101
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Fiannaca A, La Rosa M, La Paglia L, Urso A. miRTissue: a web application for the analysis of miRNA-target interactions in human tissues. BMC Bioinformatics 2018; 19:434. [PMID: 30497361 PMCID: PMC6266954 DOI: 10.1186/s12859-018-2418-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background microRNAs act as regulators of gene expression interacting with their gene targets. Current bioinformatics services, such as databases of validated miRNA-target interactions and prediction tools, usually provide interactions without any information about what tissue that interaction is more likely to appear nor information about the type of interactions, causing mRNA degradation or translation inhibition respectively. Results In this work, we introduce miRTissue, a web application that combines validated miRNA-target interactions with statistical correlation among expression profiles of miRNAs, genes and proteins in 15 different human tissues. Validated interactions are taken from the miRTarBase database, while expression profiles are downloaded from The Cancer Genome Atlas repository. As a result, the service provides a tissue-specific characterisation of each couple of miRNA and gene together with its statistical significance (p-value). The inclusion of protein data also allows providing the type of interaction. Moreover, miRTissue offers several views for analysing interactions, focusing for example on the comparison between different cancer types or different tissue conditions. All the results are freely downloadable in the most common formats. Conclusions miRTissue fills a gap concerning current bioinformatics services related to miRNA-target interactions because it provides a tissue-specific context to each validated interaction and the type of interaction itself. miRTissue is easily browsable allowing the user to select miRNAs, genes, cancer types and tissue conditions. The results can be sorted according to p-values to immediately identify those interactions that are more likely to occur in a given tissue. miRTissue is available at http://tblab.pa.icar.cnr.it/mirtissue.html. Electronic supplementary material The online version of this article (10.1186/s12859-018-2418-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonino Fiannaca
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, 90146, Italy.
| | - Massimo La Rosa
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, 90146, Italy
| | - Laura La Paglia
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, 90146, Italy
| | - Alfonso Urso
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, 90146, Italy
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102
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The central region of CNOT1 and CNOT9 stimulates deadenylation by the Ccr4-Not nuclease module. Biochem J 2018; 475:3437-3450. [PMID: 30309886 DOI: 10.1042/bcj20180456] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022]
Abstract
Regulated degradation of cytoplasmic mRNA is important for the accurate execution of gene expression programmes in eukaryotic cells. A key step in this process is the shortening and removal of the mRNA poly(A) tail, which can be achieved by the recruitment of the multi-subunit Ccr4-Not nuclease complex via sequence-specific RNA-binding proteins or the microRNA machinery. The Ccr4-Not complex contains several modules that are attached to its large subunit CNOT1. Modules include the nuclease module, which associates with the MIF4G domain of CNOT1 and contains the catalytic subunits Caf1 and Ccr4, as well as the module containing the non-catalytic CNOT9 subunit, which binds to the DUF3819 domain of CNOT1. To understand the contributions of the individual modules to the activity of the complex, we have started to reconstitute sub-complexes of the human Ccr4-Not complex containing one or several functional modules. Here, we report the reconstitution of a pentameric complex including a BTG2-Caf1-Ccr4 nuclease module, CNOT9 and the central region of CNOT1 encompassing the MIF4G and DUF3819 domains. By comparing the biochemical activities of the pentameric complex and the nuclease module, we conclude that the CNOT1-CNOT9 components stimulate deadenylation by the nuclease module. In addition, we show that a pentameric complex containing the melanoma-associated CNOT9 P131L variant is able to support deadenylation similar to a complex containing the wild-type CNOT9 protein.
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103
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Holmquist CE, Marzluff WF. Determining degradation intermediates and the pathway of 3' to 5' degradation of histone mRNA using high-throughput sequencing. Methods 2018; 155:104-115. [PMID: 30408609 DOI: 10.1016/j.ymeth.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/30/2018] [Accepted: 11/01/2018] [Indexed: 11/24/2022] Open
Abstract
The half-life of an mRNA is an important parameter contributing to the steady-state level of the mRNA. Rapid changes in mRNA levels can result from decreasing the half-life of an mRNA. Establishing the detailed pathway of mRNA degradation for a particular class of mRNAs requires the ability to isolate mRNA degradation intermediates. High-throughput sequencing provides a method for detecting these intermediates. Here we describe a method for determining the intermediates in 3' to 5' degradation. Characterizing these intermediates requires not only determining the precise 3' end of the molecule to a single nucleotide resolution, but also the ability to detect and characterize any untemplated nucleotides present on the intermediates. We achieve this by ligating a known sequence to all the 3' termini in the cell, and then sequence the 3' termini and the ligated linker to identify any alterations to the genomic reference sequence. We have applied this method to characterize the intermediates in histone mRNA metabolism, allowing us to deduce the pathway of 3' to 5' degradation. This method can potentially be applied to any RNA, and we discuss possible strategies for extending the method to include simultaneous determination of the 3' and 5' end of the same RNA molecule.
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Affiliation(s)
- Christopher E Holmquist
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States
| | - William F Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, United States.
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104
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Szádeczky-Kardoss I, Gál L, Auber A, Taller J, Silhavy D. The No-go decay system degrades plant mRNAs that contain a long A-stretch in the coding region. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:19-27. [PMID: 30107878 DOI: 10.1016/j.plantsci.2018.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 05/04/2023]
Abstract
RNA quality control systems identify and degrade aberrant mRNAs, thereby preventing the accumulation of faulty proteins. Non-stop decay (NSD) and No-go decay (NGD) are closely related RNA quality control systems that act during translation. NSD degrades mRNAs lacking a stop codon, while NGD recognizes and decays mRNAs that contain translation elongation inhibitory structures. NGD has been intensively studied in yeast and animals but it has not been described in plants yet. In yeast, NGD is induced if the elongating ribosome is stalled by a strong inhibitory structure. Then, the mRNA is cleaved by an unknown nuclease and the cleavage fragments are degraded. Here we show that NGD also operates in plant. We tested several potential NGD cis-elements and found that in plants, unlike in yeast, only long A-stretches induce NGD. These long A-stretches trigger endonucleolytic cleavage, and then the 5' fragments are degraded in a Pelota-, HBS1- and SKI2- dependent manner, while XRN4 eliminates the 3' fragment. We also show that plant NGD operates gradually, the longer the A-stretch, the more efficient the cleavage. Our data suggest that mechanistically NGD is conserved in eukaryotes, although the NGD inducing cis-elements could be different. Moreover, we found that Arabidopsis AtPelota1 functions in both NGD and NSD, while AtPelota2 represses these quality control systems. The function of plant NGD will be discussed.
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Affiliation(s)
| | - Luca Gál
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100, Gödöllő, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100, Gödöllő, Hungary
| | - János Taller
- University Pannonia Georgikon, Festetics 7, 8360, Keszthely, Hungary
| | - Dániel Silhavy
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100, Gödöllő, Hungary.
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105
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Rauch S, Jasny E, Schmidt KE, Petsch B. New Vaccine Technologies to Combat Outbreak Situations. Front Immunol 2018; 9:1963. [PMID: 30283434 PMCID: PMC6156540 DOI: 10.3389/fimmu.2018.01963] [Citation(s) in RCA: 360] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/09/2018] [Indexed: 01/07/2023] Open
Abstract
Ever since the development of the first vaccine more than 200 years ago, vaccinations have greatly decreased the burden of infectious diseases worldwide, famously leading to the eradication of small pox and allowing the restriction of diseases such as polio, tetanus, diphtheria, and measles. A multitude of research efforts focuses on the improvement of established and the discovery of new vaccines such as the HPV (human papilloma virus) vaccine in 2006. However, radical changes in the density, age distribution and traveling habits of the population worldwide as well as the changing climate favor the emergence of old and new pathogens that bear the risk of becoming pandemic threats. In recent years, the rapid spread of severe infections such as HIV, SARS, Ebola, and Zika have highlighted the dire need for global preparedness for pandemics, which necessitates the extremely rapid development and comprehensive distribution of vaccines against potentially previously unknown pathogens. What is more, the emergence of antibiotic resistant bacteria calls for new approaches to prevent infections. Given these changes, established methods for the identification of new vaccine candidates are no longer sufficient to ensure global protection. Hence, new vaccine technologies able to achieve rapid development as well as large scale production are of pivotal importance. This review will discuss viral vector and nucleic acid-based vaccines (DNA and mRNA vaccines) as new approaches that might be able to tackle these challenges to global health.
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106
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Singh SS, Naiyer S, Bharadwaj R, Kumar A, Singh YP, Ray AK, Subbarao N, Bhattacharya A, Bhattacharya S. Stress-induced nuclear depletion of Entamoeba histolytica 3'-5' exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis. J Biol Chem 2018; 293:16242-16260. [PMID: 30171071 DOI: 10.1074/jbc.ra118.004632] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/10/2018] [Indexed: 01/24/2023] Open
Abstract
The 3'-5' exoribonuclease Rrp6 is a key enzyme in RNA homeostasis involved in processing and degradation of many stable RNA precursors, aberrant transcripts, and noncoding RNAs. We previously have shown that in the protozoan parasite Entamoeba histolytica, the 5'-external transcribed spacer fragment of pre-rRNA accumulates under serum starvation-induced growth stress. This fragment is a known target of degradation by Rrp6. Here, we computationally and biochemically characterized EhRrp6 and found that it contains the catalytically important EXO and HRDC domains and exhibits exoribonuclease activity with both unstructured and structured RNA substrates, which required the conserved DEDD-Y catalytic-site residues. It lacked the N-terminal PMC2NT domain for binding of the cofactor Rrp47, but could functionally complement the growth defect of a yeast rrp6 mutant. Of note, no Rrp47 homologue was detected in E. histolytica Immunolocalization studies revealed that EhRrp6 is present both in the nucleus and cytosol of normal E. histolytica cells. However, growth stress induced its complete loss from the nuclei, reversed by proteasome inhibitors. EhRrp6-depleted E. histolytica cells were severely growth restricted, and EhRrp6 overexpression protected the cells against stress, suggesting that EhRrp6 functions as a stress sensor. Importantly EhRrp6 depletion reduced erythrophagocytosis, an important virulence determinant of E. histolytica This reduction was due to a specific decrease in transcript levels of some phagocytosis-related genes (Ehcabp3 and Ehrho1), whereas expression of other genes (Ehcabp1, Ehcabp6, Ehc2pk, and Eharp2/3) was unaffected. This is the first report of the role of Rrp6 in cell growth and stress responses in a protozoan parasite.
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Affiliation(s)
| | | | - Ravi Bharadwaj
- the School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Amarjeet Kumar
- the School of Computational and Integrative Sciences, and
| | | | | | - Naidu Subbarao
- the School of Computational and Integrative Sciences, and
| | - Alok Bhattacharya
- the School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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107
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von Brandenstein M, Bernhart SH, Pansky A, Richter C, Kohl T, Deckert M, Heidenreich A, Stadler PF, Montesinos-Rongen M, Fries JWU. Beyond the 3'UTR binding-microRNA-induced protein truncation via DNA binding. Oncotarget 2018; 9:32855-32867. [PMID: 30214689 PMCID: PMC6132356 DOI: 10.18632/oncotarget.26023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/04/2018] [Indexed: 12/31/2022] Open
Abstract
Here, we present a miR mechanism which is active in the nucleus and is essential for the production of intron included, C-terminal truncated and biologically active proteins, like e.g. Vim3. We exemplified this mechanism by miRs, miR-15a and miR-498, which are overexpressed in clear cell renal carcinoma or oncocytoma. Both miRs directly interact with DNA in an intronic region, leading to transcriptional stop, and therefore repress the full length version of the pre-mRNA, resulting in intron included truncated proteins (Mxi-2 and Vim3). A computational survey shows that this miR:DNA interactions mechanism may be generally involved in regulating the human transcriptome, with putative interaction sites in intronic regions for over 1000 genes. In this work, an entirely new mechanism is revealed how miRs can repress full length protein translation, resulting in C-terminal truncated proteins.
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Affiliation(s)
| | - Stephan H Bernhart
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Leipzig, Germany
| | - Andreas Pansky
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany
| | - Claudia Richter
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Tobias Kohl
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - Martina Deckert
- Institute of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Axel Heidenreich
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Leipzig, Germany
| | | | - Jochen W U Fries
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
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108
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Horvat F, Fulka H, Jankele R, Malik R, Jun M, Solcova K, Sedlacek R, Vlahovicek K, Schultz RM, Svoboda P. Role of Cnot6l in maternal mRNA turnover. Life Sci Alliance 2018; 1:e201800084. [PMID: 30456367 PMCID: PMC6238536 DOI: 10.26508/lsa.201800084] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 01/09/2023] Open
Abstract
Removal of poly(A) tail is an important mechanism controlling eukaryotic mRNA turnover. The major eukaryotic deadenylase complex CCR4-NOT contains two deadenylase components, CCR4 and CAF1, for which mammalian CCR4 is encoded by Cnot6 or Cnot6l paralogs. We show that Cnot6l apparently supplies the majority of CCR4 in the maternal CCR4-NOT in mouse, hamster, and bovine oocytes. Deletion of Cnot6l yielded viable mice, but Cnot6l -/- females exhibited ∼40% smaller litter size. The main onset of the phenotype was post-zygotic: fertilized Cnot6l -/- eggs developed slower and arrested more frequently than Cnot6l +/- eggs, suggesting that maternal CNOT6L is necessary for accurate oocyte-to-embryo transition. Transcriptome analysis revealed major transcriptome changes in Cnot6l -/- ovulated eggs and one-cell zygotes. In contrast, minimal transcriptome changes in preovulatory Cnot6l -/- oocytes were consistent with reported Cnot6l mRNA dormancy. A minimal overlap between transcripts sensitive to decapping inhibition and Cnot6l loss suggests that decapping and CNOT6L-mediated deadenylation selectively target distinct subsets of mRNAs during oocyte-to-embryo transition in mouse.
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Affiliation(s)
- Filip Horvat
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Helena Fulka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Animal Science, Prague, Czech Republic
| | - Radek Jankele
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ma Jun
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Katerina Solcova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v. v. i., Vestec, Czech Republic
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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109
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Valdés-Flores J, López-Rosas I, López-Camarillo C, Ramírez-Moreno E, Ospina-Villa JD, Marchat LA. Life and Death of mRNA Molecules in Entamoeba histolytica. Front Cell Infect Microbiol 2018; 8:199. [PMID: 29971219 PMCID: PMC6018208 DOI: 10.3389/fcimb.2018.00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/28/2018] [Indexed: 02/05/2023] Open
Abstract
In eukaryotic cells, the life cycle of mRNA molecules is modulated in response to environmental signals and cell-cell communication in order to support cellular homeostasis. Capping, splicing and polyadenylation in the nucleus lead to the formation of transcripts that are suitable for translation in cytoplasm, until mRNA decay occurs in P-bodies. Although pre-mRNA processing and degradation mechanisms have usually been studied separately, they occur simultaneously and in a coordinated manner through protein-protein interactions, maintaining the integrity of gene expression. In the past few years, the availability of the genome sequence of Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, coupled to the development of the so-called “omics” technologies provided new opportunities for the study of mRNA processing and turnover in this pathogen. Here, we review the current knowledge about the molecular basis for splicing, 3′ end formation and mRNA degradation in amoeba, which suggest the conservation of events related to mRNA life throughout evolution. We also present the functional characterization of some key proteins and describe some interactions that indicate the relevance of cooperative regulatory events for gene expression in this human parasite.
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Affiliation(s)
- Jesús Valdés-Flores
- Departamento de Bioquímica, CINVESTAV, Ciudad de Mexico, Mexico City, Mexico
| | - Itzel López-Rosas
- CONACyT Research Fellow - Colegio de Postgraduados Campus Campeche, Campeche, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México Ciudad de Mexico, Mexico City, Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Juan D Ospina-Villa
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Laurence A Marchat
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
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110
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Szádeczky-Kardoss I, Csorba T, Auber A, Schamberger A, Nyikó T, Taller J, Orbán TI, Burgyán J, Silhavy D. The nonstop decay and the RNA silencing systems operate cooperatively in plants. Nucleic Acids Res 2018; 46:4632-4648. [PMID: 29672715 PMCID: PMC5961432 DOI: 10.1093/nar/gky279] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent mRNA quality control systems protect the protein homeostasis of eukaryotic cells by eliminating aberrant transcripts and stimulating the decay of their protein products. Although these systems are intensively studied in animals, little is known about the translation-dependent quality control systems in plants. Here, we characterize the mechanism of nonstop decay (NSD) system in Nicotiana benthamiana model plant. We show that plant NSD efficiently degrades nonstop mRNAs, which can be generated by premature polyadenylation, and stop codon-less transcripts, which are produced by endonucleolytic cleavage. We demonstrate that in plants, like in animals, Pelota, Hbs1 and SKI2 proteins are required for NSD, supporting that NSD is an ancient and conserved eukaryotic quality control system. Relevantly, we found that NSD and RNA silencing systems cooperate in plants. Plant silencing predominantly represses target mRNAs through endonucleolytic cleavage in the coding region. Here we show that NSD is required for the elimination of 5' cleavage product of mi- or siRNA-guided silencing complex when the cleavage occurs in the coding region. We also show that NSD and nonsense-mediated decay (NMD) quality control systems operate independently in plants.
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Affiliation(s)
| | - Tibor Csorba
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Anita Schamberger
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Tünde Nyikó
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - János Taller
- University Pannonia Georgikon, Festetics 7, 8360 Keszthely, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - József Burgyán
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Dániel Silhavy
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
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111
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Darnell RB, Ke S, Darnell JE. Pre-mRNA processing includes N6 methylation of adenosine residues that are retained in mRNA exons and the fallacy of "RNA epigenetics". RNA (NEW YORK, N.Y.) 2018; 24:262-267. [PMID: 29222117 PMCID: PMC5824346 DOI: 10.1261/rna.065219.117] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
By using a cell fraction technique that separates chromatin-associated nascent RNA, newly completed nucleoplasmic mRNA and cytoplasmic mRNA, we have shown in a previous study that residues in exons are methylated (m6A) in nascent pre-mRNA and remain methylated in the same exonic residues in nucleoplasmic and cytoplasmic mRNA. Thus, there is no evidence of a substantial degree of demethylation in mRNA exons that would correspond to so-called "epigenetic" demethylation. The turnover rate of mRNA molecules is faster, depending on m6A content in HeLa cell mRNA, suggesting that specification of mRNA stability may be the major role of m6A exon modification. In mouse embryonic stem cells (mESCs) lacking Mettl3, the major mRNA methylase, the cells continue to grow, making the same mRNAs with unchanged splicing profiles in the absence (>90%) of m6A in mRNA, suggesting no common obligatory role of m6A in splicing. All these data argue strongly against a commonly used "reversible dynamic methylation/demethylation" of mRNA, calling into question the concept of "RNA epigenetics" that parallels the well-established role of dynamic DNA epigenetics.
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Affiliation(s)
- Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA
| | - Shengdong Ke
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA
| | - James E Darnell
- Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA
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112
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Abstract
Significant advancements have been made in unraveling and understanding the non-coding elements of the human genome. New insights into the structure and function of noncoding RNAs have emerged. Their relevance in the context of both physiological cellular homeostasis and human diseases is getting appreciated. As a result, exploration of noncoding RNAs, in particular microRNAs (miRs), as therapeutic agents or targets of therapeutic strategies is under way. This review summarizes and discusses in depth the current literature on the role of miRs in neurodegenerative diseases.
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Affiliation(s)
- Salil Sharma
- Department of Psychological and Brain Sciences, The Linda and Jack Gill Center for Bimolecular Sciences, Indiana University, Bloomington, IN 47405, USA
| | - Hui-Chen Lu
- Department of Psychological and Brain Sciences, The Linda and Jack Gill Center for Bimolecular Sciences, Indiana University, Bloomington, IN 47405, USA
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113
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Jiang S, Jiang L, Yang J, Peng J, Lu Y, Zheng H, Lin L, Chen J, Yan F. Over-expression of Oryza sativa Xrn4 confers plant resistance to virus infection. Gene 2018; 639:44-51. [PMID: 28987346 DOI: 10.1016/j.gene.2017.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/30/2017] [Accepted: 10/03/2017] [Indexed: 11/25/2022]
Abstract
Plant Xrn4 is a cytoplasmic 5' to 3' exoribonuclease that is reported to play an antiviral role during viral infection as demonstrated by experiments using the Xrn4s of Nicotiana benthamiana and Arabidopsis thaliana. Meanwhile, little is known about the anti-viral activity of Xrn4 from other plants. Here, we cloned the cytoplasmic Xrn4 gene of Oryza sativa (OsXrn4), and demonstrated that its over-expression elevated the 5'-3' exoribonuclease activity in rice plants and conferred resistance to rice stripe virus, a negative-sense RNA virus causing serious losses in East Asia. The accumulation of viral RNAs was also decreased. Moreover, the ectopic expression of OsXrn4 in N. benthamiana also conferred plant resistance to tobacco mosaic virus infection. These results show that the monocotyledonous plant cytoplasmic Xrn4 also has an antiviral role and thus provides a strategy for producing transgenic plants resistant to viral infection.
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Affiliation(s)
- Shanshan Jiang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liangliang Jiang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Yang
- Stake Key laboratory Breeding Base for Sustainable Control of Pest and Disease, MOA and Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiejun Peng
- Stake Key laboratory Breeding Base for Sustainable Control of Pest and Disease, MOA and Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuwen Lu
- Stake Key laboratory Breeding Base for Sustainable Control of Pest and Disease, MOA and Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hongying Zheng
- Stake Key laboratory Breeding Base for Sustainable Control of Pest and Disease, MOA and Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lin Lin
- Stake Key laboratory Breeding Base for Sustainable Control of Pest and Disease, MOA and Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianping Chen
- Stake Key laboratory Breeding Base for Sustainable Control of Pest and Disease, MOA and Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Fei Yan
- Stake Key laboratory Breeding Base for Sustainable Control of Pest and Disease, MOA and Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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McGovern F, Boland T, Ryan M, Sweeney T. Assessment of RNA Stability in Postmortem Tissue from New-Born Lambs. Anim Biotechnol 2017; 29:269-275. [PMID: 29172984 DOI: 10.1080/10495398.2017.1378226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The recovery of high quality RNA from postmortem tissue is crucial to gene expression analyses. The acquisition of postmortem tissue has inherent time delays and, hence, understanding the temporal variation in the stability of total RNA is imperative. This experiment aimed: ( 1 ) to qualitatively and quantitatively assess the integrity of total RNA derived from a range of new-born ovine tissues (liver, spleen, thyroid, skeletal muscle, ileum, and perirenal adipose tissue) which were stored at ambient temperature until extraction at 0, 3, 6, and 9 h postmortem; and ( 2 ) to analyze the stability of the reference gene(s) and expression of specific target genes in these tissues. Postmortem sampling time resulted in variable reductions in the relative integrity number (RIN) values across the tissues, ranging from 0.9 to 1.8% in liver, spleen, skeletal muscle, and ileum to 5.7-11.1% in the thyroid and perirenal adipose tissues, respectively (P < 0.05). In conclusion, tissues with small reductions in RIN value can exhibit disproportionately large differences in the normalization factor used to calculate the target gene expression. Hence, changes in transcript abundance due to RNA degradation are not always sufficiently buffered through normalization with reference genes. The normalization factor should be presented alongside the RIN value in postmortem tissue studies.
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Affiliation(s)
- Fiona McGovern
- a UCD School of Agriculture and Food Science , University College Dublin, Lyons Research Farm , Newcastle , Dublin , Ireland.,b UCD School of Veterinary Medicine , University College Dublin , Belfield , Dublin , Ireland
| | - Tommy Boland
- a UCD School of Agriculture and Food Science , University College Dublin, Lyons Research Farm , Newcastle , Dublin , Ireland
| | - Marion Ryan
- b UCD School of Veterinary Medicine , University College Dublin , Belfield , Dublin , Ireland
| | - Torres Sweeney
- b UCD School of Veterinary Medicine , University College Dublin , Belfield , Dublin , Ireland
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Abstract
Leishmania tropica, a unicellular eukaryotic parasite present in North and East Africa, the Middle East, and the Indian subcontinent, has been linked to large outbreaks of cutaneous leishmaniasis in displaced populations in Iraq, Jordan, and Syria. Here, we report the genome sequence of this pathogen and 7,863 identified protein-coding genes, and we show that the majority of clinical isolates possess high levels of allelic diversity, genetic admixture, heterozygosity, and extensive aneuploidy. By utilizing paired genome-wide high-throughput DNA sequencing (DNA-seq) with RNA-seq, we found that gene dosage, at the level of individual genes or chromosomal "somy" (a general term covering disomy, trisomy, tetrasomy, etc.), accounted for greater than 85% of total gene expression variation in genes with a 2-fold or greater change in expression. High gene copy number variation (CNV) among membrane-bound transporters, a class of proteins previously implicated in drug resistance, was found for the most highly differentially expressed genes. Our results suggest that gene dosage is an adaptive trait that confers phenotypic plasticity among natural Leishmania populations by rapid down- or upregulation of transporter proteins to limit the effects of environmental stresses, such as drug selection.IMPORTANCELeishmania is a genus of unicellular eukaryotic parasites that is responsible for a spectrum of human diseases that range from cutaneous leishmaniasis (CL) and mucocutaneous leishmaniasis (MCL) to life-threatening visceral leishmaniasis (VL). Developmental and strain-specific gene expression is largely thought to be due to mRNA message stability or posttranscriptional regulatory networks for this species, whose genome is organized into polycistronic gene clusters in the absence of promoter-mediated regulation of transcription initiation of nuclear genes. Genetic hybridization has been demonstrated to yield dramatic structural genomic variation, but whether such changes in gene dosage impact gene expression has not been formally investigated. Here we show that the predominant mechanism determining transcript abundance differences (>85%) in Leishmania tropica is that of gene dosage at the level of individual genes or chromosomal somy.
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Wang TH, Chen CC, Liang KH, Chen CY, Chuang WY, Ueng SH, Chu PH, Huang CG, Chen TC, Hsueh C. A Multivariate Evaluation of Factors Affecting the Quality of Freshly Frozen Tissue Specimens. Biopreserv Biobank 2017; 15:344-349. [DOI: 10.1089/bio.2016.0104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Tong-Hong Wang
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Research Center for Industry of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chin-Chuan Chen
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan, Taiwan
| | - Kung-Hao Liang
- Liver Research Center, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chi-Yuan Chen
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Research Center for Industry of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Wen-Yu Chuang
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Shir-Hwa Ueng
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Pao-Hsien Chu
- Healthcare Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linko, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tse-Ching Chen
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chuen Hsueh
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
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Chen P, Zhou Z, Yao X, Pang S, Liu M, Jiang W, Jiang J, Zhang Q. Capping Enzyme mRNA-cap/RNGTT Regulates Hedgehog Pathway Activity by Antagonizing Protein Kinase A. Sci Rep 2017; 7:2891. [PMID: 28588207 PMCID: PMC5460166 DOI: 10.1038/s41598-017-03165-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/21/2017] [Indexed: 02/07/2023] Open
Abstract
Hedgehog (Hh) signaling plays a pivotal role in animal development and its deregulation in humans causes birth defects and several types of cancer. Protein Kinase A (PKA) modulates Hh signaling activity through phosphorylating the transcription factor Cubitus interruptus (Ci) and G protein coupled receptor (GPCR) family protein Smoothened (Smo) in Drosophila, but how PKA activity is regulated remains elusive. Here, we identify a novel regulator of the Hh pathway, the capping-enzyme mRNA-cap, which positively regulates Hh signaling activity through modulating PKA activity. We provide genetic and biochemical evidence that mRNA-cap inhibits PKA kinase activity to promote Hh signaling. Interestingly, regulation of Hh signaling by mRNA-cap depends on its cytoplasmic capping-enzyme activity. In addition, we show that the mammalian homolog of mRNA-cap, RNGTT, can replace mRNA-cap to play the same function in the Drosophila Hh pathway and that knockdown of Rngtt in cultured mammalian cells compromised Shh pathway activity, suggesting that RNGTT is functionally conserved. Our study makes an unexpected link between the mRNA capping machinery and the Hh signaling pathway, unveils a new facet of Hh signaling regulation, and reveals a potential drug target for modulating Hh signaling activity.
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Affiliation(s)
- Ping Chen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, 210061, China
| | - Zizhang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, 210061, China
| | - Xia Yao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, 210061, China
| | - Shu Pang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, 210061, China
| | - Meijing Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, 210061, China
| | - Weirong Jiang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, 210061, China
| | - Jin Jiang
- Department of Molecular Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA. .,Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA.
| | - Qing Zhang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, 210061, China.
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118
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MicroRNA Metabolism and Dysregulation in Amyotrophic Lateral Sclerosis. Mol Neurobiol 2017; 55:2617-2630. [PMID: 28421535 DOI: 10.1007/s12035-017-0537-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/07/2017] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are a subset of endogenous, small, non-coding RNA molecules involved in the post-transcriptional regulation of eukaryotic gene expression. Dysregulation in miRNA-related pathways in the central nervous system (CNS) is associated with severe neuronal injury and cell death, which can lead to the development of neurodegenerative disorders, such as amyotrophic lateral sclerosis (ALS). ALS is a fatal adult onset disease characterized by the selective loss of upper and lower motor neurons. While the pathogenesis of ALS is still largely unknown, familial ALS forms linked to TAR DNA-binding protein 43 (TDP-43) and fused in sarcoma (FUS) gene mutations, as well as sporadic forms, display changes in several steps of RNA metabolism, including miRNA processing. Here, we review the current knowledge about miRNA metabolism and biological functions and their crucial role in ALS pathogenesis with an in-depth analysis on different pathways. A more precise understanding of miRNA involvement in ALS could be useful not only to elucidate their role in the disease etiopathogenesis but also to investigate their potential as disease biomarkers and novel therapeutic targets.
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119
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Zhou F, Wang Y, Liu H, Ready N, Han Y, Hung RJ, Brhane Y, McLaughlin J, Brennan P, Bickeböller H, Rosenberger A, Houlston RS, Caporaso N, Landi MT, Brüske I, Risch A, Ye Y, Wu X, Christiani DC, Goodman G, Chen C, Amos CI, Qingyi W. Susceptibility loci of CNOT6 in the general mRNA degradation pathway and lung cancer risk-A re-analysis of eight GWASs. Mol Carcinog 2017; 56:1227-1238. [PMID: 27805284 PMCID: PMC5354966 DOI: 10.1002/mc.22585] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/28/2016] [Accepted: 10/28/2016] [Indexed: 12/19/2022]
Abstract
PURPOSE mRNA degradation is an important regulatory step for controlling gene expression and cell functions. Genetic abnormalities involved in mRNA degradation genes were found to be associated with cancer risks. Therefore, we systematically investigated the roles of genetic variants in the general mRNA degradation pathway in lung cancer risk. EXPERIMENTAL DESIGN Meta-analyses were conducted using summary data from six lung cancer genome-wide association studies (GWASs) from the Transdisciplinary Research in Cancer of the Lung and additional two GWASs from Harvard University and deCODE in the International Lung Cancer Consortium. Expression quantitative trait loci analysis (eQTL) was used for in silico functional validation of the identified significant susceptibility loci. RESULTS This pathway-based analysis included 6816 single nucleotide polymorphisms (SNP) in 68 genes in 14 463 lung cancer cases and 44 188 controls. In the single-locus analysis, we found that 20 SNPs were associated with lung cancer risk with a false discovery rate threshold of <0.05. Among the 11 newly identified SNPs in CNOT6, which were in high linkage disequilibrium, the rs2453176 with a RegulomDB score "1f" was chosen as the tagSNP for further analysis. We found that the rs2453176 T allele was significantly associated with lung cancer risk (odds ratio = 1.11, 95% confidence interval = 1.04-1.18) in the eight GWASs. In the eQTL analysis, we found that levels of CNOT6 mRNA expression were significantly correlated with the rs2453176 T allele, which provided additional biological basis for the observed positive association. CONCLUSION The CNOT6 rs2453176 SNP may be a new functional susceptible locus for lung cancer risk. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Fei Zhou
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Oncology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080, China
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yanru Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Neal Ready
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Younghun Han
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), 69372 Lyon, France
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, 37073 Göttingen, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, 37073 Göttingen, Germany
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, the Institute of Cancer Research, London , SW7 3RP, UK
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irene Brüske
- Helmholtz Centre Munich, German Research Centre for Environmental Health, Institute of Epidemiology I, 85764 Neuherberg, Germany
| | - Angela Risch
- Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David C. Christiani
- Massachusetts General Hospital, Boston, MA 02114, USA, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115, USA
| | - Gary Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Swedish Cancer Institute, Seattle, WA 98104, USA
| | - Chu Chen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Christopher I. Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Wei Qingyi
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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120
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Shan L, Wu C, Chen D, Hou L, Li X, Wang L, Chu X, Hou Y, Wang Z. Regulators of alternative polyadenylation operate at the transition from mitosis to meiosis. J Genet Genomics 2017; 44:95-106. [DOI: 10.1016/j.jgg.2016.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/14/2016] [Accepted: 12/28/2016] [Indexed: 11/25/2022]
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121
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Yan X, Yan Z, Han Y. RRP42, a Subunit of Exosome, Plays an Important Role in Female Gametophytes Development and Mesophyll Cell Morphogenesis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:981. [PMID: 28642780 PMCID: PMC5463273 DOI: 10.3389/fpls.2017.00981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The exosome complex plays a central and essential role in RNA metabolism. However, current research on functions of exosome subunit in plants is limited. Here, we used an egg cell-specific promoter-controlled CRISPR/Cas9 system to knock out RRP42 which encodes a core subunit of the Arabidopsis exosome and presented evidence that RRP42 is essential for the development of female gametophytes. Next, we designed three different amiRNAs targeting RRP42. The rrp42 knock-down mutants mainly displayed variegated and serrated leaves, especially in cauline leaves. The internal anatomy of cauline leaves displayed irregularly shaped palisade cells and a reduced density of mesophyll cells. Interestingly, we detected highly accumulated mRNAs that encode xyloglucan endotransglucosylase/hydrolases (XTHs) and expansins (EXPAs) during later growth stages in rrp42 knock-down mutants. The mRNA decay kinetics analysis for XTH19, EXPA10, and EXPA11 revealed that RRP42 had a role in the decay of these mRNAs in the cytoplasm. RRP42 is localized to both the nucleus and cytoplasm, and RRP42 is preferentially expressed in cauline leaves during later growth stages. Altogether, our results demonstrate that RRP42 is essential for the development of female gametophytes and plays an important role in mesophyll cell morphogenesis.
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Lackey PE, Welch JD, Marzluff WF. TUT7 catalyzes the uridylation of the 3' end for rapid degradation of histone mRNA. RNA (NEW YORK, N.Y.) 2016; 22:1673-1688. [PMID: 27609902 PMCID: PMC5066620 DOI: 10.1261/rna.058107.116] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/01/2016] [Indexed: 05/03/2023]
Abstract
The replication-dependent histone mRNAs end in a stem-loop instead of the poly(A) tail present at the 3' end of all other cellular mRNAs. Following processing, the 3' end of histone mRNAs is trimmed to 3 nucleotides (nt) after the stem-loop, and this length is maintained by addition of nontemplated uridines if the mRNA is further trimmed by 3'hExo. These mRNAs are tightly cell-cycle regulated, and a critical regulatory step is rapid degradation of the histone mRNAs when DNA replication is inhibited. An initial step in histone mRNA degradation is digestion 2-4 nt into the stem by 3'hExo and uridylation of this intermediate. The mRNA is then subsequently degraded by the exosome, with stalled intermediates being uridylated. The enzyme(s) responsible for oligouridylation of histone mRNAs have not been definitively identified. Using high-throughput sequencing of histone mRNAs and degradation intermediates, we find that knockdown of TUT7 reduces both the uridylation at the 3' end as well as uridylation of the major degradation intermediate in the stem. In contrast, knockdown of TUT4 did not alter the uridylation pattern at the 3' end and had a small effect on uridylation in the stem-loop during histone mRNA degradation. Knockdown of 3'hExo also altered the uridylation of histone mRNAs, suggesting that TUT7 and 3'hExo function together in trimming and uridylating histone mRNAs.
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Affiliation(s)
- Patrick E Lackey
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joshua D Welch
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - William F Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Niinuma S, Fukaya T, Tomari Y. CCR4 and CAF1 deadenylases have an intrinsic activity to remove the post-poly(A) sequence. RNA (NEW YORK, N.Y.) 2016; 22:1550-1559. [PMID: 27484313 PMCID: PMC5029453 DOI: 10.1261/rna.057679.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/21/2016] [Indexed: 05/31/2023]
Abstract
MicroRNAs (miRNAs) recruit the CCR4-NOT complex, which contains two deadenylases, CCR4 and CAF1, to promote shortening of the poly(A) tail. Although both CCR4 and CAF1 generally have a strong preference for poly(A) RNA substrates, it has been reported from yeast to humans that they can also remove non-A residues in vitro to various degrees. However, it remains unknown how CCR4 and CAF1 remove non-A sequences. Herein we show that Drosophila miRNAs can promote the removal of 3'-terminal non-A residues in an exonucleolytic manner, but only if an upstream poly(A) sequence exists. This non-A removing reaction is directly catalyzed by both CCR4 and CAF1 and depends on the balance between the length of the internal poly(A) sequence and that of the downstream non-A sequence. These results suggest that the CCR4-NOT complex has an intrinsic activity to remove the 3'-terminal non-A modifications downstream from the poly(A) tail.
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Affiliation(s)
- Sho Niinuma
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, JapanDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Fukaya
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, JapanDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, JapanDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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124
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Kawa D, Testerink C. Regulation of mRNA decay in plant responses to salt and osmotic stress. Cell Mol Life Sci 2016; 74:1165-1176. [PMID: 27677492 PMCID: PMC5346435 DOI: 10.1007/s00018-016-2376-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 09/21/2016] [Indexed: 11/24/2022]
Abstract
Plant acclimation to environmental stresses requires fast signaling to initiate changes in developmental and metabolic responses. Regulation of gene expression by transcription factors and protein kinases acting upstream are important elements of responses to salt and drought. Gene expression can be also controlled at the post-transcriptional level. Recent analyses on mutants in mRNA metabolism factors suggest their contribution to stress signaling. Here we highlight the components of mRNA decay pathways that contribute to responses to osmotic and salt stress. We hypothesize that phosphorylation state of proteins involved in mRNA decapping affect their substrate specificity.
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Affiliation(s)
- Dorota Kawa
- Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090 GE, Amsterdam, The Netherlands
| | - Christa Testerink
- Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090 GE, Amsterdam, The Netherlands.
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125
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Abstract
Alternative precursor-mRNA splicing is a key mechanism for regulating gene expression in mammals and is controlled by specialized RNA-binding proteins. The misregulation of splicing is implicated in multiple neurological disorders. We describe recent mouse genetic studies of alternative splicing that reveal its critical role in both neuronal development and the function of mature neurons. We discuss the challenges in understanding the extensive genetic programmes controlled by proteins that regulate splicing, both during development and in the adult brain.
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Affiliation(s)
- Celine K Vuong
- Molecular Biology Interdepartmental Graduate Program, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Sika Zheng
- Division of Biomedical Sciences, University of California at Riverside, Riverside, California 92521, USA
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126
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Fuchs AL, Neu A, Sprangers R. A general method for rapid and cost-efficient large-scale production of 5' capped RNA. RNA (NEW YORK, N.Y.) 2016; 22:1454-66. [PMID: 27368341 PMCID: PMC4986899 DOI: 10.1261/rna.056614.116] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/03/2023]
Abstract
The eukaryotic mRNA 5' cap structure is indispensible for pre-mRNA processing, mRNA export, translation initiation, and mRNA stability. Despite this importance, structural and biophysical studies that involve capped RNA are challenging and rare due to the lack of a general method to prepare mRNA in sufficient quantities. Here, we show that the vaccinia capping enzyme can be used to produce capped RNA in the amounts that are required for large-scale structural studies. We have therefore designed an efficient expression and purification protocol for the vaccinia capping enzyme. Using this approach, the reaction scale can be increased in a cost-efficient manner, where the yields of the capped RNA solely depend on the amount of available uncapped RNA target. Using a large number of RNA substrates, we show that the efficiency of the capping reaction is largely independent of the sequence, length, and secondary structure of the RNA, which makes our approach generally applicable. We demonstrate that the capped RNA can be directly used for quantitative biophysical studies, including fluorescence anisotropy and high-resolution NMR spectroscopy. In combination with (13)C-methyl-labeled S-adenosyl methionine, the methyl groups in the RNA can be labeled for methyl TROSY NMR spectroscopy. Finally, we show that our approach can produce both cap-0 and cap-1 RNA in high amounts. In summary, we here introduce a general and straightforward method that opens new means for structural and functional studies of proteins and enzymes in complex with capped RNA.
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Affiliation(s)
- Anna-Lisa Fuchs
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ancilla Neu
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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127
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Wurm JP, Overbeck J, Sprangers R. The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface. RNA (NEW YORK, N.Y.) 2016; 22:1360-72. [PMID: 27354705 PMCID: PMC4986892 DOI: 10.1261/rna.057315.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/22/2016] [Indexed: 05/19/2023]
Abstract
The removal of the 5' 7-methylguanosine mRNA cap structure (decapping) is a central step in the 5'-3' mRNA degradation pathway and is performed by the Dcp1:Dcp2 decapping complex. The activity of this complex is tightly regulated to prevent premature degradation of the transcript. Here, we establish that the aromatic groove of the EVH1 domain of Schizosaccharomyces pombe Dcp1 can interact with proline-rich sequences in the exonuclease Xrn1, the scaffolding protein Pat1, the helicase Dhh1, and the C-terminal disordered region of Dcp2. We show that this region of Dcp1 can also recruit a previously unidentified enhancer of decapping protein (Edc1) and solved the crystal structure of the complex. NMR relaxation dispersion experiments reveal that the Dcp1 binding site can adopt multiple conformations, thus providing the plasticity that is required to accommodate different ligands. We show that the activator Edc1 makes additional contacts with the regulatory domain of Dcp2 and that an activation motif in Edc1 increases the RNA affinity of Dcp1:Dcp2. Our data support a model where Edc1 stabilizes the RNA in the active site, which results in enhanced decapping rates. In summary, we show that multiple decapping factors, including the Dcp2 C-terminal region, compete with Edc1 for Dcp1 binding. Our data thus reveal a network of interactions that can fine-tune the catalytic activity of the decapping complex.
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Affiliation(s)
- Jan Philip Wurm
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jan Overbeck
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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128
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Banerjee D, Bloom ALM, Panepinto JC. Opposing PKA and Hog1 signals control the post-transcriptional response to glucose availability in Cryptococcus neoformans. Mol Microbiol 2016; 102:306-320. [PMID: 27387858 DOI: 10.1111/mmi.13461] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2016] [Indexed: 12/17/2022]
Abstract
The pathogenic fungus Cryptococcus neoformans must adapt to glucose-limited conditions in the lung and glucose replete conditions upon dissemination to the brain. We report that glucose controls ribosome biogenesis and translation by modulating mRNA decay through a balance of PKA and Hog1 signalling. Glucose signalling through PKA stabilized ribosomal protein (RP) mRNAs whereas glucose starvation destabilized RP transcripts through Hog1. Glucose starvation-induced oxidative stress response genes, and treatment of glucose-fed cells with reactive oxygen species (ROS) generating compounds repressed RP transcripts, both of which were dependent on Hog1. Stabilization of RP transcripts led to retention of polysomes in a hog1Δ mutant, whereas stabilization of RP transcripts by cyclic AMP did not affect translation repression, suggesting that Hog1 alone signals translation repression. In sum, this work describes a novel antagonism between PKA and Hog1 controlling ribosome biogenesis via mRNA stability in response to glucose availability in this important human pathogen.
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Affiliation(s)
- Dithi Banerjee
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - Amanda L M Bloom
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - John C Panepinto
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York at Buffalo, Buffalo, NY, 14214, USA.
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129
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Anastasakis D, Skeparnias I, Shaukat AN, Grafanaki K, Kanellou A, Taraviras S, Papachristou DJ, Papakyriakou A, Stathopoulos C. Mammalian PNLDC1 is a novel poly(A) specific exonuclease with discrete expression during early development. Nucleic Acids Res 2016; 44:8908-8920. [PMID: 27515512 PMCID: PMC5062988 DOI: 10.1093/nar/gkw709] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/02/2016] [Indexed: 12/28/2022] Open
Abstract
PNLDC1 is a homologue of poly(A) specific ribonuclease (PARN), a known deadenylase with additional role in processing of non-coding RNAs. Both enzymes were reported recently to participate in piRNA biogenesis in silkworm and C. elegans, respectively. To get insights on the role of mammalian PNLDC1, we characterized the human and mouse enzymes. PNLDC1 shows limited conservation compared to PARN and represents an evolutionary related but distinct group of enzymes. It is expressed specifically in mouse embryonic stem cells, human and mouse testes and during early mouse embryo development, while it fades during differentiation. Its expression in differentiated cells, is suppressed through methylation of its promoter by the de novo methyltransferase DNMT3B. Both enzymes are localized mainly in the ER and exhibit in vitro specificity restricted solely to 3′ RNA or DNA polyadenylates. Knockdown of Pnldc1 in mESCs and subsequent NGS analysis showed that although the expression of the remaining deadenylases remains unaffected, it affects genes involved mainly in reprogramming, cell cycle and translational regulation. Mammalian PNLDC1 is a novel deadenylase expressed specifically in cell types which share regulatory mechanisms required for multipotency maintenance. Moreover, it could be involved both in posttranscriptional regulation through deadenylation and genome surveillance during early development.
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Affiliation(s)
- Dimitrios Anastasakis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | | | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Alexandra Kanellou
- Department of Physiology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Dionysios J Papachristou
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Athanasios Papakyriakou
- Laboratory of Chemical Biology, National Centre for Scientific Research 'Demokritos', 15341 Athens, Greece
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130
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Grudzien-Nogalska E, Kiledjian M. New insights into decapping enzymes and selective mRNA decay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27425147 DOI: 10.1002/wrna.1379] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/04/2023]
Abstract
Removal of the 5' end cap is a critical determinant controlling mRNA stability and efficient gene expression. Removal of the cap is exquisitely controlled by multiple direct and indirect regulators that influence association with the cap and the catalytic step. A subset of these factors directly stimulate activity of the decapping enzyme, while others influence remodeling of factors bound to mRNA and indirectly stimulate decapping. Furthermore, the components of the general decapping machinery can also be recruited by mRNA-specific regulatory proteins to activate decapping. The Nudix hydrolase, Dcp2, identified as a first decapping enzyme, cleaves capped mRNA and initiates 5'-3' degradation. Extensive studies on Dcp2 led to broad understanding of its activity and the regulation of transcript specific decapping and decay. Interestingly, seven additional Nudix proteins possess intrinsic decapping activity in vitro and at least two, Nudt16 and Nudt3, are decapping enzymes that regulate mRNA stability in cells. Furthermore, a new class of decapping proteins within the DXO family preferentially function on incompletely capped mRNAs. Importantly, it is now evident that each of the characterized decapping enzymes predominantly modulates only a subset of mRNAs, suggesting the existence of multiple decapping enzymes functioning in distinct cellular pathways. WIREs RNA 2017, 8:e1379. doi: 10.1002/wrna.1379 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ewa Grudzien-Nogalska
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
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131
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Singhania R, Pavey S, Payne E, Gu W, Clancy J, Jubair L, Preiss T, Saunders N, McMillan NAJ. Short interfering RNA induced generation and translation of stable 5' mRNA cleavage intermediates. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1034-42. [PMID: 27321990 DOI: 10.1016/j.bbagrm.2016.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 11/30/2022]
Abstract
Sequence-specific degradation of homologous mRNA is the main mechanism by which short-interfering RNAs (siRNAs) suppress gene expression. Generally, it is assumed that the mRNA fragments resulting from Ago2 cleavage are rapidly degraded, thus making the transcript translation-incompetent. However, the molecular mechanisms involved in the post-cleavage mRNA decay are not completely understood and the fate of cleavage intermediates has been poorly studied. Using specific siRNAs and short-hairpin RNAs (shRNAs) we show that the 5' and 3' mRNA cleavage fragments of human papilloma virus type 16 (HPV-16) E6/7 mRNA, over-expressed in cervical malignancies, are unevenly degraded. Intriguingly, the 5' mRNA fragment was more abundant and displayed a greater stability than the corresponding 3' mRNA fragment in RNAi-treated cells. Further analysis revealed that the 5' mRNA fragment was polysome-associated, indicating its active translation, and this was further confirmed by using tagged E7 protein to show that C-terminally truncated proteins were produced in treated cells. Overall, our findings provide new insight into the degradation of siRNA-targeted transcripts and show that RNAi can alter protein expression in cells as a result of preferential stabilization and translation of the 5' cleavage fragment. These results challenge the current model of siRNA-mediated RNAi and provide a significant step forward towards understanding non-canonical pathways of siRNA gene silencing.
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Affiliation(s)
- Richa Singhania
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Sandra Pavey
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Elizabeth Payne
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Wenyi Gu
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Jennifer Clancy
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Luqman Jubair
- Menzies Health Institute Queensland and School of Medical Science, Griffith University, Southport, Australia
| | - Thomas Preiss
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Nicholas Saunders
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Nigel A J McMillan
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia; Menzies Health Institute Queensland and School of Medical Science, Griffith University, Southport, Australia.
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132
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Niland CN, Jankowsky E, Harris ME. Optimization of high-throughput sequencing kinetics for determining enzymatic rate constants of thousands of RNA substrates. Anal Biochem 2016; 510:1-10. [PMID: 27296633 DOI: 10.1016/j.ab.2016.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/03/2016] [Indexed: 12/12/2022]
Abstract
Quantification of the specificity of RNA binding proteins and RNA processing enzymes is essential to understanding their fundamental roles in biological processes. High-throughput sequencing kinetics (HTS-Kin) uses high-throughput sequencing and internal competition kinetics to simultaneously monitor the processing rate constants of thousands of substrates by RNA processing enzymes. This technique has provided unprecedented insight into the substrate specificity of the tRNA processing endonuclease ribonuclease P. Here, we investigated the accuracy and robustness of measurements associated with each step of the HTS-Kin procedure. We examine the effect of substrate concentration on the observed rate constant, determine the optimal kinetic parameters, and provide guidelines for reducing error in amplification of the substrate population. Importantly, we found that high-throughput sequencing and experimental reproducibility contribute to error, and these are the main sources of imprecision in the quantified results when otherwise optimized guidelines are followed.
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Affiliation(s)
- Courtney N Niland
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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133
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Liu L, Chen X. RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants. MOLECULAR PLANT 2016; 9:826-36. [PMID: 27045817 PMCID: PMC5123867 DOI: 10.1016/j.molp.2016.03.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
RNA quality control of endogenous RNAs is an integral part of eukaryotic gene expression and often relies on exonucleolytic degradation to eliminate dysfunctional transcripts. In parallel, exogenous and selected endogenous RNAs are degraded through RNA silencing, which is a genome defense mechanism used by many eukaryotes. In plants, RNA silencing is triggered by the production of double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASEs (RDRs) and proceeds through small interfering (si) RNA-directed, ARGONAUTE (AGO)-mediated cleavage of homologous transcripts. Many studies revealed that plants avert inappropriate posttranscriptional gene silencing of endogenous coding genes by using RNA surveillance mechanisms as a safeguard to protect their transcriptome profiles. The tug of war between RNA surveillance and RNA silencing ensures the appropriate partitioning of endogenous RNA substrates among these degradation pathways. Here we review recent advances on RNA quality control and its role in the suppression of RNA silencing at endogenous genes and discuss the mechanisms underlying the crosstalk among these pathways.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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134
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Walters RW, Parker R. Coupling of Ribostasis and Proteostasis: Hsp70 Proteins in mRNA Metabolism. Trends Biochem Sci 2016; 40:552-559. [PMID: 26410596 DOI: 10.1016/j.tibs.2015.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/06/2015] [Accepted: 08/07/2015] [Indexed: 02/08/2023]
Abstract
A key aspect of the control of gene expression is the differential rates of mRNA translation and degradation, including alterations due to extracellular inputs. Surprisingly, multiple examples now argue that Hsp70 protein chaperones and their associated Hsp40 partners modulate both mRNA degradation and translation. Hsp70 proteins affect mRNA metabolism by various mechanisms including regulating nascent polypeptide chain folding, activating signal transduction pathways, promoting clearance of stress granules, and controlling mRNA degradation in an mRNA-specific manner. Taken together, these observations highlight the general principle that mRNA metabolism is coupled to the proteostatic state of the cell, often as assessed by the presence of unfolded or misfolded proteins.
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Affiliation(s)
- Robert W Walters
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO, USA.
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135
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Vuković L, Chipot C, Makino DL, Conti E, Schulten K. Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex. J Am Chem Soc 2016; 138:4069-78. [PMID: 26928279 PMCID: PMC4988868 DOI: 10.1021/jacs.5b12065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Recent experimental studies revealed structural details of 3' to 5' degradation of RNA molecules, performed by the exosome complex. ssRNA is channeled through its multisubunit ring-like core into the active site tunnel of its key exonuclease subunit Rrp44, which acts both as an enzyme and a motor. Even in isolation, Rrp44 can pull and sequentially cleave RNA nucleotides, one at a time, without any external energy input and release a final 3-5 nucleotide long product. Using molecular dynamics simulations, we identify the main factors that control these processes. Our free energy calculations reveal that RNA transfer from solution into the active site of Rrp44 is highly favorable, but dependent on the length of the RNA strand. While RNA strands formed by 5 nucleotides or more correspond to a decreasing free energy along the translocation coordinate toward the cleavage site, a 4-nucleotide RNA experiences a free energy barrier along the same direction, potentially leading to incomplete cleavage of ssRNA and the release of short (3-5) nucleotide products. We provide new insight into how Rrp44 catalyzes a localized enzymatic reaction and performs an action distributed over several RNA nucleotides, leading eventually to the translocation of whole RNA segments into the position suitable for cleavage.
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Affiliation(s)
- Lela Vuković
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- epartment of Chemistry, University of Texas at El Paso, El Paso, TX 79968, United States
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Laboratoire International Associé CNRS-University of Illinois, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Debora L. Makino
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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136
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Harnisch C, Cuzic-Feltens S, Dohm JC, Götze M, Himmelbauer H, Wahle E. Oligoadenylation of 3' decay intermediates promotes cytoplasmic mRNA degradation in Drosophila cells. RNA (NEW YORK, N.Y.) 2016; 22:428-42. [PMID: 26786835 PMCID: PMC4748820 DOI: 10.1261/rna.053942.115] [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] [Received: 08/12/2015] [Accepted: 12/08/2015] [Indexed: 05/20/2023]
Abstract
Post-transcriptional 3' end addition of nucleotides is important in a variety of RNA decay pathways. We have examined the 3' end addition of nucleotides during the decay of the Hsp70 mRNA and a corresponding reporter RNA in Drosophila S2 cells by conventional sequencing of cDNAs obtained after mRNA circularization and by deep sequencing of dedicated libraries enriched for 3' decay intermediates along the length of the mRNA. Approximately 5%-10% of 3' decay intermediates carried nonencoded oligo(A) tails with a mean length of 2-3 nucleotides. RNAi experiments showed that the oligoadenylated RNA fragments were intermediates of exosomal decay and the noncanonical poly(A) polymerase Trf4-1 was mainly responsible for A addition. A hot spot of A addition corresponded to an intermediate of 3' decay that accumulated upon inhibition of decapping, and knockdown of Trf4-1 increased the abundance of this intermediate, suggesting that oligoadenylation facilitates 3' decay. Oligoadenylated 3' decay intermediates were found in the cytoplasmic fraction in association with ribosomes, and fluorescence microscopy revealed a cytoplasmic localization of Trf4-1. Thus, oligoadenylation enhances exosomal mRNA degradation in the cytoplasm.
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Affiliation(s)
- Christiane Harnisch
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Simona Cuzic-Feltens
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Juliane C Dohm
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria
| | - Michael Götze
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
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137
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Muppavarapu M, Huch S, Nissan T. The cytoplasmic mRNA degradation factor Pat1 is required for rRNA processing. RNA Biol 2016; 13:455-65. [PMID: 26918764 DOI: 10.1080/15476286.2016.1154253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pat1 is a key cytoplasmic mRNA degradation factor, the loss of which severely increases mRNA half-lives. Several recent studies have shown that Pat1 can enter the nucleus and can shuttle between the nucleus and the cytoplasm. As a result, many nuclear roles have been proposed for Pat1. In this study, we analyzed four previously suggested nuclear roles of Pat1 and show that Pat1 is not required for efficient pre-mRNA splicing or pre-mRNA decay in yeast. However, lack of Pat1 results in accumulation of pre-rRNA processing intermediates. Intriguingly, we identified a novel genetic relationship between Pat1 and the rRNA decay machinery, specifically the exosome and the TRAMP complex. While the pre-rRNA processing intermediates that accumulate in the pat1 deletion mutant are, at least to some extent, recognized as aberrant by the rRNA degradation machinery, it is unlikely that these accumulations are the cause of their synthetic sick relationship. Here, we show that the dysregulation of the levels of mRNAs related to ribosome biogenesis could be the cause of the accumulation of the pre-rRNA processing intermediates. Although our results support a role for Pat1 in transcription, they nevertheless suggest that the primary cause of the dysregulated mRNA levels is most likely due to Pat1's role in mRNA decapping and mRNA degradation.
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Affiliation(s)
- Mridula Muppavarapu
- a Department of Molecular Biology , Umeå University , SE-901 87 Umeå , Sweden
| | - Susanne Huch
- a Department of Molecular Biology , Umeå University , SE-901 87 Umeå , Sweden
| | - Tracy Nissan
- a Department of Molecular Biology , Umeå University , SE-901 87 Umeå , Sweden
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138
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Buemo CP, Gambini A, Moro LN, Hiriart MI, Fernández-Martín R, Collas P, Salamone DF. Embryo Aggregation in Pig Improves Cloning Efficiency and Embryo Quality. PLoS One 2016; 11:e0146390. [PMID: 26894831 PMCID: PMC4760708 DOI: 10.1371/journal.pone.0146390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/16/2015] [Indexed: 11/19/2022] Open
Abstract
In this study, we analyzed the effects of the cloned embryo aggregation on in vitro embryo development and embryo quality by measuring blastocyst diameter and cell number, DNA fragmentation levels and the expression of genes associated with pluripotency, apoptosis, trophoblast and DNA methylation in the porcine. Zona-free reconstructed cloned embryos were cultured in the well of the well system, placing one (1x non aggregated group) or three (3x group) embryos per microwell. Our results showed that aggregation of three embryos increased blastocyst formation rate and blastocyst diameter of cloned pig embryos. DNA fragmentation levels in 3x aggregated cloned blastocysts were significantly decreased compared to 1x blastocysts. Levels of Oct4, Klf4, Igf2, Bax and Dnmt 1 transcripts were significantly higher in aggregated embryos, whereas Nanog levels were not affected. Transcripts of Cdx2 and Bcl-xl were essentially non-detectable. Our study suggests that embryo aggregation in the porcine may be beneficial for cloned embryo development and embryo quality, through a reduction in apoptotic levels and an improvement in cell reprogramming.
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Affiliation(s)
- Carla Paola Buemo
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - Andrés Gambini
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - Lucia Natalia Moro
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - María Inés Hiriart
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - Rafael Fernández-Martín
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, Oslo, Norway
| | - Daniel Felipe Salamone
- Laboratory of Animal Biotechnology, Faculty of Agriculture, University of Buenos Aires, Buenos Aires, Argentina
- National Institute of Scientific and Technological Research, Buenos Aires, Argentina
- * E-mail:
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139
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Lima WF, De Hoyos CL, Liang XH, Crooke ST. RNA cleavage products generated by antisense oligonucleotides and siRNAs are processed by the RNA surveillance machinery. Nucleic Acids Res 2016; 44:3351-63. [PMID: 26843429 PMCID: PMC4838368 DOI: 10.1093/nar/gkw065] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/25/2016] [Indexed: 01/22/2023] Open
Abstract
DNA-based antisense oligonucleotides (ASOs) elicit cleavage of the targeted RNA by the endoribonuclease RNase H1, whereas siRNAs mediate cleavage through the RNAi pathway. To determine the fates of the cleaved RNA in cells, we lowered the levels of the factors involved in RNA surveillance prior to treating cells with ASOs or siRNA and analyzed cleavage products by RACE. The cytoplasmic 5' to 3' exoribonuclease XRN1 was responsible for the degradation of the downstream cleavage products generated by ASOs or siRNA targeting mRNAs. In contrast, downstream cleavage products generated by ASOs targeting nuclear long non-coding RNA Malat 1 and pre-mRNA were degraded by nuclear XRN2. The downstream cleavage products did not appear to be degraded in the 3' to 5' direction as the majority of these products contained intact poly(A) tails and were bound by the poly(A) binding protein. The upstream cleavage products of Malat1 were degraded in the 3' to 5' direction by the exosome complex containing the nuclear exoribonuclease Dis3. The exosome complex containing Dis3 or cytoplasmic Dis3L1 degraded mRNA upstream cleavage products, which were not bound by the 5'-cap binding complex and, consequently, were susceptible to degradation in the 5' to 3' direction by the XRN exoribonucleases.
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Affiliation(s)
- Walt F Lima
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
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140
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Abstract
RNAs have highly complex and dynamic cellular localization patterns. Technologies for imaging RNA in living cells are important for uncovering their function and regulatory pathways. One approach for imaging RNA involves genetically encoding fluorescent RNAs using RNA mimics of green fluorescent protein (GFP). These mimics are RNA aptamers that bind fluorophores resembling those naturally found in GFP and activate their fluorescence. These RNA-fluorophore complexes, including Spinach, Spinach2, and Broccoli, can be used to tag RNAs and to image their localization in living cells. In this article, we describe the generation and optimization of these aptamers, along with strategies for expanding the spectral properties of their associated RNA-fluorophore complexes. We also discuss the structural basis for the fluorescence and photophysical properties of Spinach, and we describe future prospects for designing enhanced RNA-fluorophore complexes with enhanced photostability and increased sensitivity.
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Affiliation(s)
- Mingxu You
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York 10065; ,
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141
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Burgess HM, Mohr I. Cellular 5'-3' mRNA exonuclease Xrn1 controls double-stranded RNA accumulation and anti-viral responses. Cell Host Microbe 2015; 17:332-344. [PMID: 25766294 PMCID: PMC4826345 DOI: 10.1016/j.chom.2015.02.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/23/2014] [Accepted: 01/28/2015] [Indexed: 12/30/2022]
Abstract
By accelerating global mRNA decay, many viruses impair host protein synthesis, limiting host defenses and stimulating virus mRNA translation. Vaccinia virus (VacV) encodes two decapping enzymes (D9, D10) that remove protective 5′ caps on mRNAs, presumably generating substrates for degradation by the host exonuclease Xrn1. Surprisingly, we find VacV infection of Xrn1-depleted cells inhibits protein synthesis, compromising virus growth. These effects are aggravated by D9 deficiency and dependent upon a virus transcription factor required for intermediate and late mRNA biogenesis. Considerable double-stranded RNA (dsRNA) accumulation in Xrn1-depleted cells is accompanied by activation of host dsRNA-responsive defenses controlled by PKR and 2′-5′ oligoadenylate synthetase (OAS), which respectively inactivate the translation initiation factor eIF2 and stimulate RNA cleavage by RNase L. This proceeds despite VacV-encoded PKR and RNase L antagonists being present. Moreover, Xrn1 depletion sensitizes uninfected cells to dsRNA treatment. Thus, Xrn1 is a cellular factor regulating dsRNA accumulation and dsRNA-responsive innate immune effectors. Vaccinia virus (VacV) replication requires the host Xrn1 mRNA decay enzyme The 5′-3′ mRNA exonuclease Xrn1 limits dsRNA accumulation In the absence of Xrn1, host dsRNA-responsive innate immune defenses are activated VacV antagonists of dsRNA-responsive host defenses are Xrn1 dependent
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Affiliation(s)
- Hannah M Burgess
- Department of Microbiology and NYU Cancer Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Ian Mohr
- Department of Microbiology and NYU Cancer Institute, NYU School of Medicine, New York, NY 10016, USA.
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142
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Crenshaw E, Leung BP, Kwok CK, Sharoni M, Olson K, Sebastian NP, Ansaloni S, Schweitzer-Stenner R, Akins MR, Bevilacqua PC, Saunders AJ. Amyloid Precursor Protein Translation Is Regulated by a 3'UTR Guanine Quadruplex. PLoS One 2015; 10:e0143160. [PMID: 26618502 PMCID: PMC4664259 DOI: 10.1371/journal.pone.0143160] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 11/02/2015] [Indexed: 12/13/2022] Open
Abstract
A central event in Alzheimer’s disease is the accumulation of amyloid β (Aβ) peptides generated by the proteolytic cleavage of the amyloid precursor protein (APP). APP overexpression leads to increased Aβ generation and Alzheimer’s disease in humans and altered neuronal migration and increased long term depression in mice. Conversely, reduction of APP expression results in decreased Aβ levels in mice as well as impaired learning and memory and decreased numbers of dendritic spines. Together these findings indicate that therapeutic interventions that aim to restore APP and Aβ levels must do so within an ideal range. To better understand the effects of modulating APP levels, we explored the mechanisms regulating APP expression focusing on post-transcriptional regulation. Such regulation can be mediated by RNA regulatory elements such as guanine quadruplexes (G-quadruplexes), non-canonical structured RNA motifs that affect RNA stability and translation. Via a bioinformatics approach, we identified a candidate G-quadruplex within the APP mRNA in its 3’UTR (untranslated region) at residues 3008–3027 (NM_201414.2). This sequence exhibited characteristics of a parallel G-quadruplex structure as revealed by circular dichroism spectrophotometry. Further, as with other G-quadruplexes, the formation of this structure was dependent on the presence of potassium ions. This G-quadruplex has no apparent role in regulating transcription or mRNA stability as wild type and mutant constructs exhibited equivalent mRNA levels as determined by real time PCR. Instead, we demonstrate that this G-quadruplex negatively regulates APP protein expression using dual luciferase reporter and Western blot analysis. Taken together, our studies reveal post-transcriptional regulation by a 3’UTR G-quadruplex as a novel mechanism regulating APP expression.
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Affiliation(s)
- Ezekiel Crenshaw
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Brian P. Leung
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Chemistry, Drexel University, Philadelphia, PA, United States of America
| | - Chun Kit Kwok
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
- Department of Biochemistry & Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States of America
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michal Sharoni
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Kalee Olson
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
| | - Neeraj P. Sebastian
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Sara Ansaloni
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | | | - Michael R. Akins
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
- Department of Biochemistry & Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States of America
| | - Aleister J. Saunders
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States of America
- * E-mail:
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143
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White MR, Garcin ED. The sweet side of RNA regulation: glyceraldehyde-3-phosphate dehydrogenase as a noncanonical RNA-binding protein. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:53-70. [PMID: 26564736 DOI: 10.1002/wrna.1315] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 01/26/2023]
Abstract
The glycolytic protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has a vast array of extraglycolytic cellular functions, including interactions with nucleic acids. GAPDH has been implicated in the translocation of transfer RNA (tRNA), the regulation of cellular messenger RNA (mRNA) stability and translation, as well as the regulation of replication and gene expression of many single-stranded RNA viruses. A growing body of evidence supports GAPDH-RNA interactions serving as part of a larger coordination between intermediary metabolism and RNA biogenesis. Despite the established role of GAPDH in nucleic acid regulation, it is still unclear how and where GAPDH binds to its RNA targets, highlighted by the absence of any conserved RNA-binding sequences. This review will summarize our current understanding of GAPDH-mediated regulation of RNA function. WIREs RNA 2016, 7:53-70. doi: 10.1002/wrna.1315 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Michael R White
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Elsa D Garcin
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
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144
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Li H, Lee T, Dziubla T, Pi F, Guo S, Xu J, Li C, Haque F, Liang XJ, Guo P. RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications. NANO TODAY 2015; 10:631-655. [PMID: 26770259 PMCID: PMC4707685 DOI: 10.1016/j.nantod.2015.09.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The value of polymers is manifested in their vital use as building blocks in material and life sciences. Ribonucleic acid (RNA) is a polynucleic acid, but its polymeric nature in materials and technological applications is often overlooked due to an impression that RNA is seemingly unstable. Recent findings that certain modifications can make RNA resistant to RNase degradation while retaining its authentic folding property and biological function, and the discovery of ultra-thermostable RNA motifs have adequately addressed the concerns of RNA unstability. RNA can serve as a unique polymeric material to build varieties of nanostructures including nanoparticles, polygons, arrays, bundles, membrane, and microsponges that have potential applications in biomedical and material sciences. Since 2005, more than a thousand publications on RNA nanostructures have been published in diverse fields, indicating a remarkable increase of interest in the emerging field of RNA nanotechnology. In this review, we aim to: delineate the physical and chemical properties of polymers that can be applied to RNA; introduce the unique properties of RNA as a polymer; review the current methods for the construction of RNA nanostructures; describe its applications in material, biomedical and computer sciences; and, discuss the challenges and future prospects in this field.
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Affiliation(s)
- Hui Li
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Taek Lee
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Thomas Dziubla
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Fengmei Pi
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Sijin Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Jing Xu
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Chan Li
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Xing-Jie Liang
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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145
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Oudejans CB. Maternal plasma RNA sequencing. Clin Biochem 2015; 48:942-7. [DOI: 10.1016/j.clinbiochem.2015.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 01/08/2023]
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146
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Siwaszek A, Ukleja M, Dziembowski A. Proteins involved in the degradation of cytoplasmic mRNA in the major eukaryotic model systems. RNA Biol 2015; 11:1122-36. [PMID: 25483043 DOI: 10.4161/rna.34406] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The process of mRNA decay and surveillance is considered to be one of the main posttranscriptional gene expression regulation platforms in eukaryotes. The degradation of stable, protein-coding transcripts is normally initiated by removal of the poly(A) tail followed by 5'-cap hydrolysis and degradation of the remaining mRNA body by Xrn1. Alternatively, the exosome complex degrades mRNA in the 3'>5'direction. The newly discovered uridinylation-dependent pathway, which is present in many different organisms, also seems to play a role in bulk mRNA degradation. Simultaneously, to avoid the synthesis of incorrect proteins, special cellular machinery is responsible for the removal of faulty transcripts via nonsense-mediated, no-go, non-stop or non-functional 18S rRNA decay. This review is focused on the major eukaryotic cytoplasmic mRNA degradation pathways showing many similarities and pointing out main differences between the main model-species: yeast, Drosophila, plants and mammals.
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Affiliation(s)
- Aleksandra Siwaszek
- a Institute of Biochemistry and Biophysics ; Polish Academy of Sciences ; Warsaw , Poland
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147
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Abstract
To fully understand the regulation of gene expression, it is critical to quantitatively define whether and how RNA-binding proteins (RBPs) discriminate between alternative binding sites in RNAs. Here, we describe new methods that measure protein binding to large numbers of RNA variants, and ways to analyse and interpret data obtained by these approaches, including affinity distributions and free energy landscapes. We discuss how the new methodologies and the associated concepts enable the development of inclusive, quantitative models for RNA-protein interactions that transcend the traditional binary classification of RBPs as either specific or nonspecific.
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148
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Yartseva V, Giraldez AJ. The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming. Curr Top Dev Biol 2015; 113:191-232. [PMID: 26358874 DOI: 10.1016/bs.ctdb.2015.07.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular transitions occur at all stages of organismal life from conception to adult regeneration. Changing cellular state involves three main features: activating gene expression necessary to install the new cellular state, modifying the chromatin status to stabilize the new gene expression program, and removing existing gene products to clear out the previous cellular program. The maternal-to-zygotic transition (MZT) is one of the most profound changes in the life of an organism. It involves gene expression remodeling at all levels, including the active clearance of the maternal oocyte program to adopt the embryonic totipotency. In this chapter, we provide an overview of molecular mechanisms driving maternal mRNA clearance during the MZT, describe the developmental consequences of losing components of this gene regulation, and illustrate how remodeling of gene expression during the MZT is common to other cellular transitions with parallels to cellular reprogramming.
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Affiliation(s)
- Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.
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149
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Solich J, Kolasa M, Kusmider M, Pabian P, Faron-Gorecka A, Zurawek D, Szafran-Pilch K, Kedracka-Krok S, Jankowska U, Swiderska B, Dziedzicka-Wasylewska M. Life-long norepinephrine transporter (NET) knock-out leads to the increase in the NET mRNA in brain regions rich in norepinephrine terminals. Eur Neuropsychopharmacol 2015; 25:1099-108. [PMID: 26002194 DOI: 10.1016/j.euroneuro.2015.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 11/16/2022]
Abstract
These studies aimed to identify the genes differentially expressed in the frontal cortex of mice bearing a life-long norepinephrine transporter knock-out (NET-KO) and wild-type animals (WT). Differences in gene expression in the mouse frontal cortex were studied using a whole-genome microarray approach. Using an alternative approach, i.e. RT-PCR (reverse transcription polymerase chain reaction) with primers complementary to various exons of the NET gene, as well as TaqMan arrays, the level of mRNA encoding the NET in other brain regions of the NET-KO mice was also examined. The analyses revealed a group of 92 transcripts (27 genes) that differentiated the NET-KO mice from the WT mice. Surprisingly, the studies have shown that the mRNA encoding NET accumulated in the brain regions rich in norepinephrine nerve endings in the NET-KO mice. Because there is no other source of NET mRNA besides the noradrenergic terminals in the brain regions studied, these results might speak in favor of the presence of mRNA in axon terminals. RNA-Binding Protein Immunoprecipitation approach indicated that mRNA encoding NET was detected in the Ago2 protein/mRNA complex. In addition, the amount of Ago2 protein in the frontal cortex was significantly higher in NET-KO mice as compared with that of the WT animals. These results are important for further characterization of the NET-KO mice, which - besides other merits - might serve as a good model to study the fate of truncated mRNA in neurons.
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Affiliation(s)
- Joanna Solich
- Department of Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland.
| | - Magdalena Kolasa
- Department of Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
| | - Maciej Kusmider
- Department of Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
| | - Paulina Pabian
- Department of Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
| | - Agata Faron-Gorecka
- Department of Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
| | - Dariusz Zurawek
- Department of Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
| | - Kinga Szafran-Pilch
- Department of Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
| | - Sylwia Kedracka-Krok
- Faculty of Biochemistry, Biophysics and Biotechnology of the Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Urszula Jankowska
- Faculty of Biochemistry, Biophysics and Biotechnology of the Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Bianka Swiderska
- Faculty of Biochemistry, Biophysics and Biotechnology of the Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Marta Dziedzicka-Wasylewska
- Department of Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
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150
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Klar J, Schuster J, Khan TN, Jameel M, Mäbert K, Forsberg L, Baig SA, Baig SM, Dahl N. Whole exome sequencing identifies LRP1 as a pathogenic gene in autosomal recessive keratosis pilaris atrophicans. J Med Genet 2015; 52:599-606. [PMID: 26142438 DOI: 10.1136/jmedgenet-2014-102931] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 06/14/2015] [Indexed: 12/28/2022]
Abstract
BACKGROUND Keratosis pilaris atrophicans (KPA) is a group of rare genodermatoses characterised by perifollicular keratosis and inflammation that progresses to atrophy and scars of the facial skin. Keratosis pilaris of extensor areas of limbs is a common associated finding. Most cases with KPA are sporadic and no consistent inheritance pattern has been documented. METHODS A large consanguineous Pakistani pedigree segregating autosomal recessive KPA of a mixed type was subject to autozygosity mapping and whole exome sequencing. Quantification of mRNA and protein levels was performed on fibroblasts from affected individuals. Cellular uptake of the low-density lipoprotein (LDL) receptor-related protein 1 (LRP1) ligand α2-macroglobulin (α(2)M) was quantified using fluorescence confocal microscopy. RESULTS Genetic analyses identified a unique homozygous missense variant (K1245R) in the LRP1 in all affected family members. LRP1 encodes the LRP1, a multifunctional cell surface receptor with endocytic functions that belongs to the LDL receptor family. The LRP1 mRNA and LRP1 protein levels in fibroblasts of affected individuals were markedly reduced when compared with controls. Similarly, the LRP1-mediated cellular uptake of α(2)M was reduced in patient fibroblasts. CONCLUSIONS This is the first report on LRP1 as a pathogenic gene for autosomal recessive KPA and keratosis pilaris. The inflammatory characteristics of the KPA entity in our family suggest a link to the immune-regulatory functions of LRP1.
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Affiliation(s)
- Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Jens Schuster
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Tahir Naeem Khan
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Jameel
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Katrin Mäbert
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Lars Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Shehla Anjum Baig
- Department of Pathology, Children's Hospital, Pakistan Institute of Medical Sciences, (PIMS), Islamabad, Pakistan
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Biomedical Centre, Uppsala, Sweden
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