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Dadhwal G, Samy H, Bouvette J, El-Azzouzi F, Dagenais P, Legault P. Substrate promiscuity of Dicer toward precursors of the let-7 family and their 3'-end modifications. Cell Mol Life Sci 2024; 81:53. [PMID: 38261114 PMCID: PMC10806991 DOI: 10.1007/s00018-023-05090-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
The human let-7 miRNA family consists of thirteen members that play critical roles in many biological processes, including development timing and tumor suppression, and their levels are disrupted in several diseases. Dicer is the endoribonuclease responsible for processing the precursor miRNA (pre-miRNA) to yield the mature miRNA, and thereby plays a crucial role in controlling the cellular levels of let-7 miRNAs. It is well established that the sequence and structural features of pre-miRNA hairpins such as the 5'-phosphate, the apical loop, and the 2-nt 3'-overhang are important for the processing activity of Dicer. Exceptionally, nine precursors of the let-7 family (pre-let-7) contain a 1-nt 3'-overhang and get mono-uridylated in vivo, presumably to allow efficient processing by Dicer. Pre-let-7 are also oligo-uridylated in vivo to promote their degradation and likely prevent their efficient processing by Dicer. In this study, we systematically investigated the impact of sequence and structural features of all human let-7 pre-miRNAs, including their 3'-end modifications, on Dicer binding and processing. Through the combination of SHAPE structural probing, in vitro binding and kinetic studies using purified human Dicer, we show that despite structural discrepancies among pre-let-7 RNAs, Dicer exhibits remarkable promiscuity in binding and cleaving these substrates. Moreover, the 1- or 2-nt 3'-overhang, 3'-mono-uridylation, and 3'-oligo-uridylation of pre-let-7 substrates appear to have little effect on Dicer binding and cleavage rates. Thus, this study extends current knowledge regarding the broad substrate specificity of Dicer and provides novel insight regarding the effect of 3'-modifications on binding and cleavage by Dicer.
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Affiliation(s)
- Gunjan Dadhwal
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Hebatallah Samy
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Jonathan Bouvette
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
- Molecular Biology Department, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| | - Fatima El-Azzouzi
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
- Biochemistry Department, Wake Forest Biotech Place, 575 Patterson Avenue, Winston-Salem, NC, 27101, USA
| | - Pierre Dagenais
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Pascale Legault
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada.
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2
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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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3
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The Effect of Dicer Knockout on RNA Interference Using Various Dicer Substrate Small Interfering RNA (DsiRNA) Structures. Genes (Basel) 2022; 13:genes13030436. [PMID: 35327991 PMCID: PMC8952432 DOI: 10.3390/genes13030436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/10/2022] Open
Abstract
Small interfering RNAs (siRNAs) are artificial molecules used to silence genes of interest through the RNA interference (RNAi) pathway, mediated by the endoribonuclease Dicer. Dicer-substrate small interfering RNAs (DsiRNAs) are an alternative to conventional 21-mer siRNAs, with an increased effectiveness of up to 100-fold compared to traditional 21-mer designs. DsiRNAs have a novel asymmetric design that allows them to be processed by Dicer into the desired conventional siRNAs. DsiRNAs are a useful tool for sequence-specific gene silencing, but the molecular mechanism underlying their increased efficacy is not precisely understood. In this study, to gain a deeper understanding of Dicer function in DsiRNAs, we designed nicked DsiRNAs with and without tetra-loops to target a specific mRNA sequence, established a Dicer knockout in the HCT116 cell line, and analyzed the efficacy of various DsiRNAs on RNAi-mediated gene silencing activity. The gene silencing activity of all DsiRNAs was reduced in Dicer knockout cells. We demonstrated that tetra-looped DsiRNAs exhibited increased efficacy for gene silencing, which was mediated by Dicer protein. Thus, this study improves our understanding of Dicer function, a key component of RNAi silencing, which will inform RNAi research and applications.
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Morgan M, Kumar L, Li Y, Baptissart M. Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. Cell Mol Life Sci 2021; 78:8049-8071. [PMID: 34748024 DOI: 10.1007/s00018-021-04012-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/22/2023]
Abstract
Multiple RNA pathways are required to produce functional sperm. Here, we review RNA post-transcriptional regulation during spermatogenesis with particular emphasis on the role of 3' end modifications. From early studies in the 1970s, it became clear that spermiogenesis transcripts could be stored for days only to be translated at advanced stages of spermatid differentiation. The transition between the translationally repressed and active states was observed to correlate with the shortening of the transcripts' poly(A) tail, establishing a link between RNA 3' end metabolism and male germ cell differentiation. Since then, numerous RNA metabolic pathways have been implicated not only in the progression through spermatogenesis, but also in the maintenance of genomic integrity. Recent studies have characterized the elusive 3' biogenesis of Piwi-interacting RNAs (piRNAs), identified a critical role for messenger RNA (mRNA) 3' uridylation in meiotic progression, established the mechanisms that destabilize transcripts with long 3' untranslated regions (3'UTRs) in post-mitotic cells, and defined the physiological relevance of RNA exonucleases and deadenylases in male germ cells. In this review, we discuss RNA processing in the male germline in the light of the most recent findings. A brief recollection of different RNA-processing events will aid future studies exploring post-transcriptional regulation in spermatogenesis.
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Affiliation(s)
- Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA.
| | - Lokesh Kumar
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Marine Baptissart
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
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5
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Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases. Int J Mol Sci 2021; 22:ijms22020616. [PMID: 33435485 PMCID: PMC7827160 DOI: 10.3390/ijms22020616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.
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Fragkos M, Barra V, Egger T, Bordignon B, Lemacon D, Naim V, Coquelle A. Dicer prevents genome instability in response to replication stress. Oncotarget 2019; 10:4407-4423. [PMID: 31320994 PMCID: PMC6633883 DOI: 10.18632/oncotarget.27034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/05/2019] [Indexed: 11/25/2022] Open
Abstract
Dicer, an endoribonuclease best-known for its role in microRNA biogenesis and RNA interference pathway, has been shown to play a role in the DNA damage response and repair of double-stranded DNA breaks (DSBs) in mammalian cells. However, it remains unknown whether Dicer is also important to preserve genome integrity upon replication stress. To address this question, we focused our study on common fragile sites (CFSs), which are susceptible to breakage after replication stress. We show that inhibition of the Dicer pathway leads to an increase in CFS expression upon induction of replication stress and to an accumulation of 53BP1 nuclear bodies, indicating transmission of replication-associated damage. We also show that in absence of a functional Dicer or Drosha, the assembly into nuclear foci of the Fanconi anemia (FA) protein FANCD2 and of the replication and checkpoint factor TopBP1 in response to replication stress is impaired, and the activation of the S-phase checkpoint is defective. Based on these results, we propose that Dicer pre-vents genomic instability after replication stress, by allowing the proper recruitment to stalled forks of proteins that are necessary to maintain replication fork stability and activate the S-phase checkpoint, thus limiting cells from proceeding into mitosis with under-replicated DNA.
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Affiliation(s)
- Michalis Fragkos
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France.,Laboratory of Genetic Instability and Oncogenesis, UMR 8200 CNRS, University Paris-Sud, Gustave Roussy, Villejuif, France.,These authors contributed equally to this work
| | - Viviana Barra
- Laboratory of Genetic Instability and Oncogenesis, UMR 8200 CNRS, University Paris-Sud, Gustave Roussy, Villejuif, France.,These authors contributed equally to this work
| | - Tom Egger
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Benoit Bordignon
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Delphine Lemacon
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France.,Present address: Department of Biochemistry and Molecular Biology, Doisy Research Center, St. Louis, MO, USA
| | - Valeria Naim
- Laboratory of Genetic Instability and Oncogenesis, UMR 8200 CNRS, University Paris-Sud, Gustave Roussy, Villejuif, France.,These authors contributed equally to this work
| | - Arnaud Coquelle
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
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7
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Bouvette J, Korkut DN, Fouillen A, Amellah S, Nanci A, Durocher Y, Omichinski JG, Legault P. High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension. BMC Biotechnol 2018; 18:76. [PMID: 30522464 PMCID: PMC6282390 DOI: 10.1186/s12896-018-0485-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/21/2018] [Indexed: 01/04/2023] Open
Abstract
Background Dicer is a 219-kDa protein that plays key roles in gene regulation, particularly as the ribonuclease III enzyme responsible for cleaving precursor miRNA substrates. Its enzymatic activity is highly regulated by protein factors, and this regulation can impact on the levels of miRNAs and modulate the behavior of a cell. To better understand the underlying mechanisms of regulation, detailed enzymatic and structural characterization of Dicer are needed. However, these types of studies generally require several milligrams of recombinant protein, and efficient preparation of such quantities of pure human Dicer remains a challenge. To prepare large quantities of human Dicer, we have optimized transfection in HEK293-6E cells grown in suspension and streamlined a purification procedure. Results Transfection conditions were first optimized to achieve expression levels between 10 and 18 mg of recombinant Dicer per liter of culture. A three-step purification protocol was then developed that yields 4–9 mg of purified Dicer per liter of culture in a single day. From SEC-MALS/RI analysis and negative stain TEM, we confirmed that the purified protein is monomerically pure ( ≥ 98%) and folds with the characteristic L-shape geometry. Using an electrophoretic mobility shift assay, a dissociation constant (Kd) of 5 nM was measured for Dicer binding to pre-let-7a-1, in agreement with previous reports. However, when probing the cleavage activity of Dicer for pre-let-7a-1, we measured kcat (7.2 ± 0.5 min− 1) and KM (1.2 ± 0.3 μM) values that are much higher than previously reported due to experimental conditions that better respect the steady-state assumption. Conclusions The expression and purification protocols described here provide high yields of monomerically pure and active human Dicer. Cleavage studies of a pre-let-7 substrate with this purified Dicer reveal higher kcat and KM values than previously reported and support the current view that conformational changes are associated with substrate binding. Large quantities of highly pure Dicer will be valuable for future biochemical, biophysical and structural investigations of this key protein of the miRNA pathway. Electronic supplementary material The online version of this article (10.1186/s12896-018-0485-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan Bouvette
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, H3C 3J7, QC, Canada
| | - Dursun Nizam Korkut
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, H3C 3J7, QC, Canada
| | - Aurélien Fouillen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, H3C 3J7, QC, Canada.,Département de Stomatologie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Soumiya Amellah
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, H3C 3J7, QC, Canada
| | - Antonio Nanci
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, H3C 3J7, QC, Canada.,Département de Stomatologie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Yves Durocher
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, H3C 3J7, QC, Canada.,Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - James G Omichinski
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, H3C 3J7, QC, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, H3C 3J7, QC, Canada.
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8
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Burger K, Schlackow M, Potts M, Hester S, Mohammed S, Gullerova M. Nuclear phosphorylated Dicer processes double-stranded RNA in response to DNA damage. J Cell Biol 2017. [PMID: 28642363 PMCID: PMC5551710 DOI: 10.1083/jcb.201612131] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The endoribonuclease Dicer is a key component of the human RNA interference pathway and is known for its role in cytoplasmic microRNA production. Recent findings suggest that noncanonical Dicer generates small noncoding RNA to mediate the DNA damage response (DDR). Here, we show that human Dicer is phosphorylated in the platform-Piwi/Argonaute/Zwille-connector helix cassette (S1016) upon induction of DNA damage. Phosphorylated Dicer (p-Dicer) accumulates in the nucleus and is recruited to DNA double-strand breaks. We further demonstrate that turnover of damage-induced nuclear, double-stranded (ds) RNA requires additional phosphorylation of carboxy-terminal Dicer residues (S1728 and S1852). DNA damage-induced nuclear Dicer accumulation is conserved in mammals. Dicer depletion causes endogenous DNA damage and delays the DDR by impaired recruitment of repair factors MDC1 and 53BP1. Collectively, we place Dicer within the context of the DDR by demonstrating a DNA damage-inducible phosphoswitch that causes localized processing of nuclear dsRNA by p-Dicer to promote DNA repair.
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Affiliation(s)
- Kaspar Burger
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Martin Potts
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Svenja Hester
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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9
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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10
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Molecular mechanisms of Dicer: endonuclease and enzymatic activity. Biochem J 2017; 474:1603-1618. [PMID: 28473628 PMCID: PMC5415849 DOI: 10.1042/bcj20160759] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/12/2022]
Abstract
The enzyme Dicer is best known for its role as a riboendonuclease in the small RNA pathway. In this canonical role, Dicer is a critical regulator of the biogenesis of microRNA and small interfering RNA, as well as a growing number of additional small RNAs derived from various sources. Emerging evidence demonstrates that Dicer's endonuclease role extends beyond the generation of small RNAs; it is also involved in processing additional endogenous and exogenous substrates, and is becoming increasingly implicated in regulating a variety of other cellular processes, outside of its endonuclease function. This review will describe the canonical and newly identified functions of Dicer.
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11
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Fan F, Pabbidi MR, Ge Y, Li L, Wang S, Mims PN, Roman RJ. Knockdown of Add3 impairs the myogenic response of renal afferent arterioles and middle cerebral arteries. Am J Physiol Renal Physiol 2016; 312:F971-F981. [PMID: 27927653 PMCID: PMC5495887 DOI: 10.1152/ajprenal.00529.2016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 11/22/2022] Open
Abstract
We have reported that the myogenic response of the renal afferent arteriole (Af-art) and middle cerebral artery (MCA) and autoregulation of renal and cerebral blood flow are impaired in Fawn-Hooded Hypertensive (FHH) rats. Transfer of a region of chromosome 1 containing γ-adducin (Add3) from the Brown Norway rat rescued the vascular dysfunction and the development of renal disease. To examine whether Add3 is a viable candidate gene altering renal and cerebral hemodynamics in FHH rats, we knocked down the expression of Add3 in rat Af-arts and MCAs cultured for 36-h using a 27-mer Dicer-substrate short interfering RNA (DsiRNA). Control Af-arts constricted by 10 ± 1% in response to an elevation in pressure from 60 to 120 mmHg but dilated by 4 ± 3% when treated with Add3 DsiRNA. Add3 DsiRNA had no effect on the vasoconstrictor response of the Af-art to norepinephrine (10-7 M). Add3 DsiRNA had a similar effect on the attenuation of the myogenic response in the MCA. Peak potassium currents were threefold higher in smooth muscle cells isolated from Af-arts or MCAs transfected with Add3 DsiRNA than in nontransfected cells isolated from the same vessels. This is the first study demonstrating that Add3 plays a role in the regulation of potassium channel function and vascular reactivity. It supports the hypothesis that sequence variants in Add3, which we previously identified in FHH rats, may play a causal role in the impaired myogenic response and autoregulation in the renal and cerebral circulation.
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Affiliation(s)
- Fan Fan
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Mallikarjuna R Pabbidi
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Ying Ge
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Longyang Li
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Shaoxun Wang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Paige N Mims
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Richard J Roman
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
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12
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Kruse J, Meier D, Zenk F, Rehders M, Nellen W, Hammann C. The protein domains of the Dictyostelium microprocessor that are required for correct subcellular localization and for microRNA maturation. RNA Biol 2016; 13:1000-1010. [PMID: 27416267 PMCID: PMC5056781 DOI: 10.1080/15476286.2016.1212153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The maturation pathways of microRNAs (miRNAs) have been delineated for plants and several animals, belonging to the evolutionary supergroups of Archaeplastida and Opisthokonta, respectively. Recently, we reported the discovery of the microprocessor complex in Dictyostelium discoideum of the Amoebozoa supergroup. The complex is composed of the Dicer DrnB and the dsRBD (double-stranded RNA binding domain) containing protein RbdB. Both proteins localize at nucleoli, where they physically interact, and both are required for miRNA maturation. Here we show that the miRNA phenotype of a ΔdrnB gene deletion strain can be rescued by ectopic expression of a series of DrnB GFP fusion proteins, which consistently showed punctate perinucleolar localization in fluorescence microscopy. These punctate foci appear surprisingly stable, as they persist both disintegration of nucleoli and degradation of cellular nucleic acids. We observed that DrnB expression levels influence the number of microprocessor foci and alter RbdB accumulation. An investigation of DrnB variants revealed that its newly identified nuclear localization signal is necessary, but not sufficient for the perinucleolar localization. Biogenesis of miRNAs, which are RNA Pol II transcripts, is correlated with that localization. Besides its bidentate RNase III domains, DrnB contains only a dsRBD, which surprisingly is dispensable for miRNA maturation. This dsRBD can, however, functionally replace the homologous domain in RbdB. Based on the unique setup of the Dictyostelium microprocessor with a subcellular localization similar to plants, but a protein domain composition similar to animals, we propose a model for the evolutionary origin of RNase III proteins acting in miRNA maturation.
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Affiliation(s)
- Janis Kruse
- a Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Ribogenetics Biochemistry Lab , Jacobs University Bremen , Bremen , Germany
| | - Doreen Meier
- b Abteilung Genetik, Universität Kassel , Kassel , Germany
| | - Fides Zenk
- b Abteilung Genetik, Universität Kassel , Kassel , Germany
| | - Maren Rehders
- a Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Ribogenetics Biochemistry Lab , Jacobs University Bremen , Bremen , Germany
| | | | - Christian Hammann
- a Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Ribogenetics Biochemistry Lab , Jacobs University Bremen , Bremen , Germany
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13
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Bollmann SR, Fang Y, Press CM, Tyler BM, Grünwald NJ. Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora. FRONTIERS IN PLANT SCIENCE 2016; 7:284. [PMID: 27014308 PMCID: PMC4791657 DOI: 10.3389/fpls.2016.00284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/22/2016] [Indexed: 05/10/2023]
Abstract
Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of filamentous oomycetes, contains many devastating plant pathogens, causing multibillion-dollar damage to crops, ornamental plants, and natural environments. The genomes of several oomycetes including Phytophthora species such as the soybean pathogen P. sojae, have been sequenced, allowing evolutionary analysis of small RNA-processing enzymes. This study examined the evolutionary origins of the oomycete small RNA-related genes Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) through broad phylogenetic analyses of the key domains. Two Dicer gene homologs, DCL1 and DCL2, and one RDR homolog were cloned and analyzed from P. sojae. Gene expression analysis revealed only minor changes in transcript levels among different life stages. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs in evolutionary trees, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study that suggested the last common eukaryote ancestor possessed three RDR homologs, which were selectively retained or lost in later lineages. Our analysis clarifies the position of some Unikont and Chromalveolate RDR lineages within the tree, including oomycete homologs. Finally, we analyzed alterations in the domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain transfer of the DEAD-box helicase domain from Dicer to RDR. Implications of the oomycete domain structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed.
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Affiliation(s)
- Stephanie R. Bollmann
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
| | - Yufeng Fang
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia TechBlacksburg, VA, USA
| | - Caroline M. Press
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
| | - Brett M. Tyler
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
| | - Niklaus J. Grünwald
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
- *Correspondence: Niklaus J. Grünwald
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14
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Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicases. Int J Mol Sci 2015; 16:2269-93. [PMID: 25622248 PMCID: PMC4346836 DOI: 10.3390/ijms16022269] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 12/28/2022] Open
Abstract
The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.
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Abstract
Dicer is central to microRNA-mediated silencing and several other RNA interference phenomena that are profoundly embedded in cancer gene networks. Most recently, both germline and somatic mutations in DICER1 have been identified in diverse types of cancer. Although some of the mutations clearly reduce the dosage of this key enzyme, others dictate surprisingly specific changes in select classes of small RNAs. This Review reflects on the molecular properties of the Dicer enzymes in small RNA silencing pathways, and rationalizes the newly discovered mutations on the basis of the activities and functions of its determinants.
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Affiliation(s)
- William D Foulkes
- 1] Departments of Human Genetics, Medicine and Oncology, McGill University; Lady Davis Institute, Jewish General Hospital and Research Institute, McGill University Health Centre, Montreal, Quebec, Canada. [2]
| | | | - Thomas F Duchaine
- 1] Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada, H3A 1A3. [2]
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Hackl M, Jadhav V, Klanert G, Karbiener M, Scheideler M, Grillari J, Borth N. Analysis of microRNA transcription and post-transcriptional processing by Dicer in the context of CHO cell proliferation. J Biotechnol 2014; 190:76-84. [PMID: 24486028 PMCID: PMC4247382 DOI: 10.1016/j.jbiotec.2013.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 11/25/2022]
Abstract
The expression of Dicer is correlated to growth rate in different CHO cell lines. Global perturbation of microRNA levels via DICER knockdown or overexpression directly influences CHO growth behavior. This provides strong evidence that microRNAs are key growth regulators in CHO cell lines.
CHO cells are the mammalian cell line of choice for recombinant production of therapeutic proteins. However, their low rate of proliferation limits obtainable space-time yields due to inefficient biomass accumulation. We set out to correlate microRNA transcription to cell-specific growth-rate by microarray analysis of 5 CHO suspension cell lines with low to high specific growth rates. Global microRNA expression analysis and Pearson correlation studies showed that mature microRNA transcript levels are predominately up-regulated in a state of fast proliferation (46 positively correlated, 17 negatively correlated). To further validate this observation, the expression of three genes that are central to microRNA biogenesis (Dicer, Drosha and Dgcr8) was analyzed. The expression of Dicer, which mediates the final step in microRNA maturation, was found to be strongly correlated to growth rate. Accordingly, knockdown of Dicer impaired cell growth by reducing growth-correlating microRNA transcripts. Moderate ectopic overexpression of Dicer positively affected cell growth, while strong overexpression impaired growth, presumably due to the concomitant increase of microRNAs that inhibit cell growth. Our data therefore suggest that Dicer dependent microRNAs regulate CHO cell proliferation and that Dicer could serve as a potential surrogate marker for cellular proliferation.
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Affiliation(s)
- Matthias Hackl
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Vaibhav Jadhav
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gerald Klanert
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Michael Karbiener
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, 8010 Graz, Austria
| | - Marcel Scheideler
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, 8010 Graz, Austria
| | - Johannes Grillari
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria; ACIB GmbH, Austrian Centre of Industrial Biotechnology, Graz, Austria.
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Ahmed F, Kaundal R, Raghava GPS. PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. BMC Bioinformatics 2013; 14 Suppl 14:S9. [PMID: 24267009 PMCID: PMC3851333 DOI: 10.1186/1471-2105-14-s14-s9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Dicer, an RNase III enzyme, plays a vital role in the processing of pre-miRNAs for generating the miRNAs. The structural and sequence features on pre-miRNA which can facilitate position and efficiency of cleavage are not well known. A precise cleavage by Dicer is crucial because an inaccurate processing can produce miRNA with different seed regions which can alter the repertoire of target genes. RESULTS In this study, a novel method has been developed to predict Dicer cleavage sites on pre-miRNAs using Support Vector Machine. We used the dataset of experimentally validated human miRNA hairpins from miRBase, and extracted fourteen nucleotides around Dicer cleavage sites. We developed number of models using various types of features and achieved maximum accuracy of 66% using binary profile of nucleotide sequence taken from 5p arm of hairpin. The prediction performance of Dicer cleavage site improved significantly from 66% to 86% when we integrated secondary structure information. This indicates that secondary structure plays an important role in the selection of cleavage site. All models were trained and tested on 555 experimentally validated cleavage sites and evaluated using 5-fold cross validation technique. In addition, the performance was also evaluated on an independent testing dataset that achieved an accuracy of ~82%. CONCLUSION Based on this study, we developed a webserver PHDcleav (http://www.imtech.res.in/raghava/phdcleav/) to predict Dicer cleavage sites in pre-miRNA. This tool can be used to investigate functional consequences of genetic variations/SNPs in miRNA on Dicer cleavage site, and gene silencing. Moreover, it would also be useful in the discovery of miRNAs in human genome and design of Dicer specific pre-miRNAs for potent gene silencing.
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18
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Doyle M, Badertscher L, Jaskiewicz L, Güttinger S, Jurado S, Hugenschmidt T, Kutay U, Filipowicz W. The double-stranded RNA binding domain of human Dicer functions as a nuclear localization signal. RNA (NEW YORK, N.Y.) 2013; 19:1238-52. [PMID: 23882114 PMCID: PMC3753931 DOI: 10.1261/rna.039255.113] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Dicer is a key player in microRNA (miRNA) and RNA interference (RNAi) pathways, processing miRNA precursors and double-stranded RNA into ∼21-nt-long products ultimately triggering sequence-dependent gene silencing. Although processing of substrates in vertebrate cells occurs in the cytoplasm, there is growing evidence suggesting Dicer is also present and functional in the nucleus. To address this possibility, we searched for a nuclear localization signal (NLS) in human Dicer and identified its C-terminal double-stranded RNA binding domain (dsRBD) as harboring NLS activity. We show that the dsRBD-NLS can mediate nuclear import of a reporter protein via interaction with importins β, 7, and 8. In the context of full-length Dicer, the dsRBD-NLS is masked. However, duplication of the dsRBD localizes the full-length protein to the nucleus. Furthermore, deletion of the N-terminal helicase domain results in partial accumulation of Dicer in the nucleus upon leptomycin B treatment, indicating that CRM1 contributes to nuclear export of Dicer. Finally, we demonstrate that human Dicer has the ability to shuttle between the nucleus and the cytoplasm. We conclude that Dicer is a shuttling protein whose steady-state localization is cytoplasmic.
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Affiliation(s)
- Michael Doyle
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
- Corresponding authorsE-mail E-mail
| | - Lukas Badertscher
- Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
- Molecular Life Science Ph.D. Program, CH-8057 Zurich, Switzerland
| | - Lukasz Jaskiewicz
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | | | - Sabine Jurado
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Tabea Hugenschmidt
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
- University of Basel, CH-4056 Basel, Switzerland
- Corresponding authorsE-mail E-mail
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19
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Cawley K, Logue SE, Gorman AM, Zeng Q, Patterson J, Gupta S, Samali A. Disruption of microRNA biogenesis confers resistance to ER stress-induced cell death upstream of the mitochondrion. PLoS One 2013; 8:e73870. [PMID: 23977393 PMCID: PMC3747093 DOI: 10.1371/journal.pone.0073870] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 07/29/2013] [Indexed: 01/08/2023] Open
Abstract
Global downregulation of microRNAs (miRNAs) is a common feature of human tumors and has been shown to enhance cancer progression. Several components of the miRNA biogenesis machinery (XPO5, DICER and TRBP) have been shown to act as haploinsufficient tumor suppressors. How the deregulation of miRNA biogenesis promotes tumor development is not clearly understood. Here we show that loss of miRNA biogenesis increased resistance to endoplasmic reticulum (ER) stress-induced cell death. We observed that HCT116 cells with a DICER hypomorphic mutation (Exn5/Exn5) or where DICER or DROSHA were knocked down were resistant to ER stress-induced cell death. Extensive analysis revealed little difference in the unfolded protein response (UPR) of WT compared to Exn5/Exn5 HCT116 cells upon ER stress treatment. However, analysis of the intrinsic apoptotic pathway showed that resistance occurred upstream of the mitochondria. In particular, BAX activation and dissipation of mitochondrial membrane potential was attenuated, and there was altered expression of BCL-2 family proteins. These observations demonstrate a key role for miRNAs as critical modulators of the ER stress response. In our model, downregulation of miRNA biogenesis delays ER stress-induced apoptosis. This suggests that disrupted miRNA biogenesis may contribute to cancer progression by inhibiting ER stress-induced cell death.
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Affiliation(s)
- Karen Cawley
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
- School of Natural Sciences National University of Ireland, Galway, Ireland
| | - Susan E. Logue
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
- School of Natural Sciences National University of Ireland, Galway, Ireland
| | - Adrienne M. Gorman
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
- School of Natural Sciences National University of Ireland, Galway, Ireland
| | - Qingping Zeng
- MannKind Corporation, Valencia, California, United States of America
| | - John Patterson
- MannKind Corporation, Valencia, California, United States of America
| | - Sanjeev Gupta
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
- School of Medicine, Clinical Science Institute, National University of Ireland, Galway, Ireland
| | - Afshin Samali
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
- School of Natural Sciences National University of Ireland, Galway, Ireland
- * E-mail:
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20
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Gu S, Jin L, Zhang Y, Huang Y, Zhang F, Valdmanis PN, Kay MA. The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo. Cell 2013; 151:900-911. [PMID: 23141545 DOI: 10.1016/j.cell.2012.09.042] [Citation(s) in RCA: 220] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/20/2012] [Accepted: 09/27/2012] [Indexed: 01/02/2023]
Abstract
Short hairpin RNA (shRNA)-induced RNAi is used for biological discovery and therapeutics. Dicer, whose normal role is to liberate endogenous miRNAs from their precursors, processes shRNAs into different biologically active siRNAs, affecting their efficacy and potential for off-targeting. We found that, in cells, Dicer induced imprecise cleavage events around the expected sites based on the previously described 5'/3' counting rules. These promiscuous noncanonical cleavages were abrogated when the cleavage site was positioned 2 nt from a bulge or loop. Interestingly, we observed that the ~1/3 of mammalian endogenous pre-miRNAs that contained such structures were more precisely processed by Dicer. Implementing a "loop-counting rule," we designed potent anti-HCV shRNAs with substantially reduced off-target effects. Our results suggest that Dicer recognizes the loop/bulge structure in addition to the ends of shRNAs/pre-miRNAs for accurate processing. This has important implications for both miRNA processing and future design of shRNAs for RNAi-based genetic screens and therapies.
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Affiliation(s)
- Shuo Gu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lan Jin
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yue Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yong Huang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Paul N Valdmanis
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA.
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21
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The multiple functions of TRBP, at the hub of cell responses to viruses, stress, and cancer. Microbiol Mol Biol Rev 2013; 76:652-66. [PMID: 22933564 DOI: 10.1128/mmbr.00012-12] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The TAR RNA binding protein (TRBP) has emerged as a key player in many cellular processes. First identified as a cellular protein that facilitates the replication of human immunodeficiency virus, TRBP has since been shown to inhibit the activation of protein kinase R (PKR), a protein involved in innate immune responses and the cellular response to stress. It also binds to the PKR activator PACT and regulates its function. TRBP also contributes to RNA interference as an integral part of the minimal RNA-induced silencing complex with Dicer and Argonaute proteins. Due to its multiple functions in the cell, TRBP is involved in oncogenesis when its sequence is mutated or its expression is deregulated. The depletion or overexpression of TRBP results in malignancy, suggesting that the balance of TRBP expression is key to normal cellular function. These studies show that TRBP is multifunctional and mediates cross talk between different pathways. Its activities at the molecular level impact the cellular function from normal development to cancer and the response to infections.
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22
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Abstract
Small RNA molecules regulate eukaryotic gene expression during development and in response to stresses including viral infection. Specialized ribonucleases and RNA-binding proteins govern the production and action of small regulatory RNAs. After initial processing in the nucleus by Drosha, precursor microRNAs (pre-miRNAs) are transported to the cytoplasm, where Dicer cleavage generates mature microRNAs (miRNAs) and short interfering RNAs (siRNAs). These double-stranded products assemble with Argonaute proteins such that one strand is preferentially selected and used to guide sequence-specific silencing of complementary target mRNAs by endonucleolytic cleavage or translational repression. Molecular structures of Dicer and Argonaute proteins, and of RNA-bound complexes, have offered exciting insights into the mechanisms operating at the heart of RNA-silencing pathways.
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23
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He C, Li YX, Zhang G, Gu Z, Yang R, Li J, Lu ZJ, Zhou ZH, Zhang C, Wang J. MiRmat: mature microRNA sequence prediction. PLoS One 2012; 7:e51673. [PMID: 23300555 PMCID: PMC3531441 DOI: 10.1371/journal.pone.0051673] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 11/05/2012] [Indexed: 01/12/2023] Open
Abstract
Background MicroRNAs are known to be generated from primary transcripts mainly through the sequential cleavages by two enzymes, Drosha and Dicer. The sequence of a mature microRNA, especially the ‘seeding sequence’, largely determines its binding ability and specificity to target mRNAs. Therefore, methods that predict mature microRNA sequences with high accuracy will benefit the identification and characterization of novel microRNAs and their targets, and contribute to inferring the post-transcriptional regulation network at a genome scale. Methodology/Principal Findings We have developed a method, MiRmat, to predict the mature microRNA sequence. MiRmat is essentially composed of two parts: the prediction of Drosha processing site and the identification of Dicer processing site. Based on the analysis of microRNAs from 12 species, we found that the patterns of free energy profiles are conserved among vertebrate microRNA hairpins. Therefore, we introduced in our method the free energy distribution pattern of the downstream part of pri-microRNA secondary structure and Random Forest algorithm to predict the mature microRNA sequence. Based on the evaluation on an independent test dataset from 10 vertebrates, MiRmat was shown to identify 77.8% of the Drosha processing sites and 92.8% of the Dicer sites within a deviation of 2 nt. In a more stringent evaluation by excluding the microRNAs sharing the same family between the training set and test set, MiRmat kept a rather well performance of 71.9% and 87.2% of the identification rate on the Drosha and Dicer site respectively, which represents the ability to deal with the novel microRNA family. MiRmat outperforms other state-of-the-art methods and has a high degree of efficacy for the prediction of mature microRNA sequences of vertebrates. Conclusion MiRmat was developed for identifying microRNA mature sequence(s) by introducing the free energy distribution of RNA stem-loop structure and the Random Forest algorithm. We prove that MiRmat has better performance than the existing tools and is applicable among vertebrates. MiRmat is freely available at http://mcube.nju.edu.cn/jwang/lab/soft/MiRmat/.
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Affiliation(s)
- Chenfeng He
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Ying-Xin Li
- National Key Laboratory for Novel Software Technology, Nanjing University, Nanjing, China
- Institute of Machine Vision and Machine Intelligence, Beijing Jingwei Textile Machinery New Technology Co., Ltd., Beijing, China
| | - Guangxin Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Zuguang Gu
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Rong Yang
- Biophysics Institute, School of Physics, Nanjing University, Nanjing, China
| | - Jie Li
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Zhi John Lu
- Ministry of Education Key Lab of Bioinformatics & System Biology, School of Life Science, Tsinghua University, Beijing, China
| | - Zhi-Hua Zhou
- National Key Laboratory for Novel Software Technology, Nanjing University, Nanjing, China
- * E-mail: (ZHZ); (CZ); (JW)
| | - Chenyu Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing, China
- * E-mail: (ZHZ); (CZ); (JW)
| | - Jin Wang
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing, China
- * E-mail: (ZHZ); (CZ); (JW)
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24
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Ma E, Zhou K, Kidwell MA, Doudna JA. Coordinated activities of human dicer domains in regulatory RNA processing. J Mol Biol 2012; 422:466-76. [PMID: 22727743 DOI: 10.1016/j.jmb.2012.06.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 05/31/2012] [Accepted: 06/01/2012] [Indexed: 12/22/2022]
Abstract
The conserved ribonuclease Dicer generates microRNAs and short-interfering RNAs that guide gene silencing in eukaryotes. The specific contributions of human Dicer's structural domains to RNA product length and substrate preference are incompletely understood, due in part to the difficulties of Dicer purification. Here, we show that active forms of human Dicer can be assembled from recombinant polypeptides expressed in bacteria. Using this system, we find that three distinct modes of RNA recognition give rise to Dicer's fidelity and product length specificity. The first involves anchoring one end of a double-stranded RNA helix within the PAZ domain, which can assemble in trans with Dicer's catalytic domains to reconstitute an accurate but non-substrate-selective dicing activity. The second entails nonspecific RNA binding by the double-stranded RNA binding domain, an interaction that is essential for substrate recruitment in the absence of the PAZ domain. The third mode of recognition involves hairpin RNA loop recognition by the helicase domain, which ensures efficient processing of specific substrates. These results reveal distinct interactions of each Dicer domain with different RNA structural features and provide a facile system for investigating the molecular mechanisms of human microRNA biogenesis.
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Affiliation(s)
- Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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25
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Liu C, Axtell MJ, Fedoroff NV. The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis. PLANT PHYSIOLOGY 2012; 159:748-58. [PMID: 22474216 PMCID: PMC3406889 DOI: 10.1104/pp.112.193508] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/30/2012] [Indexed: 05/18/2023]
Abstract
Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 null mutants accumulate low levels of miRNAs and display pleiotropic developmental phenotypes. We report the identification of five new hyl1 suppressor mutants, all of which are alleles of DCL1. These new alleles affect either the helicase or the RNaseIIIa domains of DCL1, highlighting the critical functions of these domains. Biochemical analysis of the DCL1 suppressor variants reveals that they process the primary transcript (pri-miRNA) more efficiently than wild-type DCL1, with both higher K(cat) and lower K(m) values. The DCL1 variants largely rescue wild-type miRNA accumulation levels in vivo, but do not rescue the MIRNA processing precision defects of the hyl1 null mutant. In vitro, the helicase domain confers ATP dependence on DCL1-catalyzed MIRNA processing, attenuates DCL1 cleavage activity, and is required for precise MIRNA processing of some substrates.
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26
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Abstract
Superfamily 2 helicases are involved in all aspects of RNA metabolism, and many steps in DNA metabolism. This review focuses on the basic mechanistic, structural and biological properties of each of the families of helicases within superfamily 2. There are ten separate families of helicases within superfamily 2, each playing specific roles in nucleic acid metabolism. The mechanisms of action are diverse, as well as the effect on the nucleic acid. Some families translocate on single-stranded nucleic acid and unwind duplexes, some unwind double-stranded nucleic acids without translocation, and some translocate on double-stranded or single-stranded nucleic acids without unwinding.
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Affiliation(s)
- Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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27
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The molecular architecture of human Dicer. Nat Struct Mol Biol 2012; 19:436-40. [PMID: 22426548 PMCID: PMC3319852 DOI: 10.1038/nsmb.2268] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 02/22/2012] [Indexed: 12/20/2022]
Abstract
Dicer is a multi-domain enzyme that generates small RNAs for gene silencing in eukaryotes. Current understanding of Dicer structure is restricted to simple forms of the enzyme, while that of the large and complex Dicer, widespread in eukarya, is unknown. Here, we describe a novel domain localization strategy developed to determine the structure of human Dicer by electron microscopy. A rearrangement of the nuclease core, compared to the archetypal Giardia Dicer, explains how metazoan Dicers generate 21–23 nucleotide products. The helicase domains form a clamp-like structure adjacent to the RNase III active site, facilitating recognition of pre-miRNA loops or translocation on long dsRNAs. Drosophila Dicer-2 displays similar features, revealing that the three-dimensional architecture is conserved. These results illuminate the structural basis for small RNA production in eukaryotes and provide a versatile new tool for determining structures of large molecular machines.
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Dicer Proteins and Their Role in Gene Silencing Pathways. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/b978-0-12-404741-9.00001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
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29
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Small RNAs derived from longer non-coding RNAs. Biochimie 2011; 93:1905-15. [PMID: 21843590 DOI: 10.1016/j.biochi.2011.07.032] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 07/29/2011] [Indexed: 12/21/2022]
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30
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Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD, Pyle AM. Structural insights into RNA recognition by RIG-I. Cell 2011; 147:409-22. [PMID: 22000018 PMCID: PMC3222294 DOI: 10.1016/j.cell.2011.09.023] [Citation(s) in RCA: 311] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 08/02/2011] [Accepted: 09/16/2011] [Indexed: 12/19/2022]
Abstract
Intracellular RIG-I-like receptors (RLRs, including RIG-I, MDA-5, and LGP2) recognize viral RNAs as pathogen-associated molecular patterns (PAMPs) and initiate an antiviral immune response. To understand the molecular basis of this process, we determined the crystal structure of RIG-I in complex with double-stranded RNA (dsRNA). The dsRNA is sheathed within a network of protein domains that include a conserved "helicase" domain (regions HEL1 and HEL2), a specialized insertion domain (HEL2i), and a C-terminal regulatory domain (CTD). A V-shaped pincer connects HEL2 and the CTD by gripping an α-helical shaft that extends from HEL1. In this way, the pincer coordinates functions of all the domains and couples RNA binding with ATP hydrolysis. RIG-I falls within the Dicer-RIG-I clade of the superfamily 2 helicases, and this structure reveals complex interplay between motor domains, accessory mechanical domains, and RNA that has implications for understanding the nanomechanical function of this protein family and other ATPases more broadly.
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Affiliation(s)
- Dahai Luo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Steve C. Ding
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Adriana Vela
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Andrew Kohlway
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Brett D. Lindenbach
- Section of Microbial Pathogenesis, Yale University, New Haven, Connecticut 06520
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
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31
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Recognition of the pre-miRNA structure by Drosophila Dicer-1. Nat Struct Mol Biol 2011; 18:1153-8. [PMID: 21926993 DOI: 10.1038/nsmb.2125] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 07/13/2011] [Indexed: 11/09/2022]
Abstract
Drosophila melanogaster has two Dicer proteins with specialized functions. Dicer-1 liberates miRNA-miRNA* duplexes from precursor miRNAs (pre-miRNAs), whereas Dicer-2 processes long double-stranded RNAs into small interfering RNA duplexes. It was recently demonstrated that Dicer-2 is rendered highly specific for long double-stranded RNA substrates by inorganic phosphate and a partner protein R2D2. However, it remains unclear how Dicer-1 exclusively recognize pre-miRNAs. Here we show that fly Dicer-1 recognizes the single-stranded terminal loop structure of pre-miRNAs through its N-terminal helicase domain, checks the loop size and measures the distance between the 3' overhang and the terminal loop. This unique mechanism allows fly Dicer-1 to strictly inspect the authenticity of pre-miRNA structures.
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32
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Thermodynamic stability of small hairpin RNAs highly influences the loading process of different mammalian Argonautes. Proc Natl Acad Sci U S A 2011; 108:9208-13. [PMID: 21576459 DOI: 10.1073/pnas.1018023108] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs and siRNAs interact with target sequences in mRNAs, inducing cleavage- and non-cleavage-based gene repression through the RNA-induced silencing complex (RISC) that consists of one of four mammalian Argonaute proteins, Ago1-Ago4. The process of how Dicer substrate small hairpin RNAs (shRNAs) are loaded into different mammalian Agos in vivo is not well established. Here we report that shRNAs are loaded into mammalian Agos in two stepwise processes, physical association and activation, with the latter being the rate-limiting step with noncleaving RISC. We establish that, although RNA duplexes processed from shRNAs bind to Agos in cells with similar affinity, the degree by which the complexes are activated (coupled with the removal of the passenger strand) correlates with the thermodynamic instability of RNA duplexes being loaded rather than the structure of the RNA, as was previously demonstrated in Drosophila. Interestingly, Ago loading of siRNAs is less sensitive to thermostability than that of their shRNA equivalents. These results may have important implications for the future design of RNAi-based therapeutics.
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33
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Sakurai K, Amarzguioui M, Kim DH, Alluin J, Heale B, Song MS, Gatignol A, Behlke MA, Rossi JJ. A role for human Dicer in pre-RISC loading of siRNAs. Nucleic Acids Res 2010; 39:1510-25. [PMID: 20972213 PMCID: PMC3045585 DOI: 10.1093/nar/gkq846] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
RNA interference is a powerful mechanism for sequence-specific inhibition of gene expression. It is widely known that small interfering RNAs (siRNAs) targeting the same region of a target-messenger RNA can have widely different efficacies. In efforts to better understand the siRNA features that influence knockdown efficiency, we analyzed siRNA interactions with a high-molecular weight complex in whole cell extracts prepared from two different cell lines. Using biochemical tools to study the nature of the complex, our results demonstrate that the primary siRNA-binding protein in the whole cell extracts is Dicer. We find that Dicer is capable of discriminating highly functional versus poorly functional siRNAs by recognizing the presence of 2-nt 3′ overhangs and the thermodynamic properties of 2–4 bp on both ends of effective siRNAs. Our results suggest a role for Dicer in pre-selection of effective siRNAs for handoff to Ago2. This initial selection is reflective of the overall silencing potential of an siRNA.
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Affiliation(s)
- Kumi Sakurai
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, 1450 East Duarte Road, Duarte, CA 91010, USA
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34
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Saayman S, Arbuthnot P, Weinberg MS. Deriving four functional anti-HIV siRNAs from a single Pol III-generated transcript comprising two adjacent long hairpin RNA precursors. Nucleic Acids Res 2010; 38:6652-63. [PMID: 20525791 PMCID: PMC2965221 DOI: 10.1093/nar/gkq460] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Revised: 05/07/2010] [Accepted: 05/11/2010] [Indexed: 11/19/2022] Open
Abstract
Several different approaches exist to generate expressed RNA interference (RNAi) precursors for multiple target inhibition, a strategy referred to as combinatorial (co)RNAi. One such approach makes use of RNA Pol III-expressed long hairpin RNAs (lhRNAs), which are processed by Dicer to generate multiple unique short interfering siRNA effectors. However, because of inefficient intracellular Dicer processing, lhRNA duplexes have been limited to generating two independent effective siRNA species. In this study, we describe a novel strategy whereby four separate anti-HIV siRNAs were generated from a single RNA Pol III-expressed transcript. Two optimized lhRNAs, each comprising two active anti-HIV siRNAs, were placed in tandem to form a double long hairpin (dlhRNA) expression cassette, which encodes four unique and effective siRNA sequences. Processing of the 3' position lhRNA was more variable but effective multiple processing was possible by manipulating the order of the siRNA-encoding sequences. Importantly, unlike shRNAs, Pol III-expressed dlhRNAs did not compete with endogenous and exogenous microRNAs to disrupt the RNAi pathway. The versatility of expressed lhRNAs is greatly expanded and we provide a mechanism for generating transcripts with modular lhRNAs motifs that contribute to improved coRNAi.
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Affiliation(s)
| | | | - Marc S. Weinberg
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
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35
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Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res 2010; 39:675-86. [PMID: 20846955 PMCID: PMC3025573 DOI: 10.1093/nar/gkq776] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) and microRNAs are two classes of non-protein-coding RNAs with distinct functions in RNA modification or post-transcriptional gene silencing. In this study, we introduce novel insights to RNA-induced gene activity adjustments in human cells by identifying numerous snoRNA-derived molecules with miRNA-like function, including H/ACA box snoRNAs and C/D box snoRNAs. In particular, we demonstrate that several C/D box snoRNAs give rise to gene regulatory RNAs, named sno-miRNAs here. Our data are complementing the increasing number of studies in the field of small RNAs with regulatory functions. In massively deep sequencing of small RNA fractions we identified high copy numbers of sub-sequences from >30 snoRNAs with lengths of ≥18 nt. RNA secondary structure prediction indicated for a majority of candidates a location in predicted stem regions. Experimental analysis revealed efficient gene silencing for 11 box C/D sno-miRNAs, indicating cytoplasmic processing and recruitment to the RNA silencing machinery. Assays in four different human cell lines indicated variations in both the snoRNA levels and their processing to active sno-miRNAs. In addition we show that box D elements are predominantly flanking at least one of the sno-miRNA strands, while the box C element locates within the sequence of the sno-miRNA guide strand.
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Affiliation(s)
- Markus Brameier
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany.
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36
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Liu HC, Hicks JA, Trakooljul N, Zhao SH. Current knowledge of microRNA characterization in agricultural animals. Anim Genet 2010; 41:225-31. [DOI: 10.1111/j.1365-2052.2009.01995.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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37
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Snead NM, Rossi JJ. Biogenesis and function of endogenous and exogenous siRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:117-31. [PMID: 21956909 DOI: 10.1002/wrna.14] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA interference (RNAi) is a sequence-specific gene silencing, or 'knockdown', mechanism facilitated by short duplex strands of RNA with sequence complementarity to target mRNAs. RNAi has many different forms, including posttranscriptional gene silencing (PTGS), and transcriptional gene silencing (TGS). Here, we review the biogenesis and function of an endogenous set of small RNA gene regulators, called microRNAs, as well as the mechanism of exogenously delivered small interfering RNAs. The potential applications of RNAi-based therapeutics are also highlighted.
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Affiliation(s)
- Nicholas M Snead
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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38
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Gredell JA, Dittmer MJ, Wu M, Chan C, Walton SP. Recognition of siRNA asymmetry by TAR RNA binding protein. Biochemistry 2010; 49:3148-55. [PMID: 20184375 DOI: 10.1021/bi902189s] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recognition of small interfering RNAs (siRNAs) by the RNA-induced silencing complex (RISC) and its precursor, the RISC loading complex (RLC), is a key step in the RNA interference pathway that controls the subsequent sequence-specific mRNA degradation. In Drosophila, selection of the guide strand has been shown to be mediated by RLC protein R2D2, which senses the relative hybridization stability between the two ends of the siRNA. A protein with similar function has yet to be conclusively identified in humans. We show here that human TAR RNA binding protein (TRBP) alone can bind siRNAs in vitro and sense their asymmetry. We also show that TRBP can bind 21-nucleotide single-stranded RNAs, though with far lower affinity than for double-stranded siRNA, and that TRBP cross-links preferentially to the 3'-ends of the guide strands of siRNAs. This suggests that TRBP binding depends both on the sequences of the siRNA strands and on the relative hybridization stability of the ends of the duplex. Together, these results demonstrate the importance of the siRNA-TRBP interaction in the selection of the siRNA guide strand in RNAi.
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Affiliation(s)
- Joseph A Gredell
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824-1226, USA
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39
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Structure of the human Dicer-TRBP complex by electron microscopy. Structure 2010; 17:1326-32. [PMID: 19836333 DOI: 10.1016/j.str.2009.08.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 08/24/2009] [Accepted: 08/24/2009] [Indexed: 11/22/2022]
Abstract
Dicer is a specialized ribonuclease that initiates RNA interference (RNAi) by cleaving double-stranded RNA (dsRNA) into small RNA fragments about 22 nucleotides long. Here, we present the three-dimensional structure of human Dicer bound to the protein TRBP at approximately 20 A resolution determined by negative-stain electron microscopy (EM) and single-particle analysis. Our analysis reveals that the Dicer-TRBP complex is an L-shaped molecule with a long edge of 150 A and a 100 A extension on one end. A surface trench runs the length of the long edge of the molecule, defining a putative dsRNA-binding site. Docking the crystal structure of Giardia Dicer, which represents the nuclease core of human Dicer, into the EM map suggests two possible overall molecular architectures for human Dicer. These results offer insights into the structure of Dicer proteins found in multicellular organisms and provide a conceptual framework for understanding the initiation of RNAi.
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40
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Saayman SM, Arbuthnot P, Weinberg MS. Effective Pol III-expressed long hairpin RNAs targeted to multiple unique sites of HIV-1. Methods Mol Biol 2010; 629:159-74. [PMID: 20387149 DOI: 10.1007/978-1-60761-657-3_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The RNA interference (RNAi) pathway has in recent years been exploited for the development of novel antiviral therapies. The emergence of viral escape mutants, however, is a major impediment to the use of RNAi effectors to treat highly mutable viruses such as HIV-1. A combinatorial approach is therefore required for long-term inhibition of gene expression. RNA Pol III-driven long hairpin RNA (lhRNA) duplexes can be cleaved several times by Dicer, yielding multiple functional siRNAs from a single construct. Here we describe a method for the generation of ectopically expressed U6-lhRNAs encoding three separate siRNA sequences targeting unique sites in HIV-1. This methodological overview explains some crucial aspects of lhRNA design and cloning as well as facile experiments to determine their efficacy in cell culture.
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Affiliation(s)
- Sheena M Saayman
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Wits, Johannesburg, South Africa
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41
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Liu YP, von Eije KJ, Schopman NCT, Westerink JT, ter Brake O, Haasnoot J, Berkhout B. Combinatorial RNAi against HIV-1 using extended short hairpin RNAs. Mol Ther 2009; 17:1712-23. [PMID: 19672247 PMCID: PMC2835024 DOI: 10.1038/mt.2009.176] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 07/06/2009] [Indexed: 12/11/2022] Open
Abstract
RNA interference (RNAi) is a widely used gene suppression tool that holds great promise as a novel antiviral approach. However, for error-prone viruses including human immunodeficiency virus type 1(HIV-1), a combinatorial approach against multiple conserved sequences is required to prevent the emergence of RNAi-resistant escape viruses. Previously, we constructed extended short hairpin RNAs (e-shRNAs) that encode two potent small interfering RNAs (siRNAs) (e2-shRNAs). We showed that a minimal hairpin stem length of 43 base pairs (bp) is needed to obtain two functional siRNAs. In this study, we elaborated on the e2-shRNA design to make e-shRNAs encoding three or four antiviral siRNAs. We demonstrate that siRNA production and the antiviral effect is optimal for e3-shRNA of 66 bp. Further extension of the hairpin stem results in a loss of RNAi activity. The same was observed for long hairpin RNAs (lhRNAs) that target consecutive HIV-1 sequences. Importantly, we show that HIV-1 replication is durably inhibited in T cells stably transduced with a lentiviral vector containing the e3-shRNA expression cassette. These results show that e-shRNAs can be used as a combinatorial RNAi approach to target error-prone viruses.
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Affiliation(s)
- Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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42
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Davis BN, Hata A. Regulation of MicroRNA Biogenesis: A miRiad of mechanisms. Cell Commun Signal 2009; 7:18. [PMID: 19664273 PMCID: PMC3224893 DOI: 10.1186/1478-811x-7-18] [Citation(s) in RCA: 241] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 08/10/2009] [Indexed: 01/08/2023] Open
Abstract
microRNAs are small, non-coding RNAs that influence diverse biological functions through the repression of target genes during normal development and pathological responses. Widespread use of microRNA arrays to profile microRNA expression has indicated that the levels of many microRNAs are altered during development and disease. These findings have prompted a great deal of investigation into the mechanism and function of microRNA-mediated repression. However, the mechanisms which govern the regulation of microRNA biogenesis and activity are just beginning to be uncovered. Following transcription, mature microRNA are generated through a series of coordinated processing events mediated by large protein complexes. It is increasingly clear that microRNA biogenesis does not proceed in a 'one-size-fits-all' manner. Rather, individual classes of microRNAs are differentially regulated through the association of regulatory factors with the core microRNA biogenesis machinery. Here, we review the regulation of microRNA biogenesis and activity, with particular focus on mechanisms of post-transcriptional control. Further understanding of the regulation of microRNA biogenesis and activity will undoubtedly provide important insights into normal development as well as pathological conditions such as cardiovascular disease and cancer.
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Affiliation(s)
- Brandi N Davis
- Department of Biochemistry, Tufts University School of Medicine, Boston MA 02111, USA.
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43
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Flores-jasso CF, Arenas-huertero C, Reyes JL, Contreras-cubas C, Covarrubias A, Vaca L. First step in pre-miRNAs processing by human Dicer. Acta Pharmacol Sin 2009; 30:1177-85. [PMID: 19654583 DOI: 10.1038/aps.2009.108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIM To investigate the strand preference of the initial cleavage of human pre-miRNAs by human Dicer in vitro. METHODS We used a series of in vitro transcribed pre-miRNAs that were radioactively labeled at their 5' or 3' ends in cleavage reactions with recombinant human Dicer or HeLa cytoplasmic S100 extracts. Pre-miRNAs samples were purified by denaturing and native PAGE and only the stem-loop structures were used in the experiments. Products of cleavage reactions were resolved by denaturing PAGE, and scanned by phosphor-imaging. RESULTS Recombinant hDicer performs a biased first-cleavage in the pre-let-7b and hsa-pre-miR-17 3' strand. This result is recapitulated in HeLa S100 cytoplasmic extracts. CONCLUSION The differential first-nick is observed in cleavage reactions only when stem-loops are substrates for hDicer.
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44
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Kemp C, Imler JL. Antiviral immunity in drosophila. Curr Opin Immunol 2009; 21:3-9. [PMID: 19223163 DOI: 10.1016/j.coi.2009.01.007] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 01/20/2009] [Indexed: 12/21/2022]
Abstract
Genetic analysis of the drosophila antiviral response indicates that RNA interference plays a major role. This contrasts with the situation in mammals, where interferon-induced responses mediate innate antiviral host-defense. An inducible response also contributes to antiviral immunity in drosophila, and similarities in the sensing and signaling of viral infection are becoming apparent between drosophila and mammals. In particular, DExD/H box helicases appear to play a crucial role in the cytosolic detection of viral RNAs in flies and mammals.
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Affiliation(s)
- Cordula Kemp
- CNRS-UPR, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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