201
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Tomassi AH, Gagliardi D, Cambiagno DA, Manavella PA. Nonradioactive Detection of Small RNAs Using Digoxigenin-Labeled Probes. Methods Mol Biol 2017; 1640:199-210. [PMID: 28608344 DOI: 10.1007/978-1-4939-7165-7_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Small RNAs have been traditionally detected and quantified using small RNA blots, a modified Northern blot technique. The small RNAs are size-fractionated from the rest of the cellular RNA molecules by polyacrylamide gel electrophoresis and transferred by blotting onto a positively charged membrane. A radiolabeled probe was then traditionally used to detect a specific small RNA in the cellular pool. Small RNA blotting is a relatively simple, inexpensive approach to visualize small RNAs without artifacts. However, the radioactive labeling of the probe is sometimes an impediment, especially due to the requirement of specialized facilities. Here we describe a sensitive and simple method to detect and quantify small RNAs using digoxigenin-based nonradioactive RNA blots.
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Affiliation(s)
- Ariel H Tomassi
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET-FBCB), Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Delfina Gagliardi
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET-FBCB), Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET-FBCB), Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET-FBCB), Paraje El Pozo, 3000, Santa Fe, Argentina.
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202
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Xie X, Lin H, Peng X, Xu C, Sun Z, Jiang K, Huang A, Wu X, Tang N, Salvioli A, Bonfante P, Zhao B. Arbuscular Mycorrhizal Symbiosis Requires a Phosphate Transceptor in the Gigaspora margarita Fungal Symbiont. MOLECULAR PLANT 2016; 9:1583-1608. [PMID: 27688206 DOI: 10.1016/j.molp.2016.08.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 08/03/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
The majority of terrestrial vascular plants are capable of forming mutualistic associations with obligate biotrophic arbuscular mycorrhizal (AM) fungi from the phylum Glomeromycota. This mutualistic symbiosis provides carbohydrates to the fungus, and reciprocally improves plant phosphate uptake. AM fungal transporters can acquire phosphate from the soil through the hyphal networks. Nevertheless, the precise functions of AM fungal phosphate transporters, and whether they act as sensors or as nutrient transporters, in fungal signal transduction remain unclear. Here, we report a high-affinity phosphate transporter GigmPT from Gigaspora margarita that is required for AM symbiosis. Host-induced gene silencing of GigmPT hampers the development of G. margarita during AM symbiosis. Most importantly, GigmPT functions as a phosphate transceptor in G. margarita regarding the activation of the phosphate signaling pathway as well as the protein kinase A signaling cascade. Using the substituted-cysteine accessibility method, we identified residues A146 (in transmembrane domain [TMD] IV) and Val357 (in TMD VIII) of GigmPT, both of which are critical for phosphate signaling and transport in yeast during growth induction. Collectively, our results provide significant insights into the molecular functions of a phosphate transceptor from the AM fungus G. margarita.
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Affiliation(s)
- Xianan Xie
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Hui Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Xiaowei Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Congrui Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Zhongfeng Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Kexin Jiang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Antian Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Xiaohui Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Nianwu Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125 Torino, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125 Torino, Italy
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R.China.
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203
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Maillard PV, Van der Veen AG, Deddouche-Grass S, Rogers NC, Merits A, Reis e Sousa C. Inactivation of the type I interferon pathway reveals long double-stranded RNA-mediated RNA interference in mammalian cells. EMBO J 2016; 35:2505-2518. [PMID: 27815315 PMCID: PMC5167344 DOI: 10.15252/embj.201695086] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/02/2016] [Accepted: 09/12/2016] [Indexed: 12/22/2022] Open
Abstract
RNA interference (RNAi) elicited by long double-stranded (ds) or base-paired viral RNA constitutes the major mechanism of antiviral defence in plants and invertebrates. In contrast, it is controversial whether it acts in chordates. Rather, in vertebrates, viral RNAs induce a distinct defence system known as the interferon (IFN) response. Here, we tested the possibility that the IFN response masks or inhibits antiviral RNAi in mammalian cells. Consistent with that notion, we find that sequence-specific gene silencing can be triggered by long dsRNAs in differentiated mouse cells rendered deficient in components of the IFN pathway. This unveiled response is dependent on the canonical RNAi machinery and is lost upon treatment of IFN-responsive cells with type I IFN Notably, transfection with long dsRNA specifically vaccinates IFN-deficient cells against infection with viruses bearing a homologous sequence. Thus, our data reveal that RNAi constitutes an ancient antiviral strategy conserved from plants to mammals that precedes but has not been superseded by vertebrate evolution of the IFN system.
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Affiliation(s)
| | | | | | - Neil C Rogers
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
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204
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De Francesco A, Costa N, García ML. Citrus psorosis virus coat protein-derived hairpin construct confers stable transgenic resistance in citrus against psorosis A and B syndromes. Transgenic Res 2016; 26:225-235. [PMID: 27891561 DOI: 10.1007/s11248-016-0001-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/13/2016] [Indexed: 12/18/2022]
Abstract
Citrus psorosis virus (CPsV) is the causal agent of psorosis, a serious and widespread citrus disease. Two syndromes of psorosis, PsA and PsB, have been described. PsB is the most aggressive and rampant form. Previously, we obtained Pineapple sweet orange plants transformed with a hairpin construct derived from the CPsV coat protein gene (ihpCP). Some of these plants were resistant to CPsV 90-1-1, a PsA isolate homologous to the transgene. In this study, we found that expression of the ihpCP transgene and siRNA production in lines ihpCP-10 and -15 were stable with time and propagation. In particular, line ihpCP-15 has been resistant for more than 2 years, even after re-inoculation. The ihpCP plants were also resistant against a heterologous CPsV isolate that causes severe PsB syndrome. Line ihpCP-15 manifested complete resistance while line ihpCP-10 was tolerant to the virus, although with variable behaviour, showing delay and attenuation in PsB symptoms. These lines are promising for a biotech product aimed at eradicating psorosis.
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Affiliation(s)
- A De Francesco
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina
| | - N Costa
- Estación Experimental Agropecuaria, INTA Concordia, Ruta Provincial 22 y vías del Ferrocarril, 3200, Concordia, Entre Ríos, Argentina
| | - M L García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina.
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205
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Dang Y, Cheng J, Sun X, Zhou Z, Liu Y. Antisense transcription licenses nascent transcripts to mediate transcriptional gene silencing. Genes Dev 2016; 30:2417-2432. [PMID: 27856616 PMCID: PMC5131781 DOI: 10.1101/gad.285791.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022]
Abstract
In this study, Dang et al. use Neurospora to demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism. In eukaryotes, antisense transcription can regulate sense transcription by induction of epigenetic modifications. We showed previously that antisense transcription triggers Dicer-independent siRNA (disiRNA) production and disiRNA locus DNA methylation (DLDM) in Neurospora crassa. Here we show that the conserved exonuclease ERI-1 (enhanced RNAi-1) is a critical component in this process. Antisense transcription and ERI-1 binding to target RNAs are necessary and sufficient to trigger DLDM. Convergent transcription causes stalling of RNA polymerase II during transcription, which permits ERI-1 to bind nascent RNAs in the nucleus and recruit a histone methyltransferase complex that catalyzes chromatin modifications. Furthermore, we show that, in the cytoplasm, ERI-1 targets hundreds of transcripts from loci without antisense transcription to regulate RNA stability. Together, our results demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism.
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Affiliation(s)
- Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Beijing 100080, China
| | - Zhipeng Zhou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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206
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Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E. RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes. RNA Biol 2016; 13:177-95. [PMID: 26580233 PMCID: PMC4829319 DOI: 10.1080/15476286.2015.1110674] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.
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Affiliation(s)
- Anaïs Le Rhun
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Yan Yan Beer
- b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Johan Reimegård
- c Science for Life Laboratory , Department of Cell and Molecular Biology, Uppsala University, S-75003 , Uppsala , Sweden
| | - Krzysztof Chylinski
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,d Max F. Perutz Laboratories (MFPL), University of Vienna, A-1030 , Vienna , Austria
| | - Emmanuelle Charpentier
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany.,e Hannover Medical School (MHH), D-30625 , Hannover , Germany.,f Max Planck Institute for Infection Biology , Department of Regulation in Infection Biology, D-10117 , Berlin , Germany
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207
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De Santis R, Liepelt A, Mossanen JC, Dueck A, Simons N, Mohs A, Trautwein C, Meister G, Marx G, Ostareck-Lederer A, Ostareck DH. miR-155 targets Caspase-3 mRNA in activated macrophages. RNA Biol 2016; 13:43-58. [PMID: 26574931 DOI: 10.1080/15476286.2015.1109768] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
To secure the functionality of activated macrophages in the innate immune response, efficient life span control is required. Recognition of bacterial lipopolysaccharides (LPS) by toll-like receptor 4 (TLR4) induces downstream signaling pathways, which merge to induce the expression of cytokine genes and anti-apoptotic genes. MicroRNAs (miRNAs) have emerged as important inflammatory response modulators, but information about their functional impact on apoptosis is scarce. To identify miRNAs differentially expressed in response to LPS, cDNA libraries from untreated and LPS-activated murine macrophages were analyzed by deep sequencing and regulated miRNA expression was verified by Northern blotting and qPCR. Employing TargetScan(TM) we identified CASPASE-3 (CASP-3) mRNA that encodes a key player in apoptosis as potential target of LPS-induced miR-155. LPS-dependent primary macrophage activation revealed TLR4-mediated enhancement of miR-155 expression and CASP-3 mRNA reduction. Endogenous CASP-3 and cleaved CASP-3 protein declined in LPS-activated macrophages. Accumulation of miR-155 and CASP-3 mRNA in miRNA-induced silencing complexes (miRISC) was demonstrated by ARGONAUTE 2 (AGO2) immunoprecipitation. Importantly, specific antagomir transfection effectively reduced mature miR-155 and resulted in significantly elevated CASP-3 mRNA levels in activated macrophages. In vitro translation assays demonstrated that the target site in the CASP-3 mRNA 3'UTR mediates miR-155-dependent Luciferase reporter mRNA destabilization. Strikingly, Annexin V staining of macrophages transfected with antagomir-155 and stimulated with LPS prior to staurosporine (SSP) treatment implied that LPS-induced miR-155 prevents apoptosis through CASP-3 mRNA down-regulation. In conclusion, we report that miR-155-mediated CASP-3 mRNA destabilization in LPS-activated RAW 264.7 macrophages suppresses apoptosis, as a prerequisite to maintain their crucial function in inflammation.
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Affiliation(s)
- Rebecca De Santis
- a Department of Intensive Care and Intermediate Care , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
| | - Anke Liepelt
- a Department of Intensive Care and Intermediate Care , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany.,b Department of Internal Medicine III , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
| | - Jana C Mossanen
- a Department of Intensive Care and Intermediate Care , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
| | - Anne Dueck
- c Biochemistry Center Regensburg (BZR) , Laboratory for RNA Biology, University of Regensburg , Universitätsstrasse 31, 93053 , Regensburg , Germany
| | - Nadine Simons
- a Department of Intensive Care and Intermediate Care , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
| | - Antje Mohs
- b Department of Internal Medicine III , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
| | - Christian Trautwein
- b Department of Internal Medicine III , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
| | - Gunter Meister
- c Biochemistry Center Regensburg (BZR) , Laboratory for RNA Biology, University of Regensburg , Universitätsstrasse 31, 93053 , Regensburg , Germany
| | - Gernot Marx
- a Department of Intensive Care and Intermediate Care , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
| | - Antje Ostareck-Lederer
- a Department of Intensive Care and Intermediate Care , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
| | - Dirk H Ostareck
- a Department of Intensive Care and Intermediate Care , University Hospital, RWTH Aachen University , Pauwelsstrasse 30, 52074 , Aachen , Germany
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208
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Untiveros M, Olspert A, Artola K, Firth AE, Kreuze JF, Valkonen JPT. A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing. MOLECULAR PLANT PATHOLOGY 2016; 17:1111-23. [PMID: 26757490 PMCID: PMC4979677 DOI: 10.1111/mpp.12366] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/10/2015] [Accepted: 12/17/2015] [Indexed: 05/20/2023]
Abstract
The single-stranded, positive-sense RNA genome of viruses in the genus Potyvirus encodes a large polyprotein that is cleaved to yield 10 mature proteins. The first three cleavage products are P1, HCpro and P3. An additional short open reading frame (ORF), called pipo, overlaps the P3 region of the polyprotein ORF. Four related potyviruses infecting sweet potato (Ipomoea batatas) are predicted to contain a third ORF, called pispo, which overlaps the 3' third of the P1 region. Recently, pipo has been shown to be expressed via polymerase slippage at a conserved GA6 sequence. Here, we show that pispo is also expressed via polymerase slippage at a GA6 sequence, with higher slippage efficiency (∼5%) than at the pipo site (∼1%). Transient expression of recombinant P1 or the 'transframe' product, P1N-PISPO, in Nicotiana benthamiana suppressed local RNA silencing (RNAi), but only P1N-PISPO inhibited short-distance movement of the silencing signal. These results reveal that polymerase slippage in potyviruses is not limited to pipo expression, but can be co-opted for the evolution and expression of further novel gene products.
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Affiliation(s)
- Milton Untiveros
- Department of Agricultural Sciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Allan Olspert
- Department of Pathology, Division of Virology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Katrin Artola
- Department of Agricultural Sciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Andrew E Firth
- Department of Pathology, Division of Virology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | | | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki, FI-00014, Helsinki, Finland
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209
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Li F, Mei L, Zhan C, Mao Q, Yao M, Wang S, Tang L, Chen F. Liquid Hybridization and Solid Phase Detection: A Highly Sensitive and Accurate Strategy for MicroRNA Detection in Plants and Animals. Int J Mol Sci 2016; 17:E1457. [PMID: 27598139 PMCID: PMC5037736 DOI: 10.3390/ijms17091457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/31/2016] [Accepted: 08/22/2016] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in nearly every aspect of biology, including physiological, biochemical, developmental and pathological processes. Therefore, a highly sensitive and accurate method of detection of miRNAs has great potential in research on theory and application, such as the clinical approach to medicine, animal and plant production, as well as stress response. Here, we report a strategic method to detect miRNAs from multicellular organisms, which mainly includes liquid hybridization and solid phase detection (LHSPD); it has been verified in various species and is much more sensitive than traditional biotin-labeled Northern blots. By using this strategy and chemiluminescent detection with digoxigenin (DIG)-labeled or biotin-labeled oligonucleotide probes, as low as 0.01-0.25 fmol [for DIG-CDP Star (disodium2-chloro-5-(4-methoxyspiro{1,2-dioxetane-3,2'-(5'-chloro)tricyclo[3.3.1.13,7]decan}-4-yl)phenyl phosphate) system], 0.005-0.1 fmol (for biotin-CDP Star system), or 0.05-0.5 fmol (for biotin-luminol system) of miRNA can be detected and one-base difference can be distinguished between miRNA sequences. Moreover, LHSPD performed very well in the quantitative analysis of miRNAs, and the whole process can be completed within about 9 h. The strategy of LHSPD provides an effective solution for rapid, accurate, and sensitive detection and quantitative analysis of miRNAs in plants and animals.
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Affiliation(s)
- Fosheng Li
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Lanju Mei
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Cheng Zhan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Qiang Mao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
- Chengdu Botanical Garden, Chengdu 610083, Sichuan, China.
| | - Min Yao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Shenghua Wang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Lin Tang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Fang Chen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
- National and Local Joint Engineering Laboratory for Energy Plant Bio-Oil Production and Application, Chengdu 610000, Sichuan, China.
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210
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Kim W, Kim HE, Lee AR, Jun AR, Jung MG, Ahn JH, Lee JH. Base-pair opening dynamics of primary miR156a using NMR elucidates structural determinants important for its processing level and leaf number phenotype in Arabidopsis. Nucleic Acids Res 2016; 45:875-885. [PMID: 27574118 PMCID: PMC5314782 DOI: 10.1093/nar/gkw747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/28/2016] [Accepted: 08/16/2016] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs originate from primary transcripts containing hairpin structures. The levels of mature miR156 influence the leaf number prior to flowering in the life cycle of plants. To understand the molecular mechanism of biogenesis of primary miR156a (pri-miR156a) to mature miR156, a base-pair opening dynamics study was performed using model RNAs mimicking the cleavage site of wild type and B5 bulge-stabilizing mutant pri-miR156a constructs. We also determined the mature miR156 levels and measured leaf numbers at flowering of plants overexpressing the wild type and mutant constructs. Our results suggest that the stabilities and/or opening dynamics of the C15·G98 and U16·A97 base-pairs at the cleavage site are essential for formation of the active conformation and for efficient processing of pri-miR156a, and that mutations of the B5 bulge can modulate mature miR156 levels as well as miR156-driven leaf number phenotypes via changes in the base-pair stability of the cleavage site.
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Affiliation(s)
- Wanhui Kim
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hee-Eun Kim
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - A Rim Jun
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Myeong Gyo Jung
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ji Hoon Ahn
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
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211
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Kim W, Kim HE, Jun AR, Jung MG, Jin S, Lee JH, Ahn JH. Structural determinants of miR156a precursor processing in temperature-responsive flowering in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4659-4670. [PMID: 27335452 PMCID: PMC4973740 DOI: 10.1093/jxb/erw248] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
MicroRNAs originate from primary transcripts (pri-miRNAs) containing hairpin structures. Plant pri-miRNAs have highly variable structures and little is known about the information encoded in their secondary structures. Arabidopsis miR156 is an ambient temperature-responsive miRNA and plays an important role in regulating flowering time. To identify the structural determinants for miR156 processing, we analyzed the effects of mutations introduced in the upper stem of pri-miR156a on its temperature-dependent processing and flowering time. The levels of pri-miR156a and mature miR156 were opposite at different temperatures. Mutations in the upper stem, especially the region closer to the miR156a/miR156a* duplex, reduced miR156 processing at 23 °C and 16 °C and caused a less severe phenotype compared with the un-mutated construct. Mutation in the second stem near the first cleavage site of pri-miR156a affected miR156 processing at 23 °C, but not at 16 °C. This was also seen in pri-miR172a, another ambient temperature-responsive miRNA. Replacement of the upper stem of pri-miR156a with that of pri-miR172a severely affected miR156 processing and flowering time. These results suggested that the upper stem of pri-miR156a is important for miR156 processing at different temperatures. In particular, the second stem adjacent to the first cleavage site plays a role in the regulation of ambient temperature-responsive flowering.
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Affiliation(s)
- Wanhui Kim
- Creative Research Initiatives, Department of Life Sciences, Korea University, Anam-dong 5-ga, Seongbuk-Gu, Seoul 136-701, Republic of Korea
| | - Hee-Eun Kim
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea
| | - A Rim Jun
- Creative Research Initiatives, Department of Life Sciences, Korea University, Anam-dong 5-ga, Seongbuk-Gu, Seoul 136-701, Republic of Korea
| | - Myeong Gyo Jung
- Creative Research Initiatives, Department of Life Sciences, Korea University, Anam-dong 5-ga, Seongbuk-Gu, Seoul 136-701, Republic of Korea
| | - Suhyun Jin
- Creative Research Initiatives, Department of Life Sciences, Korea University, Anam-dong 5-ga, Seongbuk-Gu, Seoul 136-701, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea
| | - Ji Hoon Ahn
- Creative Research Initiatives, Department of Life Sciences, Korea University, Anam-dong 5-ga, Seongbuk-Gu, Seoul 136-701, Republic of Korea
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212
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Pawlica P, Moss WN, Steitz JA. Host miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region. RNA (NEW YORK, N.Y.) 2016; 22:1181-9. [PMID: 27335146 PMCID: PMC4931111 DOI: 10.1261/rna.054817.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 05/16/2016] [Indexed: 06/06/2023]
Abstract
Herpesvirus saimiri, an oncogenic herpesvirus, during latency produces seven small nuclear RNAs, called the Herpesvirus saimiri U RNAs (HSUR1-7). HSUR1 mediates degradation of the host microRNA, miR-27, via a process that requires imperfect base-pairing. The decreased levels of miR-27 lead to prolonged T-cell activation and likely contribute to oncogenesis. To gain insight into HSUR1-mediated degradation of miR-27, we probed the in vivo secondary structure of HSUR1 and coupled this with bioinformatic structural analyses. The results suggest that HSUR1 adopts a conformation different than previously believed and that the region complementary to miR-27 lacks stable structure. To determine whether HSUR1 structural flexibility is important for its ability to mediate miR-27 degradation, we performed structurally informative mutagenic analyses of HSUR1. HSUR1 mutants in which the miR-27 binding site sequence is preserved, but sequestered in predicted helices, lose their ability to decrease miR-27 levels. These results indicate that the HSUR1 miR27-binding region must be available in a conformationally flexible segment for noncoding RNA function.
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Affiliation(s)
- Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Walter N Moss
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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213
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Schwarzkopf M, Pierce NA. Multiplexed miRNA northern blots via hybridization chain reaction. Nucleic Acids Res 2016; 44:e129. [PMID: 27270083 PMCID: PMC5009741 DOI: 10.1093/nar/gkw503] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 05/24/2016] [Indexed: 11/13/2022] Open
Abstract
Northern blots enable detection of a target RNA of interest in a biological sample using standard benchtop equipment. miRNAs are the most challenging targets as they must be detected with a single short nucleic acid probe. With existing approaches, it is cumbersome to perform multiplexed blots in which several RNAs are detected simultaneously, impeding the study of interacting regulatory elements. Here, we address this shortcoming by demonstrating multiplexed northern blotting based on the mechanism of hybridization chain reaction (HCR). With this approach, nucleic acid probes complementary to RNA targets trigger chain reactions in which fluorophore-labeled DNA hairpins self-assemble into tethered fluorescent amplification polymers. The programmability of HCR allows multiple amplifiers to operate simultaneously and independently within a blot, enabling straightforward multiplexing. We demonstrate simultaneous detection of three endogenous miRNAs in total RNA extracted from 293T and HeLa cells. For a given target, HCR signal scales linearly with target abundance, enabling relative and absolute quantitation. Using non-radioactive HCR, sensitive and selective miRNA detection is achieved using 2'OMe-RNA probes. The HCR northern blot protocol takes ∼1.5 days independent of the number of target RNAs.
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Affiliation(s)
- Maayan Schwarzkopf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Niles A Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
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214
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Müller C, Sokol L, Vesper O, Sauert M, Moll I. Insights into the Stress Response Triggered by Kasugamycin in Escherichia coli. Antibiotics (Basel) 2016; 5:E19. [PMID: 27258317 PMCID: PMC4929434 DOI: 10.3390/antibiotics5020019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/19/2016] [Accepted: 05/23/2016] [Indexed: 01/06/2023] Open
Abstract
The bacteriostatic aminoglycoside antibiotic kasugamycin inhibits protein synthesis at an initial step without affecting translation elongation. It binds to the mRNA track of the ribosome and prevents formation of the translation initiation complex on canonical mRNAs. In contrast, translation of leaderless mRNAs continues in the presence of the drug in vivo. Previously, we have shown that kasugamycin treatment in E. coli stimulates the formation of protein-depleted ribosomes that are selective for leaderless mRNAs. Here, we provide evidence that prolonged kasugamycin treatment leads to selective synthesis of specific proteins. Our studies indicate that leaderless and short-leadered mRNAs are generated by different molecular mechanisms including alternative transcription and RNA processing. Moreover, we provide evidence for ribosome heterogeneity in response to kasugamycin treatment by alteration of the modification status of the stalk proteins bL7/L12.
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Affiliation(s)
- Christian Müller
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria.
| | - Lena Sokol
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria.
| | - Oliver Vesper
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria.
| | - Martina Sauert
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria.
| | - Isabella Moll
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria.
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215
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Song X, Cao X. Small RNA Extraction and Detection in Rice (Oryza sativa). CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:79-87. [PMID: 31725982 DOI: 10.1002/cppb.20005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Rice (Orzya sativa) small RNAs regulate almost all biological processes and agronomic traits. Characterization and dissection of small RNA functions have become an important part of rice functional genomic research. Isolation of small RNAs of desirable quality is essential for a variety of analytical techniques such as cloning, RT-PCR, northern hybridization, and microarray analysis. Among these, northern hybridization is the most convincing method to display size distribution, abundance, and expression profiles of small RNAs. This article describes protocols for extraction and detection of small RNAs from rice tissues, including procedures to enrich small RNAs from total RNA, and examination of the size and abundance of small RNAs by northern hybridization. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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216
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Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 2016; 532:517-21. [PMID: 27096362 DOI: 10.1038/nature17945] [Citation(s) in RCA: 585] [Impact Index Per Article: 73.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/30/2016] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas systems that provide defence against mobile genetic elements in bacteria and archaea have evolved a variety of mechanisms to target and cleave RNA or DNA. The well-studied types I, II and III utilize a set of distinct CRISPR-associated (Cas) proteins for production of mature CRISPR RNAs (crRNAs) and interference with invading nucleic acids. In types I and III, Cas6 or Cas5d cleaves precursor crRNA (pre-crRNA) and the mature crRNAs then guide a complex of Cas proteins (Cascade-Cas3, type I; Csm or Cmr, type III) to target and cleave invading DNA or RNA. In type II systems, RNase III cleaves pre-crRNA base-paired with trans-activating crRNA (tracrRNA) in the presence of Cas9 (refs 13, 14). The mature tracrRNA-crRNA duplex then guides Cas9 to cleave target DNA. Here, we demonstrate a novel mechanism in CRISPR-Cas immunity. We show that type V-A Cpf1 from Francisella novicida is a dual-nuclease that is specific to crRNA biogenesis and target DNA interference. Cpf1 cleaves pre-crRNA upstream of a hairpin structure formed within the CRISPR repeats and thereby generates intermediate crRNAs that are processed further, leading to mature crRNAs. After recognition of a 5'-YTN-3' protospacer adjacent motif on the non-target DNA strand and subsequent probing for an eight-nucleotide seed sequence, Cpf1, guided by the single mature repeat-spacer crRNA, introduces double-stranded breaks in the target DNA to generate a 5' overhang. The RNase and DNase activities of Cpf1 require sequence- and structure-specific binding to the hairpin of crRNA repeats. Cpf1 uses distinct active domains for both nuclease reactions and cleaves nucleic acids in the presence of magnesium or calcium. This study uncovers a new family of enzymes with specific dual endoribonuclease and endonuclease activities, and demonstrates that type V-A constitutes the most minimalistic of the CRISPR-Cas systems so far described.
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MESH Headings
- Bacterial Proteins/metabolism
- Base Sequence
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Calcium/metabolism
- Calcium/pharmacology
- Catalytic Domain
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- DNA Cleavage/drug effects
- Francisella/enzymology
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/biosynthesis
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Substrate Specificity
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Affiliation(s)
- Ines Fonfara
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Hagen Richter
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Majda Bratovič
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
- Hannover Medical School, Hannover 30625, Germany
| | - Anaïs Le Rhun
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Emmanuelle Charpentier
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
- Hannover Medical School, Hannover 30625, Germany
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217
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Cui L, Bikard D. Consequences of Cas9 cleavage in the chromosome of Escherichia coli. Nucleic Acids Res 2016; 44:4243-51. [PMID: 27060147 PMCID: PMC4872102 DOI: 10.1093/nar/gkw223] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/22/2016] [Indexed: 12/26/2022] Open
Abstract
The RNA-guided Cas9 nuclease from CRISPR-Cas systems has emerged as a powerful biotechnological tool. The specificity of Cas9 can be reprogrammed to cleave desired sequences in a cell's chromosome simply by changing the sequence of a small guide RNA. Unlike in most eukaryotes, Cas9 cleavage in the chromosome of bacteria has been reported to kill the cell. However, the mechanism of cell death remains to be investigated. Bacteria mainly rely on homologous recombination (HR) with sister chromosomes to repair double strand breaks. Here, we show that the simultaneous cleavage of all copies of the Escherichia coli chromosome at the same position cannot be repaired, leading to cell death. However, inefficient cleavage can be tolerated through continuous repair by the HR pathway. In order to kill cells reliably, HR can be blocked using the Mu phage Gam protein. Finally, the introduction of the non-homologous end joining (NHEJ) pathway from Mycobacterium tuberculosis was not able to rescue the cells from Cas9-mediated killing, but did introduce small deletions at a low frequency. This work provides a better understanding of the consequences of Cas9 cleavage in bacterial chromosomes which will be instrumental in the development of future CRISPR tools.
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Affiliation(s)
- Lun Cui
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris 75015, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris 75015, France
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218
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Liao R, He K, Chen C, Chen X, Cai C. Double-Strand Displacement Biosensor and Quencher-Free Fluorescence Strategy for Rapid Detection of MicroRNA. Anal Chem 2016; 88:4254-8. [DOI: 10.1021/acs.analchem.5b04154] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rong Liao
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Kui He
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Chunyan Chen
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Xiaoming Chen
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Changqun Cai
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
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219
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Reyes CA, Ocolotobiche EE, Marmisollé FE, Robles Luna G, Borniego MB, Bazzini AA, Asurmendi S, García ML. Citrus psorosis virus 24K protein interacts with citrus miRNA precursors, affects their processing and subsequent miRNA accumulation and target expression. MOLECULAR PLANT PATHOLOGY 2016; 17:317-29. [PMID: 26033697 PMCID: PMC6638441 DOI: 10.1111/mpp.12282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sweet orange (Citrus sinensis), one of the most important fruit crops worldwide, may suffer from disease symptoms induced by virus infections, thus resulting in dramatic economic losses. Here, we show that the infection of sweet orange plants with two isolates of Citrus psorosis virus (CPsV) expressing different symptomatology alters the accumulation of a set of endogenous microRNAs (miRNAs). Within these miRNAs, miR156, miR167 and miR171 were the most down-regulated, with almost a three-fold reduction in infected samples. This down-regulation led to a concomitant up-regulation of some of their targets, such as Squamosa promoter-binding protein-like 9 and 13, as well as Scarecrow-like 6. The processing of miRNA precursors, pre-miR156 and pre-miR171, in sweet orange seems to be affected by the virus. For instance, virus infection increases the level of unprocessed precursors, which is accompanied by a concomitant decrease in mature species accumulation. miR156a primary transcript accumulation remained unaltered, thus strongly suggesting a processing deregulation for this transcript. The co-immunoprecipitation of viral 24K protein with pre-miR156a or pre-miR171a suggests that the alteration in the processing of these precursors might be caused by a direct or indirect interaction with this particular viral protein. This result is also consistent with the nuclear localization of both miRNA precursors and the CPsV 24K protein. This study contributes to the understanding of the manner in which a virus can alter host regulatory mechanisms, particularly miRNA biogenesis and target expression.
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Affiliation(s)
- Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina
| | - Eliana E Ocolotobiche
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina
| | - Facundo E Marmisollé
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina
| | - María B Borniego
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina
| | - Ariel A Bazzini
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
| | - Sebastian Asurmendi
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
| | - María L García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina
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220
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Qu B, Cao J, Zhang F, Cui H, Teng J, Li J, Liu Z, Morehouse C, Jallal B, Tang Y, Guo Q, Yao Y, Shen N. Type I Interferon Inhibition of MicroRNA-146a Maturation Through Up-Regulation of Monocyte Chemotactic Protein-Induced Protein 1 in Systemic Lupus Erythematosus. Arthritis Rheumatol 2016; 67:3209-18. [PMID: 26315540 DOI: 10.1002/art.39398] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 08/18/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is characterized by the uncontrolled production of inflammatory cytokines, among which type I interferon (IFN) is recognized as a crucial pathogenic factor. The expression of microRNA-146a (miR-146a) is reduced in the white blood cells of SLE patients and accounts for their overactivated inflammatory responses. However, the mechanism of the reduction of miR-146a is still not fully understood. This study was undertaken to test whether the key pathogenic cytokine, type I IFN, is responsible for the dysregulation of miR-146a in SLE. METHODS Gene and protein expression was measured in all cells by reverse transcription-quantitative polymerase chain reaction, Northern blotting, or Western blotting. In THP-1 cells, expression of monocyte chemotactic protein-induced protein 1 (MCPIP-1) was knocked down with a lentivirus encoding a short hairpin RNA targeting MCPIP1. The cells were pretreated with type I IFN and assessed for gene expression levels of miR-146a. White blood cells from patients with SLE were analyzed for the expression of the IFN-inducible genes MCPIP1 and miR-146a, and the gene expression data were compared for correlation. RESULTS Pretreatment of THP-1 cells with type I IFN attenuated the induction of miR-146a posttranscriptionally, by down-regulating the expression of pre-miR-146a but not pri-miR-146a or its original unspliced transcript. Expression of MCPIP-1, which was enhanced by type I IFN, was found to be responsible for the inhibition of miR-146a. In white blood cells from patients with SLE, MCPIP1 expression was elevated, and its expression correlated positively with the IFN score and negatively with the miR-146a transcript level. CONCLUSION Type I IFN inhibits the maturation of miR-146a through the up-regulation of MCPIP-1, and thus contributes to the uncontrolled inflammation and excessive inflammatory gene expression in SLE.
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Affiliation(s)
- Bo Qu
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Institute of Health Sciences of Shanghai Institutes for Biological Sciences, and Chinese Academy of Sciences, Shanghai, China
| | - Jianchang Cao
- Institute of Health Sciences of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feifei Zhang
- Institute of Health Sciences of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huijuan Cui
- Renji Hospital and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialin Teng
- Renji Hospital and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Li
- Renji Hospital and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | | | - Yuanjia Tang
- Renji Hospital and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiang Guo
- Renji Hospital and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Nan Shen
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Institute of Health Sciences of Shanghai Institutes for Biological Sciences, and Chinese Academy of Sciences, Shanghai, China, and Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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221
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Chi BZ, Liang RP, Zhang L, Qiu JD. Sensitive and homogeneous microRNA detection using branched cascade enzymatic amplification. Chem Commun (Camb) 2016; 51:10543-6. [PMID: 26040236 DOI: 10.1039/c5cc02864g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This assay, termed branched cascade enzymatic amplification (BCEA), can be a novel and straightforward method for sensitive and specific microRNA detection in crude cellular extracts of cancer cells at physiological temperature, by coupling two ordinary polymerases, Klenow fragment exo(-) and terminal deoxynucleotidyl transferase.
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Affiliation(s)
- Bao-Zhu Chi
- Department of Chemistry, Nanchang University, Nanchang 330031, People's Republic of China.
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222
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Jakob L, Treiber T, Treiber N, Gust A, Kramm K, Hansen K, Stotz M, Wankerl L, Herzog F, Hannus S, Grohmann D, Meister G. Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA (NEW YORK, N.Y.) 2016; 22:383-396. [PMID: 26769856 PMCID: PMC4748816 DOI: 10.1261/rna.055426.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/02/2015] [Indexed: 06/05/2023]
Abstract
In the microRNA (miRNA) pathway, Dicer processes precursors to mature miRNAs. For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. In flies, Loquacious (Loqs) interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. Here, we have solved the structure of the third double-stranded RNA-binding domain (dsRBD) of Loqs and define specific structural elements that interact with dmDcr1. In addition, we show that the linker preceding dsRBD3 contributes significantly to dmDcr1 binding. Furthermore, our structural work demonstrates that the third dsRBD of Loqs forms homodimers. Mutations in the dimerization interface abrogate dmDcr1 interaction. Loqs, however, binds to dmDcr1 as a monomer using the identified dimerization surface, which suggests that Loqs might form dimers under conditions where dmDcr1 is absent or not accessible. Since critical sequence elements are conserved, we suggest that dimerization might be a general feature of dsRBD proteins in gene silencing.
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Affiliation(s)
- Leonhard Jakob
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Alexander Gust
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Kramm
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kerrin Hansen
- Intana Bioscience GmbH, 82152 Planegg, Martinsried, Germany
| | - Mathias Stotz
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Ludwig Wankerl
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Franz Herzog
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany
| | - Stefan Hannus
- Intana Bioscience GmbH, 82152 Planegg, Martinsried, Germany
| | - Dina Grohmann
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
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Miesen P, Ivens A, Buck AH, van Rij RP. Small RNA Profiling in Dengue Virus 2-Infected Aedes Mosquito Cells Reveals Viral piRNAs and Novel Host miRNAs. PLoS Negl Trop Dis 2016; 10:e0004452. [PMID: 26914027 PMCID: PMC4767436 DOI: 10.1371/journal.pntd.0004452] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/21/2016] [Indexed: 11/18/2022] Open
Abstract
In Aedes mosquitoes, infections with arthropod-borne viruses (arboviruses) trigger or modulate the expression of various classes of viral and host-derived small RNAs, including small interfering RNAs (siRNAs), PIWI interacting RNAs (piRNAs), and microRNAs (miRNAs). Viral siRNAs are at the core of the antiviral RNA interference machinery, one of the key pathways that limit virus replication in invertebrates. Besides siRNAs, Aedes mosquitoes and cells derived from these insects produce arbovirus-derived piRNAs, the best studied examples being viruses from the Togaviridae or Bunyaviridae families. Host miRNAs modulate the expression of a large number of genes and their levels may change in response to viral infections. In addition, some viruses, mostly with a DNA genome, express their own miRNAs to regulate host and viral gene expression. Here, we perform a comprehensive analysis of both viral and host-derived small RNAs in Aedes aegypti Aag2 cells infected with dengue virus 2 (DENV), a member of the Flaviviridae family. Aag2 cells are competent in producing all three types of small RNAs and provide a powerful tool to explore the crosstalk between arboviral infection and the distinct RNA silencing pathways. Interestingly, besides the well-characterized DENV-derived siRNAs, a specific population of viral piRNAs was identified in infected Aag2 cells. Knockdown of Piwi5, Ago3 and, to a lesser extent, Piwi6 results in reduction of vpiRNA levels, providing the first genetic evidence that Aedes PIWI proteins produce DENV-derived small RNAs. In contrast, we do not find convincing evidence for the production of virus-derived miRNAs. Neither do we find that host miRNA expression is strongly changed upon DENV2 infection. Finally, our deep-sequencing analyses detect 30 novel Aedes miRNAs, complementing the repertoire of regulatory small RNAs in this important vector species. Mosquitoes of the Aedes family transmit many important viruses, including dengue virus, between their vertebrate hosts. In the mosquito, the growth of these viruses is limited by the antiviral RNA interference pathway. Key to this pathway is a class of small non-coding RNAs known as small interfering RNAs (siRNAs). In addition, two related but distinct small RNA pathways known as the microRNA (miRNA) and the PIWI-interacting RNA (piRNA) pathway are implicated in regulating virus replication in mosquitoes. Thus, since small RNAs may critically influence the transmission of dengue virus, we set out to analyze the populations of viral and mosquito small RNAs that are produced in infected Aedes mosquito cells. We found that besides the well-known viral siRNAs, dengue virus-derived piRNAs were produced in these cells and we identified the PIWI proteins that these small RNAs rely on. In addition, we found that viral miRNAs were not expressed from the dengue virus genome and that the levels of mosquito miRNAs were barely changed upon infection. Finally, our data allowed for the identification of novel Aedes miRNAs, complementing the repertoire of these important regulatory RNAs in vector mosquitoes.
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Affiliation(s)
- Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Alasdair Ivens
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy H. Buck
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Ronald P. van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- * E-mail:
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224
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Ren M, Wang S, Cai C, Chen C, Chen X. A simple and sensitive resonance light scattering method based on aggregation of gold nanoparticles for selective detection of microRNA-21. RSC Adv 2016. [DOI: 10.1039/c6ra12366j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel resonance light scattering method based on analyte-induced aggregation of gold nanoparticles for the determination of microRNAs was developed.
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Affiliation(s)
- Ming Ren
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
| | - Shijun Wang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
| | - Changqun Cai
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
| | - Chunyan Chen
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
| | - Xiaoming Chen
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
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225
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Pacak A, Barciszewska-Pacak M, Swida-Barteczka A, Kruszka K, Sega P, Milanowska K, Jakobsen I, Jarmolowski A, Szweykowska-Kulinska Z. Heat Stress Affects Pi-related Genes Expression and Inorganic Phosphate Deposition/Accumulation in Barley. FRONTIERS IN PLANT SCIENCE 2016; 7:926. [PMID: 27446155 PMCID: PMC4919326 DOI: 10.3389/fpls.2016.00926] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/10/2016] [Indexed: 05/07/2023]
Abstract
Phosphorus (P) in plants is taken from soil as an inorganic phosphate (Pi) and is one of the most important macroelements in growth and development. Plants actively react to Pi starvation by the induced expression of Pi transporters, MIR399, MIR827, and miR399 molecular sponge - IPS1 genes and by the decreased expression of the ubiquitin-conjugating enzyme E2 (PHOSPHATE2 - PHO2) and Pi sensing and transport SPX-MFS genes. The PHO2 protein is involved in the degradation of Pi transporters PHT1;1 (from soil to roots) and PHO1 (from roots to shoots). The decreased expression of PHO2 leads to Pi accumulation in shoots. In contrast, the pho1 mutant shows a decreased level of Pi concentration in shoots. Finally, Pi starvation leads to decreased Pi concentration in all plant tissues. Little is known about plant Pi homeostasis in other abiotic stress conditions. We found that, during the first hour of heat stress, Pi accumulated in barley shoots but not in the roots, and transcriptomic data analysis as well as RT-qPCR led us to propose an explanation for this phenomenon. Pi transport inhibition from soil to roots is balanced by lower Pi efflux from roots to shoots directed by the PHO1 transporter. In shoots, the PHO2 mRNA level is decreased, leading to an increased Pi level. We concluded that Pi homeostasis in barley during heat stress is maintained by dynamic changes in Pi-related genes expression.
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Affiliation(s)
- Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
- *Correspondence: Andrzej Pacak,
| | - Maria Barciszewska-Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Pawel Sega
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Kaja Milanowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Iver Jakobsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of CopenhagenCopenhagen, Denmark
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
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226
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Baksa I, Nagy T, Barta E, Havelda Z, Várallyay É, Silhavy D, Burgyán J, Szittya G. Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics 2015; 16:1025. [PMID: 26626050 PMCID: PMC4667520 DOI: 10.1186/s12864-015-2209-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for protein expression and purification. To discover and characterize the miRNAs and their cleaved target mRNAs in N. benthamiana, we sequenced small RNA transcriptomes and degradomes of two N. benthamiana accessions and validated them by Northern blots. RESULTS We used a comprehensive molecular approach to detect and to experimentally validate N. benthamiana miRNAs and their target mRNAs from various tissues. We identified 40 conserved miRNA families and 18 novel microRNA candidates and validated their target mRNAs with a genomic scale approach. The accumulation of thirteen novel miRNAs was confirmed by Northern blot analysis. The conserved and novel miRNA targets were found to be involved in various biological processes including transcription, RNA binding, DNA modification, signal transduction, stress response and metabolic process. Among the novel miRNA targets we found the mRNA of REPRESSOR OF SILENCING (ROS1). Regulation of ROS1 by a miRNA provides a new regulatory layer to reinforce transcriptional gene silencing by a post-transcriptional repression of ROS1 activity. CONCLUSIONS The identified conserved and novel miRNAs along with their target mRNAs also provides a tissue specific atlas of known and new miRNA expression and their cleaved target mRNAs of N. benthamiana. Thus this study will serve as a valuable resource to the plant research community that will be beneficial well into the future.
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Affiliation(s)
- Ivett Baksa
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Tibor Nagy
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Endre Barta
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Zoltán Havelda
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Éva Várallyay
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Dániel Silhavy
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - József Burgyán
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - György Szittya
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
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227
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Benitez AA, Spanko LA, Bouhaddou M, Sachs D, tenOever BR. Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response. Cell Rep 2015; 13:1456-1466. [PMID: 26549455 DOI: 10.1016/j.celrep.2015.10.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/10/2015] [Accepted: 10/07/2015] [Indexed: 12/20/2022] Open
Abstract
Although the intrinsic antiviral cell defenses of many kingdoms utilize pathogen-specific small RNAs, the antiviral response of chordates is primarily protein based and not uniquely tailored to the incoming microbe. In an effort to explain this evolutionary bifurcation, we determined whether antiviral RNAi was sufficient to replace the protein-based type I interferon (IFN-I) system of mammals. To this end, we recreated an RNAi-like response in mammals and determined its effectiveness to combat influenza A virus in vivo in the presence and absence of the canonical IFN-I system. Mammalian antiviral RNAi, elicited by either host- or virus-derived small RNAs, effectively attenuated virus and prevented disease independently of the innate immune response. These data find that chordates could have utilized RNAi as their primary antiviral cell defense and suggest that the IFN-I system emerged as a result of natural selection imposed by ancient pathogens.
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Affiliation(s)
- Asiel Arturo Benitez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Adrienne Spanko
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mehdi Bouhaddou
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Sachs
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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228
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Campillo Pedroza N, Franco Salazar JP, Gallego Gómez JC. Estandarización de un protocolo para Northern blot no radioactivo usado en la detección de pequeños RNA en células Vero. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2015. [DOI: 10.15446/rev.colomb.biote.v17n2.48522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p><strong>Título en ingles:</strong> <strong>Standardization of<em> Northern blot </em>non-radioactive protocol used in the detection of small RNAs in Vero line cells</strong></p><p>El interés en la detección, identificación, y caracterización funcional de los pequeños RNAs no codificantes (sRNAs), ha generado la necesidad de optimizar las metodologías comúnmente usadas en su detección, la reacción en cadena de la polimerasa cuantitativa (RT-qPCR) y <em>Northern blot</em>, con el fin de que sean más sensibles y específicas. A pesar de la baja sensibilidad del <em>Northern blot</em>, esta metodología continúa siendo de uso común en la detección de sRNAs porque permite detectar el RNA pequeño así como a sus precursores, razón por la cual se usa como una metodología complementaria en este tipo de investigaciones. En este trabajo se describe la implementación de un nuevo protocolo para <em>Northern blot</em> no radioactivo, con modificaciones dirigidas a mejorar su sensibilidad y especificidad. El diseños de la sonda con la tecnología LNA, el marcaje de esta con Digoxigenina y por último la fijación del RNA a la membrana mediante 1-Ethyl-3-(-3-dimethylaminopropyl) carboniimide (EDC) y finalmente se discuten los fundamentos teóricos de estos cambios.</p>
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229
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Ku YS, Wong JWH, Mui Z, Liu X, Hui JHL, Chan TF, Lam HM. Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods. Int J Mol Sci 2015; 16:24532-54. [PMID: 26501263 PMCID: PMC4632763 DOI: 10.3390/ijms161024532] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/21/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022] Open
Abstract
To survive under abiotic stresses in the environment, plants trigger a reprogramming of gene expression, by transcriptional regulation or translational regulation, to turn on protective mechanisms. The current focus of research on how plants cope with abiotic stresses has transitioned from transcriptomic analyses to small RNA investigations. In this review, we have summarized and evaluated the current methodologies used in the identification and validation of small RNAs and their targets, in the context of plant responses to abiotic stresses.
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Affiliation(s)
- Yee-Shan Ku
- Center for Soybean Research of State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Johanna Wing-Hang Wong
- Center for Soybean Research of State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Zeta Mui
- Center for Soybean Research of State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Xuan Liu
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Jerome Ho-Lam Hui
- Center for Soybean Research of State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Ting-Fung Chan
- Center for Soybean Research of State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Hon-Ming Lam
- Center for Soybean Research of State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
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230
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Park JH, Shin C. Slicer-independent mechanism drives small-RNA strand separation during human RISC assembly. Nucleic Acids Res 2015; 43:9418-33. [PMID: 26384428 PMCID: PMC4627090 DOI: 10.1093/nar/gkv937] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/08/2015] [Indexed: 11/17/2022] Open
Abstract
Small RNA silencing is mediated by the effector RNA-induced silencing complex (RISC) that consists of an Argonaute protein (AGOs 1–4 in humans). A fundamental step during RISC assembly involves the separation of two strands of a small RNA duplex, whereby only the guide strand is retained to form the mature RISC, a process not well understood. Despite the widely accepted view that ‘slicer-dependent unwinding’ via passenger-strand cleavage is a prerequisite for the assembly of a highly complementary siRNA into the AGO2-RISC, here we show by careful re-examination that ‘slicer-independent unwinding’ plays a more significant role in human RISC maturation than previously appreciated, not only for a miRNA duplex, but, unexpectedly, for a highly complementary siRNA as well. We discovered that ‘slicer-dependency’ for the unwinding was affected primarily by certain parameters such as temperature and Mg2+. We further validate these observations in non-slicer AGOs (1, 3 and 4) that can be programmed with siRNAs at the physiological temperature of humans, suggesting that slicer-independent mechanism is likely a common feature of human AGOs. Our results now clearly explain why both miRNA and siRNA are found in all four human AGOs, which is in striking contrast to the strict small-RNA sorting system in Drosophila.
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Affiliation(s)
- June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Republic of Korea
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231
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Goldman SR, Nair NU, Wells CD, Nickels BE, Hochschild A. The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo. eLife 2015; 4. [PMID: 26371553 PMCID: PMC4604602 DOI: 10.7554/elife.10514] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
The σ subunit of bacterial RNA polymerase (RNAP) confers on the enzyme the ability to initiate promoter-specific transcription. Although σ factors are generally classified as initiation factors, σ can also remain associated with, and modulate the behavior of, RNAP during elongation. Here we establish that the primary σ factor in Escherichia coli, σ70, can function as an elongation factor in vivo by loading directly onto the transcription elongation complex (TEC) in trans. We demonstrate that σ70 can bind in trans to TECs that emanate from either a σ70-dependent promoter or a promoter that is controlled by an alternative σ factor. We further demonstrate that binding of σ70 to the TEC in trans can have a particularly large impact on the dynamics of transcription elongation during stationary phase. Our findings establish a mechanism whereby the primary σ factor can exert direct effects on the composition of the entire transcriptome, not just that portion that is produced under the control of σ70-dependent promoters. DOI:http://dx.doi.org/10.7554/eLife.10514.001 Proteins are made following instructions that are encoded by sections of DNA called genes. In the first step of protein production, an enzyme called RNA polymerase uses the gene as a template to make molecules of messenger ribonucleic acid (mRNA). This process—known as transcription—starts when RNA polymerase binds to a site at the start of a gene. The enzyme then moves along the DNA, assembling the mRNA as it goes. This stage of transcription is known as elongation and continues until the RNA polymerase reaches the end of the gene. In bacteria, RNA polymerase needs a family of proteins called sigma factors to help it identify and bind to the start sites associated with the genes that will be transcribed. In the well studied bacterium known as E. coli, the primary sigma factor that is required for transcription initiation on most genes is called sigma 70. Recent research has shown that sigma 70 also influences the activity of RNA polymerase during elongation. During this stage, the RNA polymerase and several other proteins interact to form a complex called the transcription elongation complex (or TEC for short). However, it is not clear how sigma 70 gains access to this complex: does it simply remain with RNA polymerase after transcription starts, or is it freshly incorporated into the TEC during elongation? Goldman, Nair et al. found that sigma 70 is able to incorporate into TECs during elongation and causes them to pause at specific sites in the gene. Sigma 70 can even incorporate into TECs on genes where transcription was initiated by a different sigma factor. These findings indicate that sigma 70 can directly influence the transcription of all genes, not just the genes with start sites that are recognized by this sigma factor. Goldman et al. also observed that in cells that were growing and dividing rapidly, the pauses that occurred due to sigma 70 associating with TECs were of shorter duration than those in cells that were growing slowly. This implies that the growth status of the cells modulates the pausing of RNA polymerase during transcription. In the future, it will be important to understand how much influence the primary sigma factor has on RNA polymerase during elongation in E. coli and other bacteria. DOI:http://dx.doi.org/10.7554/eLife.10514.002
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Affiliation(s)
- Seth R Goldman
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States.,Department of Genetics, Waksman Institute, Rutgers University, New Brunswick, United States
| | - Nikhil U Nair
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Christopher D Wells
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Bryce E Nickels
- Department of Genetics, Waksman Institute, Rutgers University, New Brunswick, United States
| | - Ann Hochschild
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
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232
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Abstract
During microRNA (miRNA)-guided gene silencing, Argonaute (Ago) proteins interact with a member of the TNRC6/GW protein family. Here we used a short GW protein-derived peptide fused to GST and demonstrate that it binds to Ago proteins with high affinity. This allows for the simultaneous isolation of all Ago protein complexes expressed in diverse species to identify associated proteins, small RNAs, or target mRNAs. We refer to our method as "Ago protein Affinity Purification by Peptides" (Ago-APP). Furthermore, expression of this peptide competes for endogenous TNRC6 proteins, leading to global inhibition of miRNA function in mammalian cells.
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233
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Title AC, Denzler R, Stoffel M. Uptake and Function Studies of Maternal Milk-derived MicroRNAs. J Biol Chem 2015; 290:23680-91. [PMID: 26240150 PMCID: PMC4583031 DOI: 10.1074/jbc.m115.676734] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of cell-autonomous gene expression that influence many biological processes. They are also released from cells and are present in virtually all body fluids, including blood, urine, saliva, sweat, and milk. The functional role of nutritionally obtained extracellular miRNAs is controversial, and irrefutable demonstration of exogenous miRNA uptake by cells and canonical miRNA function is still lacking. Here we show that miRNAs are present at high levels in the milk of lactating mice. To investigate intestinal uptake of miRNAs in newborn mice, we employed genetic models in which newborn miR-375 and miR-200c/141 knockout mice received milk from wild-type foster mothers. Analysis of the intestinal epithelium, blood, liver, and spleen revealed no evidence for miRNA uptake. miR-375 levels in hepatocytes were at the limit of detection and remained orders of magnitude below the threshold for target gene regulation (between 1000 and 10,000 copies/cell). Furthermore, our study revealed rapid degradation of milk miRNAs in intestinal fluid. Together, our results indicate a nutritional rather than gene-regulatory role of miRNAs in the milk of newborn mice.
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Affiliation(s)
- Alexandra C Title
- From the Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland and
| | - Rémy Denzler
- From the Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland and
| | - Markus Stoffel
- From the Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland and the Faculty of Medicine, University of Zurich, 8091 Zurich, Switzerland
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234
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Quantitative Analysis of MicroRNAs in Vaccinia virus Infection Reveals Diversity in Their Susceptibility to Modification and Suppression. PLoS One 2015; 10:e0131787. [PMID: 26161560 PMCID: PMC4498801 DOI: 10.1371/journal.pone.0131787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/08/2015] [Indexed: 12/26/2022] Open
Abstract
Vaccinia virus (VACV) is a large cytoplasmic DNA virus that causes dramatic alterations to many cellular pathways including microRNA biogenesis. The virus encodes a poly(A) polymerase which was previously shown to add poly(A) tails to the 3’ end of cellular miRNAs, resulting in their degradation by 24 hours post infection (hpi). Here we used small RNA sequencing to quantify the impact of VACV infection on cellular miRNAs in human cells at both early (6 h) and late (24 h) times post infection. A detailed quantitative analysis of individual miRNAs revealed marked diversity in the extent of their modification and relative change in abundance during infection. Some miRNAs became highly modified (e.g. miR-29a-3p, miR-27b-3p) whereas others appeared resistant (e.g. miR-16-5p). Furthermore, miRNAs that were highly tailed at 6 hpi were not necessarily among the most reduced at 24 hpi. These results suggest that intrinsic features of human cellular miRNAs cause them to be differentially polyadenylated and altered in abundance during VACV infection. We also demonstrate that intermediate and late VACV gene expression are required for optimal repression of some miRNAs including miR-27-3p. Overall this work reveals complex and varied consequences of VACV infection on host miRNAs and identifies miRNAs which are largely resistant to VACV-induced polyadenylation and are therefore present at functional levels during the initial stages of infection and replication.
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235
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Bitton L, Klaiman D, Kaufmann G. Phage T4-induced DNA breaks activate a tRNA repair-defying anticodon nuclease. Mol Microbiol 2015; 97:898-910. [PMID: 26031711 DOI: 10.1111/mmi.13074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2015] [Indexed: 01/13/2023]
Abstract
The natural role of the conserved bacterial anticodon nuclease (ACNase) RloC is not known, but traits that set it apart from the homologous phage T4-excluding ACNase PrrC could provide relevant clues. PrrC is silenced by a genetically linked DNA restriction-modification (RM) protein and turned on by a phage-encoded DNA restriction inhibitor. In contrast, RloC is rarely linked to an RM protein, and its ACNase is regulated by an internal switch responsive to double-stranded DNA breaks. Moreover, PrrC nicks the tRNA substrate, whereas RloC excises the wobble nucleotide. These distinctions suggested that (i) T4 and related phage that degrade their host DNA will activate RloC and (ii) the tRNA species consequently disrupted will not be restored by phage tRNA repair enzymes that counteract PrrC. Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation. Moreover, host and T4 tRNA species disrupted by the activated ACNase were not restored by T4's tRNA repair system. Nonetheless, T4's plating efficiency was inefficiently impaired by AbaRloC, presumably due to a decoy function of the phage encoded tRNA target, the absence of which exacerbated the restriction.
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Affiliation(s)
- Lital Bitton
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Klaiman
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Gabriel Kaufmann
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
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236
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Friedrich M, Meier D, Schuster I, Nellen W. A Simple Retroelement Based Knock-Down System in Dictyostelium: Further Insights into RNA Interference Mechanisms. PLoS One 2015; 10:e0131271. [PMID: 26110905 PMCID: PMC4482531 DOI: 10.1371/journal.pone.0131271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/01/2015] [Indexed: 12/21/2022] Open
Abstract
CHARACTERISTICS OF DIRS-1 MEDIATED KNOCK-DOWNS We have previously shown that the most abundant Dictyostelium discoideum retroelement DIRS-1 is suppressed by RNAi mechanisms. Here we provide evidence that both inverted terminal repeats have strong promoter activity and that bidirectional expression apparently generates a substrate for Dicer. A cassette containing the inverted terminal repeats and a fragment of a gene of interest was sufficient to activate the RNAi response, resulting in the generation of ~21 nt siRNAs, a reduction of mRNA and protein expression of the respective endogene. Surprisingly, no transitivity was observed on the endogene. This was in contrast to previous observations, where endogenous siRNAs caused spreading on an artificial transgene. Knock-down was successful on seven target genes that we examined. In three cases a phenotypic analysis proved the efficiency of the approach. One of the target genes was apparently essential because no knock-out could be obtained; the RNAi mediated knock-down, however, resulted in a very slow growing culture indicating a still viable reduction of gene expression. ADVANTAGES OF THE DIRS-1–RNAI SYSTEM: The knock-down system required a short DNA fragment (~400 bp) of the target gene as an initial trigger. Further siRNAs were generated by RdRPs since we have shown some siRNAs with a 5'-triphosphate group. Extrachromosomal vectors facilitate the procedure and allowed for molecular and phenotypic analysis within one week. The system provides an efficient and rapid method to reduce protein levels including those of essential genes.
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Affiliation(s)
| | - Doreen Meier
- Abt. Genetik, FB 10, Universität Kassel, Kassel, Germany
| | | | - Wolfgang Nellen
- Abt. Genetik, FB 10, Universität Kassel, Kassel, Germany
- * E-mail:
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237
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Miesen P, Girardi E, van Rij RP. Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Res 2015; 43:6545-56. [PMID: 26068474 PMCID: PMC4513867 DOI: 10.1093/nar/gkv590] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/22/2015] [Indexed: 11/13/2022] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway is essential for transposon silencing in many model organisms. Its remarkable efficiency relies on a sophisticated amplification mechanism known as the ping-pong loop. In Alphavirus-infected Aedes mosquitoes, piRNAs with sequence features that suggest ping-pong-dependent biogenesis are produced from viral RNA. The PIWI family in Aedes mosquitoes is expanded when compared to other model organisms, raising the possibility that individual PIWI proteins have functionally diversified in these insects. Here, we show that Piwi5 and Ago3, but none of the other PIWI family members, are essential for piRNA biogenesis from Sindbis virus RNA in infected Aedes aegypti cells. In contrast, the production of piRNAs from transposons relies on a more versatile set of PIWI proteins, some of which do not contribute to viral piRNA biogenesis. These results indicate that functional specialization allows distinct mosquito PIWI proteins to process RNA from different endogenous and exogenous sources.
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Affiliation(s)
- Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Erika Girardi
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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238
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Iwasaki S, Sasaki HM, Sakaguchi Y, Suzuki T, Tadakuma H, Tomari Y. Defining fundamental steps in the assembly of the Drosophila RNAi enzyme complex. Nature 2015; 521:533-6. [PMID: 25822791 DOI: 10.1038/nature14254] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 01/23/2015] [Indexed: 02/07/2023]
Abstract
Small RNAs such as small interfering RNAs (siRNAs) and microRNAs (miRNAs) silence the expression of their complementary target messenger RNAs via the formation of effector RNA-induced silencing complexes (RISCs), which contain Argonaute (Ago) family proteins at their core. Although loading of siRNA duplexes into Drosophila Ago2 requires the Dicer-2-R2D2 heterodimer and the Hsc70/Hsp90 (Hsp90 also known as Hsp83) chaperone machinery, the details of RISC assembly remain unclear. Here we reconstitute RISC assembly using only Ago2, Dicer-2, R2D2, Hsc70, Hsp90, Hop, Droj2 (an Hsp40 homologue) and p23. By following the assembly of single RISC molecules, we find that, in the absence of the chaperone machinery, an siRNA bound to Dicer-2-R2D2 associates with Ago2 only transiently. The chaperone machinery extends the dwell time of the Dicer-2-R2D2-siRNA complex on Ago2, in a manner dependent on recognition of the 5'-phosphate on the siRNA guide strand. We propose that the chaperone machinery supports a productive state of Ago2, allowing it to load siRNA duplexes from Dicer-2-R2D2 and thereby assemble RISC.
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Affiliation(s)
- Shintaro Iwasaki
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroshi M Sasaki
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hisashi Tadakuma
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- 1] Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. [2] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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239
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The Baculovirus Antiapoptotic p35 Protein Functions as an Inhibitor of the Host RNA Interference Antiviral Response. J Virol 2015; 89:8182-92. [PMID: 26018163 DOI: 10.1128/jvi.00802-15] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/18/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED RNA interference (RNAi) is considered an ancient antiviral defense in diverse organisms, including insects. Virus infections generate double-strand RNAs (dsRNAs) that trigger the RNAi machinery to process dsRNAs into virus-derived short interfering RNAs (vsiRNAs), which target virus genomes, mRNAs, or replication intermediates. Viruses, in turn, have evolved viral suppressors of RNAi (VSRs) to counter host antiviral RNAi. Following recent discoveries that insects mount an RNAi response against DNA viruses, in this study, we found that Autographa californica multiple nucleopolyhedrovirus (AcMNPV) infection similarly induces an RNAi response in Spodoptera frugiperda cells by generating a large number of vsiRNAs postinfection. Interestingly, we found that AcMNPV expresses a potent VSR to counter RNAi. The viral p35 gene, which is well known as an inhibitor of apoptosis, was found to be responsible for the suppression of RNAi in diverse insect and mammalian cells. The VSR activity of p35 was further confirmed by a p35-null AcMNPV that did not suppress the response. In addition, our results showed that the VSR activity is not due to inhibition of dsRNA cleavage by Dicer-2 but acts downstream in the RNAi pathway. Furthermore, we found that the VSR activity is not linked to the antiapoptotic activity of the protein. Overall, our results provide evidence for the existence of VSR activity in a double-stranded DNA virus and identify the responsible gene, which is involved in the inhibition of RNAi as well as apoptosis. IMPORTANCE Our findings demonstrate the occurrence of an insect RNAi response against a baculovirus (AcMNPV) that is highly utilized in microbial control, biological and biomedical research, and protein expression. Moreover, our investigations led to the identification of a viral suppressor of RNAi activity and the gene responsible for the activity. Notably, this gene is also a potent inhibitor of apoptosis. The outcomes signify the dual role of a virus-encoded protein in nullifying two key antiviral responses, apoptosis and RNAi.
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240
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Bozzetti MP, Specchia V, Cattenoz PB, Laneve P, Geusa A, Sahin HB, Di Tommaso S, Friscini A, Massari S, Diebold C, Giangrande A. The Drosophila fragile X mental retardation protein participates in the piRNA pathway. J Cell Sci 2015; 128:2070-84. [PMID: 25908854 DOI: 10.1242/jcs.161810] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 04/10/2015] [Indexed: 12/19/2022] Open
Abstract
RNA metabolism controls multiple biological processes, and a specific class of small RNAs, called piRNAs, act as genome guardians by silencing the expression of transposons and repetitive sequences in the gonads. Defects in the piRNA pathway affect genome integrity and fertility. The possible implications in physiopathological mechanisms of human diseases have made the piRNA pathway the object of intense investigation, and recent work suggests that there is a role for this pathway in somatic processes including synaptic plasticity. The RNA-binding fragile X mental retardation protein (FMRP, also known as FMR1) controls translation and its loss triggers the most frequent syndromic form of mental retardation as well as gonadal defects in humans. Here, we demonstrate for the first time that germline, as well as somatic expression, of Drosophila Fmr1 (denoted dFmr1), the Drosophila ortholog of FMRP, are necessary in a pathway mediated by piRNAs. Moreover, dFmr1 interacts genetically and biochemically with Aubergine, an Argonaute protein and a key player in this pathway. Our data provide novel perspectives for understanding the phenotypes observed in Fragile X patients and support the view that piRNAs might be at work in the nervous system.
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Affiliation(s)
- Maria Pia Bozzetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Valeria Specchia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Pierre B Cattenoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Pietro Laneve
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Annamaria Geusa
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - H Bahar Sahin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Silvia Di Tommaso
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Antonella Friscini
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Serafina Massari
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Celine Diebold
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Angela Giangrande
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
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241
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Tsetsarkin KA, Liu G, Kenney H, Bustos-Arriaga J, Hanson CT, Whitehead SS, Pletnev AG. Dual miRNA targeting restricts host range and attenuates neurovirulence of flaviviruses. PLoS Pathog 2015; 11:e1004852. [PMID: 25906260 PMCID: PMC4408003 DOI: 10.1371/journal.ppat.1004852] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/03/2015] [Indexed: 12/31/2022] Open
Abstract
Mosquito-borne flaviviruses are among the most significant arboviral pathogens worldwide. Vaccinations and mosquito population control programs remain the most reliable means for flavivirus disease prevention, and live attenuated viruses remain one of the most attractive flavivirus vaccine platforms. Some live attenuated viruses are capable of infecting principle mosquito vectors, as demonstrated in the laboratory, which in combination with their intrinsic genetic instability could potentially lead to a vaccine virus reversion back to wild-type in nature, followed by introduction and dissemination of potentially dangerous viral strains into new geographic locations. To mitigate this risk we developed a microRNA-targeting approach that selectively restricts replication of flavivirus in the mosquito host. Introduction of sequences complementary to a mosquito-specific mir-184 and mir-275 miRNAs individually or in combination into the 3’NCR and/or ORF region resulted in selective restriction of dengue type 4 virus (DEN4) replication in mosquito cell lines and adult Aedes mosquitos. Moreover a combined targeting of DEN4 genome with mosquito-specific and vertebrate CNS-specific mir-124 miRNA can silence viral replication in two evolutionally distant biological systems: mosquitoes and mouse brains. Thus, this approach can reinforce the safety of newly developed or existing vaccines for use in humans and could provide an additional level of biosafety for laboratories using viruses with altered pathogenic or transmissibility characteristics. Despite advances in developing flavivirus live attenuated vaccine (LAV) candidates, a concern exists that they might not be safe in the environment due to their intrinsic genetic instability leading to potential reversion back to wild-type that could be associated with possible dissemination of these mutated viruses by mosquitoes. Here, we describe a miRNA targeting approach that can be adapted to support the design of environmentally-safe LAV restricted in their ability to infect and be transmitted by competent vectors, thereby limiting the possibility of subsequent viral evolution and unpredictable consequences. A combined co-targeting of flavivirus genome with mosquito- and vertebrate brain- specific miRNAs resulted in simultaneous restriction of dengue virus infection and replication in mosquitoes and in brains of newborn mice indicating that the miRNA-mediated approach for virus attenuation represents an alternative to non-specific strategies for the control of viral tissue tropism and pathogenesis in the vertebrate host and replicative efficacy in permissive vectors.
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Affiliation(s)
- Konstantin A. Tsetsarkin
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Guangping Liu
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Heather Kenney
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jose Bustos-Arriaga
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher T. Hanson
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen S. Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexander G. Pletnev
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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242
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Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z. Amplification-based method for microRNA detection. Biosens Bioelectron 2015; 71:322-331. [PMID: 25930002 DOI: 10.1016/j.bios.2015.04.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/20/2022]
Abstract
Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zuhong Lu
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
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243
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Dhir A, Dhir S, Proudfoot NJ, Jopling CL. Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs. Nat Struct Mol Biol 2015; 22:319-27. [PMID: 25730776 PMCID: PMC4492989 DOI: 10.1038/nsmb.2982] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/05/2015] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) play a major part in the post-transcriptional regulation of gene expression. Mammalian miRNA biogenesis begins with cotranscriptional cleavage of RNA polymerase II (Pol II) transcripts by the Microprocessor complex. Although most miRNAs are located within introns of protein-coding transcripts, a substantial minority of miRNAs originate from long noncoding (lnc) RNAs, for which transcript processing is largely uncharacterized. We show, by detailed characterization of liver-specific lnc-pri-miR-122 and genome-wide analysis in human cell lines, that most lncRNA transcripts containing miRNAs (lnc-pri-miRNAs) do not use the canonical cleavage-and-polyadenylation pathway but instead use Microprocessor cleavage to terminate transcription. Microprocessor inactivation leads to extensive transcriptional readthrough of lnc-pri-miRNA and transcriptional interference with downstream genes. Consequently we define a new RNase III-mediated, polyadenylation-independent mechanism of Pol II transcription termination in mammalian cells.
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Affiliation(s)
- Ashish Dhir
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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244
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Bhushan L, Abraham A, Choudhury NR, Rana VS, Mukherjee SK, Savithri HS. Demonstration of helicase activity in the nonstructural protein, NSs, of the negative-sense RNA virus, groundnut bud necrosis virus. Arch Virol 2015; 160:959-67. [PMID: 25643815 DOI: 10.1007/s00705-014-2331-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/30/2014] [Indexed: 12/22/2022]
Abstract
The nonstructural protein NSs, encoded by the S RNA of groundnut bud necrosis virus (GBNV) (genus Tospovirus, family Bunyaviridae) has earlier been shown to possess nucleic-acid-stimulated NTPase and 5' α phosphatase activity. ATP hydrolysis is an essential function of a true helicase. Therefore, NSs was tested for DNA helicase activity. The results demonstrated that GBNV NSs possesses bidirectional DNA helicase activity. An alanine mutation in the Walker A motif (K189A rNSs) decreased DNA helicase activity substantially, whereas a mutation in the Walker B motif resulted in a marginal decrease in this activity. The parallel loss of the helicase and ATPase activity in the K189A mutant confirms that NSs acts as a non-canonical DNA helicase. Furthermore, both the wild-type and K189A NSs could function as RNA silencing suppressors, demonstrating that the suppressor activity of NSs is independent of its helicase or ATPase activity. This is the first report of a true helicase from a negative-sense RNA virus.
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Affiliation(s)
- Lokesh Bhushan
- Department of Biochemistry, New Biological Sciences, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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245
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Samarakkody A, Abbas A, Scheidegger A, Warns J, Nnoli O, Jokinen B, Zarns K, Kubat B, Dhasarathy A, Nechaev S. RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. Nucleic Acids Res 2015; 43:3938-49. [PMID: 25820424 PMCID: PMC4417172 DOI: 10.1093/nar/gkv263] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/17/2015] [Indexed: 12/26/2022] Open
Abstract
Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the epithelial to mesenchymal transition (EMT). We find that the gene for EMT master regulator Snail (SNAI1), but not Slug (SNAI2), shows evidence of Pol II pausing before activation. Transcriptional activation of the paused SNAI1 gene is accompanied by a further increase in Pol II pausing signal, whereas activation of non-paused SNAI2 gene results in the acquisition of a typical pausing signature. The increase in pausing signal reflects increased transcription initiation without changes in Pol II pausing. Activation of the heat shock HSP70 gene involves pausing release that speeds up Pol II turnover, but does not change pausing location. We suggest that Pol II pausing is retained during transcriptional activation and can further undergo regulated release in a signal-specific manner.
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Affiliation(s)
- Ann Samarakkody
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Ata Abbas
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Adam Scheidegger
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Jessica Warns
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Oscar Nnoli
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Bradley Jokinen
- Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Kris Zarns
- Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Brooke Kubat
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Archana Dhasarathy
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Sergei Nechaev
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
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246
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Rosas-Cárdenas FDF, Escobar-Guzmán R, Cruz-Hernández A, Marsch-Martínez N, de Folter S. An efficient method for miRNA detection and localization in crop plants. FRONTIERS IN PLANT SCIENCE 2015; 6:99. [PMID: 25784917 PMCID: PMC4347446 DOI: 10.3389/fpls.2015.00099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/06/2015] [Indexed: 05/28/2023]
Abstract
microRNAs are a class of non-coding small RNAs (sRNAs) that are important regulators of gene expression at the post-transcriptional level by mRNA cleavage or translation inhibition. Another class of sRNAs are siRNAs, which also regulate gene expression but by causing DNA methylation. This epigenetic regulatory role has been observed for some miRNAs as well. The use of sRNAs allows the development of biotechnological applications in plants. To develop these types of applications, and to better understand the natural roles they play, it is important to be able to detect and to localize these sRNAs at the plant tissue level. Sometimes, in crop plants this can be challenging. Therefore, we developed a tissue printing hybridization protocol for easy and efficient detection of sRNAs and demonstrate this by the analysis of the spatio-temporal expression patterns of the miRNAs miR159 and miR164 in fruits of various crop plants. Moreover, we show the possibility to also detect the expression of miRNAs in fruit juice using a dot blot hybridization approach.
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Affiliation(s)
- Flor de Fátima Rosas-Cárdenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalGuanajuato, México
- Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico NacionalTlaxcala, México
| | - Rocío Escobar-Guzmán
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalGuanajuato, México
| | | | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalGuanajuato, México
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalGuanajuato, México
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Kawamura K, Ikoma K, Maruoka Y, Hisamoto H. Separation Behavior of Short Oligonucleotides by Ion-Pair Reversed-Phase Capillary Liquid Chromatography Using a Silica-Based Monolithic Column Applied to Simple Detection of SNPs. Chromatographia 2015. [DOI: 10.1007/s10337-015-2855-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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248
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Rosas-Cárdenas FDF, Caballero-Pérez J, Gutiérrez-Ramos X, Marsch-Martínez N, Cruz-Hernández A, de Folter S. miRNA expression during prickly pear cactus fruit development. PLANTA 2015; 241:435-48. [PMID: 25366556 DOI: 10.1007/s00425-014-2193-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/14/2014] [Indexed: 05/06/2023]
Abstract
miRNAs are a class of small non-coding RNAs that regulate gene expression. They are involved in the control of many developmental processes, including fruit development. The increasing amount of information on miRNAs, on their expression, abundance, and conservation between various species, provides a new opportunity to study the role of miRNAs in non-model plant species. In this work, we used a combination of Northern blot and tissue print hybridization analysis to identify conserved miRNAs expressed during prickly pear cactus (Opuntia ficus indica) fruit development. Comparative profiling detected the expression of 34 miRNAs, which were clustered in three different groups that were associated with the different phases of fruit development. Variation in the level of miRNA expression was observed. Gradual expression increase of several miRNAs was observed during fruit development, including miR164. miR164 was selected for stem-loop RT-PCR and for a detailed spatial-temporal expression analysis. At early floral stages, miR164 was mainly localized in meristematic tissues, boundaries and fusion zones, while it was more homogenously expressed in fruit tissues. Our results provide the first evidence of miRNA expression in the prickly pear cactus and provide the basis for future research on miRNAs in Opuntia. Moreover, our analyses suggest that miR164 plays different roles during prickly pear cactus fruit development.
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Affiliation(s)
- Flor de Fátima Rosas-Cárdenas
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico,
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249
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Aungier SR, Ohmori H, Clinton M, Mabbott NA. MicroRNA-100-5p indirectly modulates the expression of Il6, Ptgs1/2 and Tlr4 mRNA in the mouse follicular dendritic cell-like cell line, FL-Y. Immunology 2015; 144:34-44. [PMID: 24944008 PMCID: PMC4264908 DOI: 10.1111/imm.12342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/13/2014] [Accepted: 06/13/2014] [Indexed: 01/09/2023] Open
Abstract
Follicular dendritic cells (FDC) are important stromal cells within the B-cell follicles and germinal centres (GC) of secondary lymphoid tissues. FDC trap and retain native antigens on their surfaces in the form of immune complexes that they display to B cells, in order to select those cells with the highest antigen affinity. MicroRNAs are short, non-coding RNAs that are approximately 18-25 nucleotides in length that regulate gene expression at the post-transcriptional level by repressing the translation of target genes. In the current study, in vivo and in vitro systems were used to identify microRNAs that were potentially expressed by FDC. Constitutive lymphotoxin-β receptor (LTβR) stimulation is required to maintain FDC in their differentiated state. We show that the rapid de-differentiation of spleen FDC that accompanied LTβR-blockade, coincided with a significant decrease in the expression of mmu-miR-100-5p, mmu-miR-138-5p and mmu-miR-2137. These microRNAs were shown to be expressed in the FDC-like cell line, FL-YB, and specific inhibition of mmu-miR-100-5p significantly enhanced expression of Il6, Ptgs1/2 and Tlr4 mRNA in this cell line. The expression of Il6, Ptgs1/2 and Tlr4 by FDC play important roles in regulating GC size and promoting high-affinity antibody responses, so it is plausible that mmu-miR-100-5p may help to regulate the expression of these genes during GC reactions.
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Affiliation(s)
- Susan R Aungier
- The Roslin Institute and R(D)SVS, University of EdinburghMidlothian, UK
| | - Hitoshi Ohmori
- Department of Bioscience and Biotechnology, Okayama University Graduate School of Natural Science and TechnologyOkayama, Japan
| | - Michael Clinton
- The Roslin Institute and R(D)SVS, University of EdinburghMidlothian, UK
| | - Neil A Mabbott
- The Roslin Institute and R(D)SVS, University of EdinburghMidlothian, UK
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250
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Kilic T, Erdem A, Erac Y, Seydibeyoglu MO, Okur S, Ozsoz M. Electrochemical Detection of a Cancer Biomarker mir‐21 in Cell Lysates Using Graphene Modified Sensors. ELECTROANAL 2014. [DOI: 10.1002/elan.201400518] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tugba Kilic
- Izmir Katip Celebi University, Faculty of Engineering and Architecture, Department of Biomedical Engineering, 35620, Cigli, Turkey
| | - Arzum Erdem
- Ege University, Faculty of Pharmacy, Department of Analytical Chemistry, 35100 Bornova, Turkey tel: +90 (232) 311 5131
| | - Yasemin Erac
- Ege University, Faculty of Pharmacy, Department of Pharmacology, 35100 Bornova, Turkey
| | - M. Ozgur Seydibeyoglu
- Izmir Katip Celebi University, Faculty of Engineering and Architecture, Department of Materials Science and Engineering, 35620, Cigli, Turkey
| | - Salih Okur
- Izmir Katip Celebi University, Faculty of Engineering and Architecture, Department of Materials Science and Engineering, 35620, Cigli, Turkey
| | - Mehmet Ozsoz
- Gediz University, Faculty of Engineering and Architecture, Department of Biomedical Engineering, 35665, Seyrek, Turkey tel: +90 (232) 355 23 20
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