic splicing silencer ISS-N1, which controls survival of motor neuron exon 7 splicing. RRM2 binds to the upstream motif and RRM1 to the downstream motif. Combining the insights from the structure with in cell splicing assays we show that the architecture and organization of the two RRMs is essential to hnRNP A1 function. The disruption of the inter-RRM interaction or the loss of RNA binding capacity of either RRM impairs splicing repression by hnRNP A1. Furthermore, both binding sites within the ISS-N1 are important for splicing repression and their contributions are cumulative rather than synergistic. DOI:http://dx.doi.org/10.7554/eLife.25736.001
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Affiliation(s)
- Irene Beusch
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Pierre Barraud
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.,Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Laboratoire d'expression génétique microbienne, UMR 8261, CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de biologie physico-chimique, Paris, France
| | - Ahmed Moursy
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Frédéric Hai-Trieu Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
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11
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Fernandez N, Cordiner RA, Young RS, Hug N, Macias S, Cáceres JF. Genetic variation and RNA structure regulate microRNA biogenesis. Nat Commun 2017; 8:15114. [PMID: 28466845 PMCID: PMC5418625 DOI: 10.1038/ncomms15114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
MiRNA biogenesis is highly regulated at the post-transcriptional level; however, the role of sequence and secondary RNA structure in this process has not been extensively studied. A single G to A substitution present in the terminal loop of pri-mir-30c-1 in breast and gastric cancer patients had been previously described to result in increased levels of mature miRNA. Here, we report that this genetic variant directly affects Drosha-mediated processing of pri-mir-30c-1 in vitro and in cultured cells. Structural analysis of this variant revealed an altered RNA structure that facilitates the interaction with SRSF3, an SR protein family member that promotes pri-miRNA processing. Our results are compatible with a model whereby a genetic variant in pri-mir-30c-1 leads to a secondary RNA structure rearrangement that facilitates binding of SRSF3 resulting in increased levels of miR-30c. These data highlight that primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.
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Affiliation(s)
- Noemi Fernandez
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ross A. Cordiner
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Robert S. Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sara Macias
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Javier F. Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
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12
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Mao R, Yang R, Chen X, Harhaj EW, Wang X, Fan Y. Regnase-1, a rapid response ribonuclease regulating inflammation and stress responses. Cell Mol Immunol 2017; 14:412-422. [PMID: 28194024 PMCID: PMC5423090 DOI: 10.1038/cmi.2016.70] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins (RBPs) are central players in post-transcriptional regulation and immune homeostasis. The ribonuclease and RBP Regnase-1 exerts critical roles in both immune cells and non-immune cells. Its expression is rapidly induced under diverse conditions including microbial infections, treatment with inflammatory cytokines and chemical or mechanical stimulation. Regnase-1 activation is transient and is subject to negative feedback mechanisms including proteasome-mediated degradation or mucosa-associated lymphoid tissue 1 (MALT1) mediated cleavage. The major function of Regnase-1 is promoting mRNA decay via its ribonuclease activity by specifically targeting a subset of genes in different cell types. In monocytes, Regnase-1 downregulates IL-6 and IL-12B mRNAs, thus mitigating inflammation, whereas in T cells, it restricts T-cell activation by targeting c-Rel, Ox40 and Il-2 transcripts. In cancer cells, Regnase-1 promotes apoptosis by inhibiting anti-apoptotic genes including Bcl2L1, Bcl2A1, RelB and Bcl3. Together with up-frameshift protein-1 (UPF1), Regnase-1 specifically cleaves mRNAs that are active during translation by recognizing a stem-loop (SL) structure within the 3'UTRs of these genes in endoplasmic reticulum-bound ribosomes. Through this mechanism, Regnase-1 rapidly shapes mRNA profiles and associated protein expression, restricts inflammation and maintains immune homeostasis. Dysregulation of Regnase-1 has been described in a multitude of pathological states including autoimmune diseases, cancer and cardiovascular diseases. Here, we provide a comprehensive update on the function, regulation and molecular mechanisms of Regnase-1, and we propose that Regnase-1 may function as a master rapid response gene for cellular adaption triggered by microenvironmental changes.
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Affiliation(s)
- Renfang Mao
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Riyun Yang
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Xia Chen
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Edward W Harhaj
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Xiaoying Wang
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Yihui Fan
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
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13
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Early Prediction of Sepsis Incidence in Critically Ill Patients Using Specific Genetic Polymorphisms. Biochem Genet 2016; 55:193-203. [PMID: 27943002 DOI: 10.1007/s10528-016-9785-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/02/2016] [Indexed: 01/13/2023]
Abstract
Several diagnostic methods for the evaluation and monitoring were used to find out the pro-inflammatory status, as well as incidence of sepsis in critically ill patients. One such recent method is based on investigating the genetic polymorphisms and determining the molecular and genetic links between them, as well as other sepsis-associated pathophysiologies. Identification of genetic polymorphisms in critical patients with sepsis can become a revolutionary method for evaluating and monitoring these patients. Similarly, the complications, as well as the high costs associated with the management of patients with sepsis, can be significantly reduced by early initiation of intensive care.
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14
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Terasaka N, Futai K, Katoh T, Suga H. A human microRNA precursor binding to folic acid discovered by small RNA transcriptomic SELEX. RNA (NEW YORK, N.Y.) 2016; 22:1918-1928. [PMID: 27852928 PMCID: PMC5113211 DOI: 10.1261/rna.057737.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/12/2016] [Indexed: 05/17/2023]
Abstract
RNA aptamers are structured motifs that bind to specific molecules. A growing number of RNAs bearing aptamer elements, whose functions are modulated by direct binding of metabolites, have been found in living cells. Recent studies have suggested that more small RNAs binding to metabolites likely exist and may be involved in diverse cellular processes. However, conventional methods are not necessarily suitable for the discovery of such RNA aptamer elements in small RNAs with lengths ranging from 50 to 200 nucleotides, due to the far more abundant tRNAs in this size range. Here, we describe a new in vitro selection method to uncover naturally occurring small RNAs capable of binding to a ligand of interest, referred to as small RNA transcriptomic SELEX (smaRt-SELEX). By means of this method, we identified a motif in human precursor microRNA 125a (hsa-pre-miR-125a) that interacts with folic acid. Mutation studies revealed that the terminal loop region of hsa-pre-miR-125a is important for this binding interaction. This method has potential for the discovery of new RNA aptamer elements or catalytic motifs in biological small RNA fractions.
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Affiliation(s)
- Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuki Futai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST, CREST, The University of Tokyo, Tokyo 113-0033, Japan
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15
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Hou J, Meng F, Chan LWC, Cho WCS, Wong SCC. Circulating Plasma MicroRNAs As Diagnostic Markers for NSCLC. Front Genet 2016; 7:193. [PMID: 27857721 PMCID: PMC5093122 DOI: 10.3389/fgene.2016.00193] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/18/2016] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is the most common cause of cancer deaths all over the world, in which non-small cell lung cancer (NSCLC) accounts for ~85% of cases. It is well known that microRNAs (miRNAs) play a critical role in various cellular processes, mediating post-transcriptional silencing either by mRNA degradation through binding the 3' UTR of target mRNA or by translational inhibition of the protein. In the past decade, miRNAs have also been increasingly identified in biological fluids such as human serum or plasma known as circulating or cell-free miRNAs, and may function as non-invasive diagnostic markers for various cancer types including NSCLC. Circulating tumor cells (CTCs) are those cells that are shed from solid tumors and then migrate into the circulation. However, reports concerning the roles of CTCs are quite rare, which may be attributed to the difficulties in the enrichment and detection of CTCs in the circulation. Although, there have been reassuring advances in identifying circulating miRNA-panels, which are assumed to be of diagnostic value in NSCLC early stage, some issues remain concerning the reliability of using miRNA panels as a diagnostic tool for NSCLC. In the current review, we are aiming at providing insights into the miRNAs biology, the mechanisms of miRNAs release into the bloodstream, cell-free miRNAs as the diagnostic markers for NSCLC and the current limitations of CTCs as diagnostic markers in NSCLC.
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Affiliation(s)
- Jinpao Hou
- Department of Health Technology and Informatics, Hong Kong Polytechnic University Hong Kong, Hong Kong
| | - Fei Meng
- Department of Health Technology and Informatics, Hong Kong Polytechnic University Hong Kong, Hong Kong
| | - Lawrence W C Chan
- Department of Health Technology and Informatics, Hong Kong Polytechnic University Hong Kong, Hong Kong
| | - William C S Cho
- Department of Clinical Oncology, The Queen Elizabeth Hospital Kowloon, Hong Kong, Hong Kong
| | - S C Cesar Wong
- Department of Health Technology and Informatics, Hong Kong Polytechnic University Hong Kong, Hong Kong
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16
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Chen Y, Yang F, Zubovic L, Pavelitz T, Yang W, Godin K, Walker M, Zheng S, Macchi P, Varani G. Targeted inhibition of oncogenic miR-21 maturation with designed RNA-binding proteins. Nat Chem Biol 2016; 12:717-23. [PMID: 27428511 PMCID: PMC4990487 DOI: 10.1038/nchembio.2128] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 05/02/2016] [Indexed: 02/07/2023]
Abstract
The RNA Recognition Motif (RRM) is the largest family of eukaryotic RNA-binding proteins. Engineered RRMs with new specificity would provide valuable tools and an exacting test of our understanding of specificity. We have achieved the first successful re-design of the specificity of an RRM using rational methods and demonstrated re-targeting of activity in cells. We engineered the conserved RRM of human Rbfox proteins to specifically bind to the terminal loop of miR-21 precursor with high affinity and inhibit its processing by Drosha and Dicer. We further engineered Giardia Dicer by replacing its PAZ domain with the designed RRM. The reprogrammed enzyme degrades pre-miR-21 specifically in vitro and suppresses mature miR-21 levels in cells, which results in increased expression of PDCD4 and significantly decreased viability for cancer cells. The results demonstrate the feasibility of engineering the sequence-specificity of RRMs and of using this ubiquitous platform for diverse biological applications.
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Affiliation(s)
- Yu Chen
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Lorena Zubovic
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Tom Pavelitz
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Katherine Godin
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Matthew Walker
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Suxin Zheng
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Paolo Macchi
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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17
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Bedreag OH, Rogobete AF, Dumache R, Sarandan M, Cradigati AC, Papurica M, Craciunescu MC, Popa DM, Luca L, Nartita R, Sandesc D. Use of circulating microRNAs as biomarkers in critically ill polytrauma patients. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.bgm.2015.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Morgan CE, Meagher JL, Levengood JD, Delproposto J, Rollins C, Stuckey JA, Tolbert BS. The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein. J Mol Biol 2015; 427:3241-3257. [PMID: 26003924 PMCID: PMC4586317 DOI: 10.1016/j.jmb.2015.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/29/2015] [Accepted: 05/15/2015] [Indexed: 01/01/2023]
Abstract
The heterogeneous nuclear ribonucleoprotein (hnRNP) A1 protein is a multifunctional RNA binding protein implicated in a wide range of biological functions. Mechanisms and putative hnRNP A1-RNA interactions have been inferred primarily from the crystal structure of its UP1 domain bound to ssDNA. RNA stem loops represent an important class of known hnRNP A1 targets, yet little is known about the structural basis of hnRNP A1-RNA recognition. Here, we report the first high-resolution structure (1.92Å) of UP1 bound to a 5'-AGU-3' trinucleotide that resembles sequence elements of several native hnRNP A1-RNA stem loop targets. UP1 interacts specifically with the AG dinucleotide sequence via a "nucleobase pocket" formed by the β-sheet surface of RRM1 and the inter-RRM linker; RRM2 does not contact the RNA. The inter-RRM linker forms the lid of the nucleobase pocket and we show using structure-guided mutagenesis that the conserved salt-bridge interactions (R75:D155 and R88:D157) on the α-helical side of the RNA binding surface stabilize the linker in a geometry poised to bind RNA. We further investigated the structural basis of UP1 binding HIViSL3(ESS3) by determining a structural model of the complex scored by small-angle X-ray scattering. UP1 docks on the apical loop of SL3(ESS3) using its RRM1 domain and inter-RRM linker only. The biophysical implications of the structural model were tested by measuring kinetic binding parameters, where mutations introduced within the apical loop reduce binding affinities by slowing down the rate of complex formation. Collectively, the data presented here provide the first insights into hnRNP A1-RNA interactions.
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Affiliation(s)
- Christopher E Morgan
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey D Levengood
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - James Delproposto
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carrie Rollins
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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19
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Choudhury NR, Nowak JS, Zuo J, Rappsilber J, Spoel SH, Michlewski G. Trim25 Is an RNA-Specific Activator of Lin28a/TuT4-Mediated Uridylation. Cell Rep 2015; 9:1265-72. [PMID: 25457611 PMCID: PMC4542301 DOI: 10.1016/j.celrep.2014.10.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 09/30/2014] [Accepted: 10/03/2014] [Indexed: 12/27/2022] Open
Abstract
RNA binding proteins have thousands of cellular RNA targets and often exhibit opposite or passive molecular functions. Lin28a is a conserved RNA binding protein involved in pluripotency and tumorigenesis that was previously shown to trigger TuT4-mediated pre-let-7 uridylation, inhibiting its processing and targeting it for degradation. Surprisingly, despite binding to other pre-microRNAs (pre-miRNAs), only pre-let-7 is efficiently uridylated by TuT4. Thus, we hypothesized the existence of substrate-specific cofactors that stimulate Lin28a-mediated pre-let-7 uridylation or restrict its functionality on non-let-7 pre-miRNAs. Through RNA pull-downs coupled with quantitative mass spectrometry, we identified the E3 ligase Trim25 as an RNA-specific cofactor for Lin28a/TuT4-mediated uridylation. We show that Trim25 binds to the conserved terminal loop (CTL) of pre-let-7 and activates TuT4, allowing for more efficient Lin28a-mediated uridylation. These findings reveal that protein-modifying enzymes, only recently shown to bind RNA, can guide the function of canonical ribonucleoprotein (RNP) complexes in cis, thereby providing an additional level of specificity. Lin28a binding to a pre-miRNA is insufficient to trigger TuT4-mediated uridylation The E3 ligase Trim25 binds to the conserved terminal loop of pre-let-7 Trim25 is an RNA-specific cofactor for Lin28a/TuT4-mediated uridylation
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20
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Abstract
MicroRNAs are 20-24-nucleotide-long noncoding RNAs that bind to the 3' UTR (untranslated region) of target mRNAs. Since their discovery, microRNAs have been gaining attention for their ability to contribute to gene expression regulation under various physiological conditions. Consequently, deregulated expression of microRNAs has been linked to different disease states. Here, a brief overview of the canonical and alternative microRNA biogenesis pathways and microRNA functions in biological systems is given based on recent developments. In addition, newly emerging regulatory mechanisms, such as alternative polyadenylation, in connection with microRNA-dependent gene expression regulation are discussed.
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21
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Mattioli C, Pianigiani G, Pagani F. Cross talk between spliceosome and microprocessor defines the fate of pre-mRNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:647-58. [DOI: 10.1002/wrna.1236] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/14/2014] [Accepted: 03/21/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Chiara Mattioli
- Human Molecular Genetics; International Centre for Genetic Engineering and Biotechnology; Trieste Italy
| | - Giulia Pianigiani
- Human Molecular Genetics; International Centre for Genetic Engineering and Biotechnology; Trieste Italy
| | - Franco Pagani
- Human Molecular Genetics; International Centre for Genetic Engineering and Biotechnology; Trieste Italy
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22
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Nowak JS, Choudhury NR, de Lima Alves F, Rappsilber J, Michlewski G. Lin28a regulates neuronal differentiation and controls miR-9 production. Nat Commun 2014; 5:3687. [PMID: 24722317 PMCID: PMC4035284 DOI: 10.1038/ncomms4687] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 03/18/2014] [Indexed: 01/23/2023] Open
Abstract
microRNAs shape the identity and function of cells by regulating gene expression. It is known that brain-specific miR-9 is controlled transcriptionally; however, it is unknown whether post-transcriptional processes contribute to establishing its levels. Here, we show that miR-9 is regulated transcriptionally and post-transcriptionally during neuronal differentiation of the embryonic carcinoma cell line P19. We demonstrate that miR-9 is more efficiently processed in differentiated than undifferentiated cells. We reveal that Lin28a affects miR-9 by inducing the degradation of its precursor through a uridylation-independent mechanism. Furthermore, we show that constitutively expressed untagged but not GFP-tagged Lin28a decreases differentiation capacity of P19 cells, which coincides with reduced miR-9 levels. Finally, using an inducible system we demonstrate that Lin28a can also reduce miR-9 levels in differentiated P19 cells. Together, our results shed light on the role of Lin28a in neuronal differentiation and increase our understanding of the mechanisms regulating the level of brain-specific microRNAs.
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Affiliation(s)
- Jakub S Nowak
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - Nila Roy Choudhury
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - Flavia de Lima Alves
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - Juri Rappsilber
- 1] Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK [2] Department of Biotechnology, Technische Universität Berlin, 13353 Berlin, Germany
| | - Gracjan Michlewski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
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23
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Siddeek B, Inoubli L, Lakhdari N, Rachel PB, Fussell KC, Schneider S, Mauduit C, Benahmed M. MicroRNAs as potential biomarkers in diseases and toxicology. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 764-765:46-57. [PMID: 24486656 DOI: 10.1016/j.mrgentox.2014.01.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 01/20/2014] [Accepted: 01/20/2014] [Indexed: 02/06/2023]
Abstract
MiRNAs (microRNAs) are single-stranded non-coding RNAs of approximately 21-23 nucleotides in length whose main function is to inhibit gene expression by interfering with mRNA processes. MicroRNAs suppress gene expression by affecting mRNA (messenger RNAs) stability, targeting the mRNA for degradation, or both. In this review, we have examined how microRNA expression could be altered following exposure to chemicals and how they could represent appropriate tissue and more interestingly circulating biomarkers. Among the key questions before using the microRNA for evaluation of risk toxicity, it remains still to clarify how they could be causally involved in the adverse effects and how stable their changes are.
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Affiliation(s)
- Bénazir Siddeek
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France; BASF Agro, Ecully F-69130, France
| | - Lilia Inoubli
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France
| | - Nadjem Lakhdari
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France
| | - Paul Bellon Rachel
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France
| | | | - Steffen Schneider
- BASF SE, experimental toxicology and ecology, 67056 Ludwigshafen, Germany
| | - Claire Mauduit
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France; Université Lyon 1, UFR Médecine Lyon Sud, Lyon, F-69921, France; Hospices Civils de Lyon, Hôpital Lyon Sud, laboratoire d'anatomie et de cytologie pathologiques, Pierre-Bénite, F-69495, France
| | - Mohamed Benahmed
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France; Centre Hospitalier Universitaire de Nice, Pôle Digestif, Gynécologie, Obstetrique, Centre de Reproduction, Nice, F-06202, France.
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24
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Abstract
Regulating the expression of individual miRNAs (microRNAs) is important for cell development and function. The up- or down-regulation of the processing of specific miRNA precursors to the mature active form represents one tool to control miRNA concentration and is mediated by proteins that recognize the terminal loop of the RNA precursors. Terminal loop recognition is achieved by the combined action of several RNA-binding domains. The proteins can then regulate the processing by recruiting RNA enzymes, changing the RNA structure and preventing or enhancing the accessibility and processing activity of the core processing complexes. The present review focuses on how terminal loop-binding proteins recognize their RNA targets and mediate their regulatory function(s), and highlights how terminal loop-mediated regulation relates to the broader regulation of mRNA metabolism.
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25
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Abstract
The human nervous system expresses approximately 70% of all miRNAs (microRNAs). Changing levels of certain ubiquitous and brain-specific miRNAs shape the development and function of the nervous system. It is becoming clear that misexpression of some miRNAs can contribute towards neurodevelopmental disorders. In the present article, we review the current knowledge of the role of miRNAs in development and pathogenesis of the nervous system.
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26
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Gebert LFR, Rebhan MAE, Crivelli SEM, Denzler R, Stoffel M, Hall J. Miravirsen (SPC3649) can inhibit the biogenesis of miR-122. Nucleic Acids Res 2013; 42:609-21. [PMID: 24068553 PMCID: PMC3874169 DOI: 10.1093/nar/gkt852] [Citation(s) in RCA: 261] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs, which bind to messenger RNAs and regulate protein expression. The biosynthesis of miRNAs includes two precursors, a primary miRNA transcript (pri-miRNA) and a shorter pre-miRNA, both of which carry a common stem-loop bearing the mature miRNA. MiR-122 is a liver-specific miRNA with an important role in the life cycle of hepatitis C virus (HCV). It is the target of miravirsen (SPC3649), an antimiR drug candidate currently in clinical testing for treatment of HCV infections. Miravirsen is composed of locked nucleic acid (LNAs) ribonucleotides interspaced throughout a DNA phosphorothioate sequence complementary to mature miR-122. The LNA modifications endow the drug with high affinity for its target and provide resistance to nuclease degradation. While miravirsen is thought to work mainly by hybridizing to mature miR-122 and blocking its interaction with HCV RNA, its target sequence is also present in pri- and pre-miR-122. Using new in vitro and cellular assays specifically developed to discover ligands that suppress biogenesis of miR-122, we show that miravirsen binds to the stem-loop structure of pri- and pre-miR-122 with nanomolar affinity, and inhibits both Dicer- and Drosha-mediated processing of miR-122 precursors. This inhibition may contribute to the pharmacological activity of the drug in man.
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Affiliation(s)
- Luca F R Gebert
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, CH-8093, Switzerland and Institute of Molecular Health Sciences, ETH Zurich, Zurich, CH-8093, Switzerland
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27
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Libri V, Miesen P, van Rij RP, Buck AH. Regulation of microRNA biogenesis and turnover by animals and their viruses. Cell Mol Life Sci 2013; 70:3525-44. [PMID: 23354060 PMCID: PMC3771402 DOI: 10.1007/s00018-012-1257-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 12/27/2012] [Accepted: 12/27/2012] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are a ubiquitous component of gene regulatory networks that modulate the precise amounts of proteins expressed in a cell. Despite their small size, miRNA genes contain various recognition elements that enable specificity in when, where and to what extent they are expressed. The importance of precise control of miRNA expression is underscored by functional studies in model organisms and by the association between miRNA mis-expression and disease. In the last decade, identification of the pathways by which miRNAs are produced, matured and turned-over has revealed many aspects of their biogenesis that are subject to regulation. Studies in viral systems have revealed a range of mechanisms by which viruses target these pathways through viral proteins or non-coding RNAs in order to regulate cellular gene expression. In parallel, a field of study has evolved around the activation and suppression of antiviral RNA interference (RNAi) by viruses. Virus encoded suppressors of RNAi can impact miRNA biogenesis in cases where miRNA and small interfering RNA pathways converge. Here we review the literature on the mechanisms by which miRNA biogenesis and turnover are regulated in animals and the diverse strategies that viruses use to subvert or inhibit these processes.
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Affiliation(s)
- Valentina Libri
- Centre for Immunity, Infection and Evolution, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
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28
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Multiple cis-elements and trans-acting factors regulate dynamic spatio-temporal transcription of let-7 in Caenorhabditis elegans. Dev Biol 2012. [PMID: 23201578 DOI: 10.1016/j.ydbio.2012.11.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The let-7 microRNA (miRNA) is highly conserved across animal phyla and generally regulates cellular differentiation and developmental timing pathways. In Caenorhabditis elegans, the mature let-7 miRNA starts to accumulate in the last stages of larval development where it directs cellular differentiation programs required for adult fates. Here, we show that expression of the let-7 gene in C. elegans is under complex transcriptional control. The onset of let-7 transcription begins as early as the first larval stage in some tissues, and as late as the third larval stage in others, and is abrogated at the gravid adult stage. Transcription from two different start sites in the let-7 promoter oscillates during each larval stage. We show that transcription is regulated by two distinct cis-elements in the promoter of let-7, the previously described temporal regulatory element (TRE), and a novel element downstream of the TRE that we have named the let-7 transcription element (LTE). These elements play distinct and redundant roles in regulating let-7 expression in specific tissues. In the absence of the TRE and LTE, transcription of let-7 is undetectable and worms exhibit the lethal phenotype characteristic of let-7 null mutants. We also identify several genes that affect the transcription of let-7 generally and tissue-specifically. Overall, spatio-temporal regulation of let-7 transcription is orchestrated by multiple cis- and trans-acting factors to ensure appropriate expression of this essential miRNA during worm development.
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