101
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Donohoe OH, Henshilwood K, Way K, Hakimjavadi R, Stone DM, Walls D. Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs. PLoS One 2015; 10:e0125434. [PMID: 25928140 PMCID: PMC4416013 DOI: 10.1371/journal.pone.0125434] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/17/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.
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Affiliation(s)
- Owen H. Donohoe
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | | | - Keith Way
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom
| | - Roya Hakimjavadi
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | - David M. Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom
| | - Dermot Walls
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
- * E-mail:
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102
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Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJP, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MMG, Blaxter ML, Bourke AFG, Brown MJF, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FCP, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HMG, Leask M, Lockett GA, Mallon EB, Antonio DSM, Marxer M, Meeus I, Moritz RFA, Nair A, Näpflin K, Nissen I, Niu J, Nunes FMF, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZLP, Soares MPM, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KKO, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol 2015; 16:76. [PMID: 25908251 PMCID: PMC4414376 DOI: 10.1186/s13059-015-0623-3] [Citation(s) in RCA: 249] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/10/2015] [Indexed: 12/25/2022] Open
Abstract
Background The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0623-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ben M Sadd
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA. .,Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Seth M Barribeau
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland. .,Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Guy Bloch
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Dirk C de Graaf
- Laboratory of Zoophysiology, Faculty of Sciences, Ghent University, Krijgslaan 281, S2, 9000, Ghent, Belgium.
| | - Peter Dearden
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Christine G Elsik
- Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. .,Department of Biology, Georgetown University, Washington, DC, 20057, USA.
| | - Jürgen Gadau
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
| | - Cornelis J P Grimmelikhuijzen
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Martin Hasselmann
- University of Hohenheim, Institute of Animal Science, Garbenstrasse 17, 70599, Stuttgart, Germany.
| | - Jeffrey D Lozier
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA.
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Eckart Stolle
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Matthias Van Vaerenbergh
- Laboratory of Zoophysiology, Faculty of Sciences, Ghent University, Krijgslaan 281, S2, 9000, Ghent, Belgium.
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
| | - Erich Bornberg-Bauer
- Westfalian Wilhelms University, Institute of Evolution and Biodiversity, Huefferstrasse 1, 48149, Muenster, Germany.
| | - Steffen Klasberg
- Westfalian Wilhelms University, Institute of Evolution and Biodiversity, Huefferstrasse 1, 48149, Muenster, Germany.
| | - Anna K Bennett
- Department of Biology, Georgetown University, Washington, DC, 20057, USA.
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Katharina Hoff
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Monica Munoz-Torres
- Department of Biology, Georgetown University, Washington, DC, 20057, USA. .,Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Terence Murphy
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Gro V Amdam
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Food Science, N-1432, Aas, Norway.
| | - Matthew Beckers
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Martin Beye
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Matthias Biewer
- University of Hohenheim, Institute of Animal Science, Garbenstrasse 17, 70599, Stuttgart, Germany. .,University of Cologne, Institute of Genetics, Cologne, Germany.
| | - Márcia M G Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, Brazil.
| | - Mark L Blaxter
- Institute of Evolutionary Biology and Edinburgh Genomics, The Ashworth Laboratories, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, London, UK.
| | - Severine D Buechel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Rossanah Cameron
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Kaat Cappelle
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - James C Carolan
- Maynooth University Department of Biology, Maynooth University, Co, Kildare, Ireland.
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Kate L Ciborowski
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | | | - Thomas J Colgan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland.
| | - David H Collins
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Stephanie Dreier
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Louis du Plessis
- Theoretical Biology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Computational Evolution, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Elizabeth Duncan
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Silvio Erler
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Jay Evans
- USDA-ARS Bee Research Laboratory, Maryland, USA.
| | - Tiago Falcon
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Kevin Flores
- Center for Research in Scientific Computation, North Carolina State University Raleigh, Raleigh, NC, USA.
| | - Flávia C P Freitas
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Taro Fuchikawa
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. .,Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Tanja Gempe
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Sophie Helbing
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Fernanda C Humann
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, 15991-502, Matão, Brazil.
| | - Frano Irvine
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | | | - Claire E Johnson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Reed M Johnson
- Department of Entomology, The Ohio State University, Wooster, OH, 44791, USA.
| | - Andrew K Jones
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.
| | - Jonathan H Kidner
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Vasco Koch
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Arian Köhler
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - F Bernhard Kraus
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,Department of Laboratory Medicine, University Hospital Halle (Saale), Halle, Germany.
| | - H Michael G Lattorff
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Megan Leask
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | | | - Eamonn B Mallon
- Department of Biology, University of Leicester, Leicester, UK.
| | - David S Marco Antonio
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Monika Marxer
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Robin F A Moritz
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Ajay Nair
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Kathrin Näpflin
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Inga Nissen
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Jinzhi Niu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Francis M F Nunes
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, 13565-905, São Carlos, Brazil.
| | | | - Amy Osborne
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Marianne Otte
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Daniel G Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, 14884-900, Jaboticabal, Brazil.
| | - Nina Rossié
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27403, USA.
| | - Carolina G Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Regula Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Björn D Schmitt
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Christina Schulte
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Zilá L P Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, Brazil.
| | - Michelle P M Soares
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Luc Swevers
- Institute of Biosciences & Applications, National Center for Scientific Research Demokritos, Athens, Greece.
| | | | - Florian Wolschin
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Food Science, N-1432, Aas, Norway.
| | - Na Yu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland.
| | - Peshtewani K Aqrawi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kerstin P Blankenburg
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Marcus Coyle
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Liezl Francisco
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Michael Holder
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Matthew E Hudson
- Department of Crop Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - LaRonda Jackson
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Joy Jayaseelan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Vandita Joshi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Christie Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Robert Mata
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Tittu Mathew
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Irene F Newsham
- Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 2, Houston, TX, 77025, USA.
| | - Robin Ngo
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Geoffrey Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Christopher Pham
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Ling-Ling Pu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Nehad Saada
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - DeNard Simmons
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Aarti Venkat
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Yuan-Qing Wu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Griet Debyser
- Laboratory of Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Bart Devreese
- Laboratory of Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Claire Asher
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Julie Blommaert
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Ariel D Chipman
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Lars Chittka
- Department of Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Bertrand Fouks
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27403, USA.
| | - Jisheng Liu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium. .,School of Life Sciences, Guangzhou University, Guangzhou, China.
| | - Meaghan P O'Neill
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Seirian Sumner
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Steven E Scherer
- School of Life Sciences, Guangzhou University, Guangzhou, China.
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, Department of Entomology, Neuroscience Program, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Paul Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
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103
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Trieu TA, Calo S, Nicolás FE, Vila A, Moxon S, Dalmay T, Torres-Martínez S, Garre V, Ruiz-Vázquez RM. A non-canonical RNA silencing pathway promotes mRNA degradation in basal Fungi. PLoS Genet 2015; 11:e1005168. [PMID: 25875805 PMCID: PMC4395119 DOI: 10.1371/journal.pgen.1005168] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/20/2015] [Indexed: 12/04/2022] Open
Abstract
The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing. Most eukaryotic organisms produce different classes of endogenous small RNA (esRNA) molecules that suppress gene expression through RNA interference (RNAi) pathways. These pathways, which may differ among organisms, are normally involved in genome defense, heterochromatin formation and regulation of genes involved in multiple cellular functions. In the basal fungus Mucor circinelloides, an opportunistic human pathogen, we previously demonstrated that biogenesis of a large group of esRNA molecules requires a basic RNAi machinery consisting of a Dicer-like protein, an Argonaute nuclease and two RNA-dependent RNA polymerases. This canonical dicer-dependent pathway regulates different cellular processes, such as vegetative sporulation. Besides those esRNAs generated by this canonical RNAi pathway, we have identified a new rdrp-dependent dicer-independent esRNA class. These esRNAs are produced by a degradation pathway in which the RdRP proteins signal specific transcripts that will be degraded by a newly identified RNase. This RNase, named R3B2, presents unique domain architecture, can only be found in basal fungi and it is also involved in the canonical dicer-dependent RNAi pathway. Our results expand the role of RdRPs in gene silencing and reveal the involvement of these proteins in a new RNA degradation process that could represent the first step in the evolution of RNAi.
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Affiliation(s)
- Trung Anh Trieu
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Silvia Calo
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | | | - Ana Vila
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Simon Moxon
- The Genome Analysis Centre, University of East Anglia, Norwich, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Victoriano Garre
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Rosa M. Ruiz-Vázquez
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
- * E-mail:
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104
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Xu P, Billmeier M, Mohorianu I, Green D, Fraser WD, Dalmay T. An improved protocol for small RNA library construction using High Definition adapters. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/mngs-2015-0001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractNext generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems. However, cDNA libraries of sRNAs are biased for molecules that are ligated to adapters more or less efficiently than other molecules. One approach to reduce this ligation bias is to use a pool of adapters instead of a single adapter sequence, which allows many sRNAs to be ligated efficiently. We previously developed High Definition (HD) adapters for the Illumina sequencing platform, which contain degenerate nucleotides at the ligating ends of the adapters. However, the current commercial kits produced a large amount of 5’ adapter – 3’ adapter ligation product without the cDNA insert when HD adapters were used to replace the kit adapters. Here, we report a protocol to generate sRNA libraries using HD adapters with greatly reduced proportion of adapter-adapter products due to the degradation of nonligated 3’ adapters. The libraries can be completed within two days and can be used for various biological and clinical samples. As examples for using this protocol, we constructed sRNA libraries using total RNA extracted from cultured mammalian cells and plant leaf tissue.
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105
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Asgari S. Regulatory role of cellular and viral microRNAs in insect-virus interactions. CURRENT OPINION IN INSECT SCIENCE 2015; 8:104-110. [PMID: 32846658 DOI: 10.1016/j.cois.2014.12.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/17/2014] [Accepted: 12/17/2014] [Indexed: 06/11/2023]
Abstract
The discovery of microRNAs (miRNAs) and their functions has led to a paradigm shift in our understanding of the regulation of gene expression, adding an extra layer of complexity for the mechanisms of gene expression. Both cellular and virus encoded miRNAs play important roles in virus-host interactions that may affect virus replication and the outcome of infection. Recent developments in RNA-seq platforms and bioinformatics tools have accelerated the discovery of miRNAs, their targets, and a myriad of associated research in various species. Here, recent findings and developments in miRNA research pertinent to insect host-virus interactions are reviewed and analyzed.
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Affiliation(s)
- Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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106
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Deep sequencing of virus-derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscapes of a plant virus population. J Virol 2015; 89:4760-9. [PMID: 25673712 DOI: 10.1128/jvi.03685-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED RNA viruses exist within a host as a population of mutant sequences, often referred to as quasispecies. Within a host, sequences of RNA viruses constitute several distinct but interconnected pools, such as RNA packed in viral particles, double-stranded RNA, and virus-derived small interfering RNAs. We aimed to test if the same representation of within-host viral population structure could be obtained by sequencing different viral sequence pools. Using ultradeep Illumina sequencing, the diversity of two coexisting Potato virus Y sequence pools present within a plant was investigated: RNA isolated from viral particles and virus-derived small interfering RNAs (the derivatives of a plant RNA silencing mechanism). The mutational landscape of the within-host virus population was highly similar between both pools, with no notable hotspots across the viral genome. Notably, all of the single-nucleotide polymorphisms with a frequency of higher than 1.6% were found in both pools. Some unique single-nucleotide polymorphisms (SNPs) with very low frequencies were found in each of the pools, with more of them occurring in the small RNA (sRNA) pool, possibly arising through genetic drift in localized virus populations within a plant and the errors introduced during the amplification of silencing signal. Sequencing of the viral particle pool enhanced the efficiency of consensus viral genome sequence reconstruction. Nonhomologous recombinations were commonly detected in the viral particle pool, with a hot spot in the 3' untranslated and coat protein regions of the genome. We stress that they present an important but often overlooked aspect of virus population diversity. IMPORTANCE This study is the most comprehensive whole-genome characterization of a within-plant virus population to date and the first study comparing diversity of different pools of viral sequences within a host. We show that both virus-derived small RNAs and RNA from viral particles could be used for diversity assessment of within-plant virus population, since they show a highly congruent portrayal of the virus mutational landscape within a plant. The study is an important baseline for future studies of virus population dynamics, for example, during the adaptation to a new host. The comparison of the two virus sequence enrichment techniques, sequencing of virus-derived small interfering RNAs and RNA from purified viral particles, shows the strength of the latter for the detection of recombinant viral genomes and reconstruction of complete consensus viral genome sequence.
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107
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Pirovano W, Miozzi L, Boetzer M, Pantaleo V. Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population. Front Microbiol 2015; 5:790. [PMID: 25674078 PMCID: PMC4307218 DOI: 10.3389/fmicb.2014.00790] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022] Open
Abstract
Over the past years deep sequencing experiments have opened novel doors to reconstruct viral populations in a high-throughput and cost-effective manner. Currently a substantial number of studies have been performed which employ next generation sequencing techniques to either analyze known viruses by means of a reference-guided approach or to discover novel viruses using a de novo-based strategy. Taking advantage of the well-known Cymbidium ringspot virus we have carried out a comparison of different bioinformatics tools to reconstruct the viral genome based on 21–27 nt short (s)RNA sequencing with the aim to identify the most efficient pipeline. The same approach was applied to a population of plants constituting an ancient variety of Cicer arietinum with red seeds. Among the discovered viruses, we describe the presence of a Tobamovirus referring to the Tomato mottle mosaic virus (NC_022230), which was not yet observed on C. arietinum nor revealed in Europe and a viroid referring to Hop stunt viroid (NC_001351.1) never reported in chickpea. Notably, a reference sequence guided approach appeared the most efficient in such kind of investigation. Instead, the de novo assembly reached a non-appreciable coverage although the most prominent viral species could still be identified. Advantages and limitations of viral metagenomics analysis using sRNAs are discussed.
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Affiliation(s)
- Walter Pirovano
- Genome Analysis and Technology Department, BaseClear B. V. Leiden, Netherlands
| | - Laura Miozzi
- Institute for Sustainable Plant Protection of National Research Council Torino, Italy
| | - Marten Boetzer
- Genome Analysis and Technology Department, BaseClear B. V. Leiden, Netherlands
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection of National Research Council, Bari Research Unit Bari, Italy
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108
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Kang W, Friedländer MR. Computational Prediction of miRNA Genes from Small RNA Sequencing Data. Front Bioeng Biotechnol 2015; 3:7. [PMID: 25674563 PMCID: PMC4306309 DOI: 10.3389/fbioe.2015.00007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/07/2015] [Indexed: 01/19/2023] Open
Abstract
Next-generation sequencing now for the first time allows researchers to gage the depth and variation of entire transcriptomes. However, now as rare transcripts can be detected that are present in cells at single copies, more advanced computational tools are needed to accurately annotate and profile them. microRNAs (miRNAs) are 22 nucleotide small RNAs (sRNAs) that post-transcriptionally reduce the output of protein coding genes. They have established roles in numerous biological processes, including cancers and other diseases. During miRNA biogenesis, the sRNAs are sequentially cleaved from precursor molecules that have a characteristic hairpin RNA structure. The vast majority of new miRNA genes that are discovered are mined from small RNA sequencing (sRNA-seq), which can detect more than a billion RNAs in a single run. However, given that many of the detected RNAs are degradation products from all types of transcripts, the accurate identification of miRNAs remain a non-trivial computational problem. Here, we review the tools available to predict animal miRNAs from sRNA sequencing data. We present tools for generalist and specialist use cases, including prediction from massively pooled data or in species without reference genome. We also present wet-lab methods used to validate predicted miRNAs, and approaches to computationally benchmark prediction accuracy. For each tool, we reference validation experiments and benchmarking efforts. Last, we discuss the future of the field.
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Affiliation(s)
- Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University , Stockholm , Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University , Stockholm , Sweden
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109
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Copy number variable microRNAs in schizophrenia and their neurodevelopmental gene targets. Biol Psychiatry 2015; 77:158-66. [PMID: 25034949 PMCID: PMC4464826 DOI: 10.1016/j.biopsych.2014.05.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/16/2014] [Accepted: 05/18/2014] [Indexed: 01/12/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are key regulators of gene expression in the human genome and may contribute to risk for neuropsychiatric disorders. miRNAs play an acknowledged role in the strongest of genetic risk factors for schizophrenia, 22q11.2 deletions. We hypothesized that in schizophrenia there would be an enrichment of other rare copy number variants (CNVs) that overlap miRNAs. METHODS Using high-resolution genome-wide microarrays and rigorous methods, we compared the miRNA content of rare CNVs in well-characterized cohorts of schizophrenia cases (n = 420) and comparison subjects, excluding 22q11.2 CNVs. We also performed a gene-set enrichment analysis of the predicted miRNA target genes. RESULTS The schizophrenia group was enriched for the proportion of individuals with a rare CNV overlapping a miRNA (3.29-fold increase over comparison subjects, p < .0001). The presence of a rare CNV overlapping a miRNA remained a significant predictor of schizophrenia case status (p = .0072) in a multivariate logistic regression model correcting for total CNV size. In contrast, comparable analyses correcting for CNV size showed no enrichment of rare CNVs overlapping protein-coding genes. A gene-set enrichment analysis indicated that predicted target genes of recurrent CNV-overlapped miRNAs in schizophrenia may be functionally enriched for neurodevelopmental processes, including axonogenesis and neuron projection development. Predicted gene targets driving these results included CAPRIN1, NEDD4, NTRK2, PAK2, RHOA, and SYNGAP1. CONCLUSIONS These data are the first to demonstrate a genome-wide role for CNVs overlapping miRNAs in the genetic risk for schizophrenia. The results provide support for an expanded multihit model of causation, with potential implications for miRNA-based therapeutics.
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110
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Abstract
Viruses are obligate intracellular entities that infect all forms of life. In plants, invading viral nucleic acids trigger RNA silencing machinery and it results in the accumulation of viral short interfering RNAs (v-siRNAs). The study of v-siRNAs population in biological samples has become a major part of many research projects aiming to identify viruses infecting them, including unknown viruses, even at extremely low titer. Currently, siRNA populations are investigated by high-throughput sequencing approaches, which generate very large data sets. The major difficulty in these studies is to properly analyze such huge amount of data. In this regard, easy-to-use bioinformatics tools to groom and decipher siRNA libraries and to draw out v-siRNAs are needed. Here we describe a workflow, which permit users with little experience in bioinformatics to draw out v-siRNAs from raw data sequences obtained by Illumina technology. Such pipeline has been released in the context of Galaxy, an open source Web-based platform for bioinformatics analyses.
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Affiliation(s)
- Laura Miozzi
- Institute for Sustainable Plant Protection of CNR, Strada delle Cacce 73, Turin, Italy
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111
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Heyer EE, Ozadam H, Ricci EP, Cenik C, Moore MJ. An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments. Nucleic Acids Res 2014; 43:e2. [PMID: 25505164 PMCID: PMC4288154 DOI: 10.1093/nar/gku1235] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Deep sequencing of strand-specific cDNA libraries is now a ubiquitous tool for identifying and quantifying RNAs in diverse sample types. The accuracy of conclusions drawn from these analyses depends on precise and quantitative conversion of the RNA sample into a DNA library suitable for sequencing. Here, we describe an optimized method of preparing strand-specific RNA deep sequencing libraries from small RNAs and variably sized RNA fragments obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs. Our approach works across a wide range of input amounts (400 pg to 200 ng), is easy to follow and produces a library in 2–3 days at relatively low reagent cost, all while giving the user complete control over every step. Because all enzymatic reactions were optimized and driven to apparent completion, sequence diversity and species abundance in the input sample are well preserved.
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Affiliation(s)
- Erin E Heyer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Hakan Ozadam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Emiliano P Ricci
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Can Cenik
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Melissa J Moore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
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112
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Rajeswaran R, Golyaev V, Seguin J, Zvereva AS, Farinelli L, Pooggin MM. Interactions of Rice tungro bacilliform pararetrovirus and its protein P4 with plant RNA-silencing machinery. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:1370-8. [PMID: 25122481 DOI: 10.1094/mpmi-07-14-0201-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Small interfering RNA (siRNA)-directed gene silencing plays a major role in antiviral defense. Virus-derived siRNAs inhibit viral replication in infected cells and potentially move to neighboring cells, immunizing them from incoming virus. Viruses have evolved various ways to evade and suppress siRNA production or action. Here, we show that 21-, 22-, and 24-nucleotide (nt) viral siRNAs together constitute up to 19% of total small RNA population of Oryza sativa plants infected with Rice tungro bacilliform virus (RTBV) and cover both strands of the RTBV DNA genome. However, viral siRNA hotspots are restricted to a short noncoding region between transcription and reverse-transcription start sites. This region generates double-stranded RNA (dsRNA) precursors of siRNAs and, in pregenomic RNA, forms a stable secondary structure likely inaccessible to siRNA-directed cleavage. In transient assays, RTBV protein P4 suppressed cell-to-cell spread of silencing but enhanced cell-autonomous silencing, which correlated with reduced 21-nt siRNA levels and increased 22-nt siRNA levels. Our findings imply that RTBV generates decoy dsRNA that restricts siRNA production to the structured noncoding region and thereby protects other regions of the viral genome from repressive action of siRNAs, while the viral protein P4 interferes with cell-to-cell spread of antiviral silencing.
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113
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Merico D, Costain G, Butcher NJ, Warnica W, Ogura L, Alfred SE, Brzustowicz LM, Bassett AS. MicroRNA Dysregulation, Gene Networks, and Risk for Schizophrenia in 22q11.2 Deletion Syndrome. Front Neurol 2014; 5:238. [PMID: 25484875 PMCID: PMC4240070 DOI: 10.3389/fneur.2014.00238] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/02/2014] [Indexed: 01/20/2023] Open
Abstract
The role of microRNAs (miRNAs) in the etiology of schizophrenia is increasingly recognized. Microdeletions at chromosome 22q11.2 are recurrent structural variants that impart a high risk for schizophrenia and are found in up to 1% of all patients with schizophrenia. The 22q11.2 deletion region overlaps gene DGCR8, encoding a subunit of the miRNA microprocessor complex. We identified miRNAs overlapped by the 22q11.2 microdeletion and for the first time investigated their predicted target genes, and those implicated by DGCR8, to identify targets that may be involved in the risk for schizophrenia. The 22q11.2 region encompasses seven validated or putative miRNA genes. Employing two standard prediction tools, we generated sets of predicted target genes. Functional enrichment profiles of the 22q11.2 region miRNA target genes suggested a role in neuronal processes and broader developmental pathways. We then constructed a protein interaction network of schizophrenia candidate genes and interaction partners relevant to brain function, independent of the 22q11.2 region miRNA mechanisms. We found that the predicted gene targets of the 22q11.2 deletion miRNAs, and targets of the genome-wide miRNAs predicted to be dysregulated by DGCR8 hemizygosity, were significantly represented in this schizophrenia network. The findings provide new insights into the pathway from 22q11.2 deletion to expression of schizophrenia, and suggest that hemizygosity of the 22q11.2 region may have downstream effects implicating genes elsewhere in the genome that are relevant to the general schizophrenia population. These data also provide further support for the notion that robust genetic findings in schizophrenia may converge on a reasonable number of final pathways.
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Affiliation(s)
- Daniele Merico
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON , Canada
| | - Gregory Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health , Toronto, ON , Canada
| | - Nancy J Butcher
- Clinical Genetics Research Program, Centre for Addiction and Mental Health , Toronto, ON , Canada ; Institute of Medical Science, University of Toronto , Toronto, ON , Canada
| | - William Warnica
- Clinical Genetics Research Program, Centre for Addiction and Mental Health , Toronto, ON , Canada
| | - Lucas Ogura
- Clinical Genetics Research Program, Centre for Addiction and Mental Health , Toronto, ON , Canada
| | - Simon E Alfred
- Clinical Genetics Research Program, Centre for Addiction and Mental Health , Toronto, ON , Canada
| | - Linda M Brzustowicz
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University , Piscataway, NJ , USA
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health , Toronto, ON , Canada ; Institute of Medical Science, University of Toronto , Toronto, ON , Canada ; The Dalglish Family Hearts and Minds Clinic for 22q11.2 Deletion Syndrome, Toronto General Hospital, University Health Network , Toronto, ON , Canada ; Department of Psychiatry, Toronto General Research Institute, University Health Network , Toronto, ON , Canada ; Department of Psychiatry, University of Toronto , Toronto, ON , Canada
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114
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Beatty M, Guduric-Fuchs J, Brown E, Bridgett S, Chakravarthy U, Hogg RE, Simpson DA. Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma. BMC Genomics 2014; 15:933. [PMID: 25344700 PMCID: PMC4230795 DOI: 10.1186/1471-2164-15-933] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 10/16/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived. RESULTS Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin. In addition, extremely abundant small RNAs derived from human Y RNAs were detected. CONCLUSIONS A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.
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Affiliation(s)
| | | | | | | | | | | | - David Arthur Simpson
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.
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115
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Necsulea A, Kaessmann H. Evolutionary dynamics of coding and non-coding transcriptomes. Nat Rev Genet 2014; 15:734-48. [PMID: 25297727 DOI: 10.1038/nrg3802] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive assessments of transcript sequences and expression levels. Here, we review the initial wave of the new generation of comparative transcriptomic studies in mammals and vertebrate outgroup species in the context of earlier work. Together with various large-scale genomic and epigenomic data, these studies have unveiled commonalities and differences in the dynamics of gene expression evolution for various types of coding and non-coding genes across mammalian lineages, organs, developmental stages, chromosomes and sexes. They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes.
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Affiliation(s)
- Anamaria Necsulea
- Laboratory of Developmental Genomics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Henrik Kaessmann
- 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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116
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Abstract
Across taxa, female behavior and physiology change significantly following the receipt of ejaculate molecules during mating. For example, receipt of sex peptide (SP) in female Drosophila melanogaster significantly alters female receptivity, egg production, lifespan, hormone levels, immunity, sleep, and feeding patterns. These changes are underpinned by distinct tissue- and time-specific changes in diverse sets of mRNAs. However, little is yet known about the regulation of these gene expression changes, and hence the potential role of microRNAs (miRNAs), in female postmating responses. A preliminary screen of genomic responses in females to receipt of SP suggested that there were changes in the expression of several miRNAs. Here we tested directly whether females lacking four of the candidate miRNAs highlighted (miR-279, miR-317, miR-278, and miR-184) showed altered fecundity, receptivity, and lifespan responses to receipt of SP, when mated once or continually to SP null or control males. The results showed that miRNA-lacking females mated to SP null males exhibited altered receptivity, but not reproductive output, in comparison to controls. However, these effects interacted significantly with the genetic background of the miRNA-lacking females. No significant survival effects were observed in miRNA-lacking females housed continually with SP null or control males. However, continual exposure to control males that transferred SP resulted in significantly higher variation in miRNA-lacking female lifespan than did continual exposure to SP null males. The results provide the first insight into the effects and importance of miRNAs in regulating postmating responses in females.
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117
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Zhang Z, Lee JE, Riemondy K, Anderson EM, Yi R. High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing. Genome Biol 2014; 14:R109. [PMID: 24098942 PMCID: PMC3983620 DOI: 10.1186/gb-2013-14-10-r109] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/25/2013] [Indexed: 01/28/2023] Open
Abstract
Small RNA cloning and sequencing is uniquely positioned as a genome-wide approach to quantify miRNAs with single-nucleotide resolution. However, significant biases introduced by RNA ligation in current protocols lead to inaccurate miRNA quantification by 1000-fold. Here we report an RNA cloning method that achieves over 95% efficiency for both 5′ and 3′ ligations. It achieves accurate quantification of synthetic miRNAs with less than two-fold deviation from the anticipated value and over a dynamic range of four orders of magnitude. Taken together, this high-efficiency RNA cloning method permits accurate genome-wide miRNA profiling from total RNAs.
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118
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Schnettler E, Tykalová H, Watson M, Sharma M, Sterken MG, Obbard DJ, Lewis SH, McFarlane M, Bell-Sakyi L, Barry G, Weisheit S, Best SM, Kuhn RJ, Pijlman GP, Chase-Topping ME, Gould EA, Grubhoffer L, Fazakerley JK, Kohl A. Induction and suppression of tick cell antiviral RNAi responses by tick-borne flaviviruses. Nucleic Acids Res 2014; 42:9436-46. [PMID: 25053841 PMCID: PMC4132761 DOI: 10.1093/nar/gku657] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Arboviruses are transmitted by distantly related arthropod vectors such as mosquitoes (class Insecta) and ticks (class Arachnida). RNA interference (RNAi) is the major antiviral mechanism in arthropods against arboviruses. Unlike in mosquitoes, tick antiviral RNAi is not understood, although this information is important to compare arbovirus/host interactions in different classes of arbovirus vectos. Using an Ixodes scapularis-derived cell line, key Argonaute proteins involved in RNAi and the response against tick-borne Langat virus (Flaviviridae) replication were identified and phylogenetic relationships characterized. Analysis of small RNAs in infected cells showed the production of virus-derived small interfering RNAs (viRNAs), which are key molecules of the antiviral RNAi response. Importantly, viRNAs were longer (22 nucleotides) than those from other arbovirus vectors and mapped at highest frequency to the termini of the viral genome, as opposed to mosquito-borne flaviviruses. Moreover, tick-borne flaviviruses expressed subgenomic flavivirus RNAs that interfere with tick RNAi. Our results characterize the antiviral RNAi response in tick cells including phylogenetic analysis of genes encoding antiviral proteins, and viral interference with this pathway. This shows important differences in antiviral RNAi between the two major classes of arbovirus vectors, and our data broadens our understanding of arthropod antiviral RNAi.
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Affiliation(s)
- Esther Schnettler
- MRC - University of Glasgow Centre for Virus Research, Glasgow G11 5JR, UK The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Hana Tykalová
- Faculty of Science, University of South Bohemia and Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Mayuri Sharma
- Markey Centre for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette IN 47907, USA
| | - Mark G Sterken
- Laboratory of Virology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Darren J Obbard
- Institute of Evolutionary Biology and Centre for Infection Immunity and Evolution, University of Edinburgh, EH9 3JT, UK
| | - Samuel H Lewis
- Institute of Evolutionary Biology and Centre for Infection Immunity and Evolution, University of Edinburgh, EH9 3JT, UK
| | - Melanie McFarlane
- MRC - University of Glasgow Centre for Virus Research, Glasgow G11 5JR, UK
| | - Lesley Bell-Sakyi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Gerald Barry
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Sabine Weisheit
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Sonja M Best
- Innate Immunity and Pathogenesis Unit, Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Richard J Kuhn
- Markey Centre for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette IN 47907, USA
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | | | - Ernest A Gould
- Unité des Virus Emergents, Faculté de Médicine Timone, 13385 Marseille Cedex 05, France Centre for Hydrology and Ecology, Maclean Building, Oxon OX10 8BB, UK
| | - Libor Grubhoffer
- Faculty of Science, University of South Bohemia and Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
| | - John K Fazakerley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Alain Kohl
- MRC - University of Glasgow Centre for Virus Research, Glasgow G11 5JR, UK The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
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119
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Xu P, Mohorianu I, Yang L, Zhao H, Gao Z, Dalmay T. Small RNA profile in moso bamboo root and leaf obtained by high definition adapters. PLoS One 2014; 9:e103590. [PMID: 25079776 PMCID: PMC4117519 DOI: 10.1371/journal.pone.0103590] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/30/2014] [Indexed: 11/23/2022] Open
Abstract
Moso bamboo (Phyllostachy heterocycla cv. pubescens L.) is an economically important fast-growing tree. In order to gain better understanding of gene expression regulation in this important species we used next generation sequencing to profile small RNAs in leaf and roots of young seedlings. Since standard kits to produce cDNA of small RNAs are biased for certain small RNAs, we used High Definition adapters that reduce ligation bias. We identified and experimentally validated five new microRNAs and a few other small non-coding RNAs that were not microRNAs. The biological implication of microRNA expression levels and targets of microRNAs are discussed.
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Affiliation(s)
- Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Li Yang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Centre for Bamboo, Rattan, Beijing, China
| | - Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Centre for Bamboo, Rattan, Beijing, China
| | - Zhimin Gao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Centre for Bamboo, Rattan, Beijing, China
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- * E-mail:
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120
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Sterling CH, Veksler-Lublinsky I, Ambros V. An efficient and sensitive method for preparing cDNA libraries from scarce biological samples. Nucleic Acids Res 2014; 43:e1. [PMID: 25056322 PMCID: PMC4288208 DOI: 10.1093/nar/gku637] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in tissues and in biofluids has grown substantially with the findings that small RNAs can serve as indicators of biological conditions and disease states. Here we describe a novel and straightforward method to clone cDNA libraries from small quantities of input RNA. This method permits the generation of cDNA libraries from sub-picogram quantities of RNA robustly, efficiently and reproducibly. We demonstrate that the method provides a significant improvement in sensitivity compared to previous cloning methods while maintaining reproducible identification of diverse small RNA species. This method should have widespread applications in a variety of contexts, including biomarker discovery from scarce samples of human tissue or body fluids.
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Affiliation(s)
- Catherine H Sterling
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Isana Veksler-Lublinsky
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
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121
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Jackson TJ, Spriggs RV, Burgoyne NJ, Jones C, Willis AE. Evaluating bias-reducing protocols for RNA sequencing library preparation. BMC Genomics 2014; 15:569. [PMID: 25001197 PMCID: PMC4117970 DOI: 10.1186/1471-2164-15-569] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/26/2014] [Indexed: 12/17/2022] Open
Abstract
Background Next-generation sequencing does not yield fully unbiased estimates for read abundance, which may impact on the conclusions that can be drawn from sequencing data. The ligation step in RNA sequencing library generation is a known source of bias, motivating developments in enzyme technology and library construction protocols. We present the first comparison of the standard duplex adaptor protocol supplied by Life Technologies for use on the Ion Torrent PGM with an alternate single adaptor approach involving CircLigase (CircLig protocol). A correlation between over-representation in sequenced libraries and degree of secondary structure has been reported previously, therefore we also investigated whether bias could be reduced by ligation with an enzyme that functions at a temperature not permissive for such structure. Results A pool of small RNA fragments of known composition was converted into a sequencing library using one of three protocols and sequenced on an Ion Torrent PGM. The CircLig protocol resulted in less over-representation of specific sequences than the standard protocol. Over-represented sequences are more likely to be predicted to have secondary structure and to co-fold with adaptor sequences. However, use of the thermostable ligase Methanobacterium thermoautotrophicum RNA ligase K97A (Mth K97A) was not sufficient to reduce bias. Conclusions The single adaptor CircLigase-based approach significantly reduces, but does not eliminate, bias in Ion Torrent data. Ligases that function at temperatures to remove the possible influence of secondary structure on library generation may be of value, although Mth K97A is not effective in this case. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-569) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas J Jackson
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, UK.
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122
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Warnefors M, Liechti A, Halbert J, Valloton D, Kaessmann H. Conserved microRNA editing in mammalian evolution, development and disease. Genome Biol 2014; 15:R83. [PMID: 24964909 PMCID: PMC4197820 DOI: 10.1186/gb-2014-15-6-r83] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/25/2014] [Indexed: 01/31/2023] Open
Abstract
Background Mammalian microRNAs (miRNAs) are sometimes subject to adenosine-to-inosine RNA editing, which can lead to dramatic changes in miRNA target specificity or expression levels. However, although a few miRNAs are known to be edited at identical positions in human and mouse, the evolution of miRNA editing has not been investigated in detail. In this study, we identify conserved miRNA editing events in a range of mammalian and non-mammalian species. Results We demonstrate deep conservation of several site-specific miRNA editing events, including two that date back to the common ancestor of mammals and bony fishes some 450 million years ago. We also find evidence of a recent expansion of an edited miRNA family in placental mammals and show that editing of these miRNAs is associated with changes in target mRNA expression during primate development and aging. While global patterns of miRNA editing tend to be conserved across species, we observe substantial variation in editing frequencies depending on tissue, age and disease state: editing is more frequent in neural tissues compared to heart, kidney and testis; in older compared to younger individuals; and in samples from healthy tissues compared to tumors, which together suggests that miRNA editing might be associated with a reduced rate of cell proliferation. Conclusions Our results show that site-specific miRNA editing is an evolutionarily conserved mechanism, which increases the functional diversity of mammalian miRNA transcriptomes. Furthermore, we find that although miRNA editing is rare compared to editing of long RNAs, miRNAs are greatly overrepresented among conserved editing targets.
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123
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Nassirpour R, Mathur S, Gosink MM, Li Y, Shoieb AM, Wood J, O'Neil SP, Homer BL, Whiteley LO. Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms. BMC Genomics 2014; 15:485. [PMID: 24942259 PMCID: PMC4079956 DOI: 10.1186/1471-2164-15-485] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 06/09/2014] [Indexed: 12/17/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small, non-coding RNAs that regulate protein levels post-transcriptionally. miRNAs play important regulatory roles in many cellular processes and have been implicated in several diseases. Recent studies have reported significant levels of miRNAs in a variety of body fluids, raising the possibility that miRNAs could serve as useful biomarkers. Next-generation sequencing (NGS) is increasingly employed in biomedical investigations. Although concordance between this platform and qRT-PCR based assays has been reported in high quality specimens, information is lacking on comparisons in biofluids especially urine. Here we describe the changes in miRNA expression patterns in a rodent model of renal tubular injury (gentamicin). Our aim is to compare RNA sequencing and qPCR based miRNA profiling in urine specimen from control and rats with confirmed tubular injury. Results Our preliminary examination of the concordance between miRNA-seq and qRT-PCR in urine specimen suggests minimal agreement between platforms probably due to the differences in sensitivity. Our results suggest that although miRNA-seq has superior specificity, it may not detect low abundant miRNAs in urine samples. Specifically, miRNA-seq did not detect some sequences which were identified by qRT-PCR. On the other hand, the qRT-PCR analysis was not able to detect the miRNA isoforms, which made up the majority of miRNA changes detected by NGS. Conclusions To our knowledge, this is the first time that miRNA profiling platforms including NGS have been compared in urine specimen. miRNAs identified by both platforms, let-7d, miR-203, and miR-320, may potentially serve as promising novel urinary biomarkers for drug induced renal tubular epithelial injury.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Laurence O Whiteley
- Drug Safety, Pfizer Worldwide Research and Development, 1 Burtt Rd, Andover, MA 01810, USA.
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124
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Contrant M, Fender A, Chane-Woon-Ming B, Randrianjafy R, Vivet-Boudou V, Richer D, Pfeffer S. Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs. Nucleic Acids Res 2014; 42:7981-96. [PMID: 24831544 PMCID: PMC4081064 DOI: 10.1093/nar/gku424] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNAs themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNA accumulation. To this end, we used the Kaposi's sarcoma herpesvirus, which encodes a cluster of 12 pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNAs could be as high as 60-fold. Using high-throughput selective 2′-hydroxyl acylation analyzed by primer extension, we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops or by targeted mutagenesis of selected miRNAs, which resulted in a perturbed accumulation of the mature miRNA.
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Affiliation(s)
- Maud Contrant
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Aurélie Fender
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Béatrice Chane-Woon-Ming
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Ramy Randrianjafy
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Valérie Vivet-Boudou
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Delphine Richer
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
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125
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Small RNA cloning and sequencing strategy affects host and viral microRNA expression signatures. J Biotechnol 2014; 181:35-44. [PMID: 24746587 DOI: 10.1016/j.jbiotec.2014.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/26/2014] [Accepted: 04/04/2014] [Indexed: 01/04/2023]
Abstract
The establishment of the microRNA (miRNA) expression signatures is the basic element to investigate the role played by these regulatory molecules in the biology of an organism. Marek's disease virus 1 (MDV-1) is an avian herpesvirus that naturally infects chicken and induces T cells lymphomas. During latency, MDV-1, like other herpesviruses, expresses a limited subset of transcripts. These include three miRNA clusters. Several studies identified the expression of virus and host encoded miRNAs from MDV-1 infected cell cultures and chickens. But a high discrepancy was observed when miRNA cloning frequencies obtained from different cloning and sequencing protocols were compared. Thus, we analyzed the effect of small RNA library preparation and sequencing on the miRNA frequencies obtained from the same RNA samples collected during MDV-1 infection of chicken at different steps of the oncoviral pathogenesis. Qualitative and quantitative variations were found in the data, depending on the strategy used. One of the mature miRNA derived from the latency-associated-transcript (LAT), mdv1-miR-M7-5p, showed the highest variation. Its cloning frequency was 50% of the viral miRNA counts when a small scale sequencing approach was used. Its frequency was 100 times less abundant when determined through the deep sequencing approach. Northern blot analysis showed a better correlation with the miRNA frequencies found by the small scale sequencing approach. By analyzing the cellular miRNA repertoire, we also found a gap between the two sequencing approaches. Collectively, our study indicates that next-generation sequencing data considered alone are limited for assessing the absolute copy number of transcripts. Thus, the quantification of small RNA should be addressed by compiling data obtained by using different techniques such as microarrays, qRT-PCR and NB analysis in support of high throughput sequencing data. These observations should be considered when miRNA variations are studied prior addressing functional studies.
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126
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Song Y, Liu KJ, Wang TH. Elimination of ligation dependent artifacts in T4 RNA ligase to achieve high efficiency and low bias microRNA capture. PLoS One 2014; 9:e94619. [PMID: 24722341 PMCID: PMC3983213 DOI: 10.1371/journal.pone.0094619] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/18/2014] [Indexed: 01/22/2023] Open
Abstract
Adapter ligation is a critical first step in many microRNA analysis methods including microarray, qPCR, and sequencing. Previous studies have shown that ligation bias can have dramatic effects on both the fidelity of expression profiles and reproducibility across samples. We have developed a method for high efficiency and low bias microRNA capture by 3′ adapter ligation using T4 RNA ligase that does not require pooled adapters. Using a panel of 20 microRNA, we investigated the effects of ligase type, PEG concentration, ligase amount, adapter concentration, incubation time, incubation temperature, and adapter design on capture efficiency and bias. Of these factors, high PEG% was found to be critical in suppressing ligation bias. We obtained high average capture efficiency and low CV across the 20 microRNA panel, both in idealized buffer conditions (86%±10%) and total RNA spiking conditions (64%±17%). We demonstrate that this method is reliable across microRNA species that previous studies have had difficulty capturing and that our adapter design performs significantly better than the common adapter designs. Further, we demonstrate that the optimization methodology must be specifically designed for minimizing bias in order to obtain the ideal reaction parameters.
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Affiliation(s)
- Yunke Song
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kelvin J. Liu
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Circulomics Inc, Baltimore, Maryland, United States of America
- * E-mail: (THW); (KJL)
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (THW); (KJL)
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127
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Xia J, Zhang W. A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5'-isoforms in four model species. Nucleic Acids Res 2014; 42:1427-41. [PMID: 24178030 PMCID: PMC3919606 DOI: 10.1093/nar/gkt967] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 09/12/2013] [Accepted: 10/01/2013] [Indexed: 12/20/2022] Open
Abstract
MicroRNA (miRNA) 5'-isoforms, or 5'-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5' ends shifted from the 5' ends of the miRNAs by a few nucleotides. Although 5'-isomiRs have been reported, their origins, properties and potential functions remain to be examined. We systematically studied 5'-isomiRs in human, mouse, fruitfly and worm by analysing a large collection of small non-coding RNA and mRNA profiling data. The results revealed a broad existence of 5'-isomiRs in the four species, many of which were conserved and could arise from genomic loci of canonical and non-canonical miRNAs. The well-conserved 5'-isomiRs have several features, including a preference of the 3p over the 5p arms of hairpins of conserved mammalian miRNAs, altered 5'-isomiRs across species and across tissues, and association with structural variations of miRNA hairpins. Importantly, 5'-isomiRs and their major miRNAs may have different mRNA targets and thus potentially play distinct roles of gene regulation, as shown by an integrative analysis combining miRNA and mRNA profiling data from psoriatic and normal human skin and from murine miRNA knockout assays. Indeed, 18 5'-isomiRs had aberrant expression in psoriatic human skin, suggesting their potential function in psoriasis pathogenesis. The results of the current study deepened our understanding of the diversity and conservation of miRNAs, their plasticity in gene regulation and potential broad function in complex diseases.
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Affiliation(s)
- Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China, Department of Computer Science and Engineering, Washington University in Saint Louis, One Brookings Drive, St. Louis, MO 63130, USA and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China, Department of Computer Science and Engineering, Washington University in Saint Louis, One Brookings Drive, St. Louis, MO 63130, USA and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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128
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Randomized Adapters for Reducing Bias in Small RNA-Seq Libraries. Biotechniques 2014. [DOI: 10.2144/000114138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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129
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Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 2014; 56:61-4, 66, 68, passim. [PMID: 24502796 DOI: 10.2144/000114133] [Citation(s) in RCA: 343] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/21/2014] [Indexed: 01/03/2023] Open
Abstract
High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries from DNA and RNA sources. Factors such as the quantity and physical characteristics of the RNA or DNA source material as well as the desired application (i.e., genome sequencing, targeted sequencing, RNA-seq, ChIP-seq, RIP-seq, and methylation) are addressed in the context of preparing high quality sequencing libraries. In addition, the current methods for preparing NGS libraries from single cells are also discussed.
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Affiliation(s)
- Steven R Head
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA
| | - H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Thomas Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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130
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Library preparation methods for next-generation sequencing: tone down the bias. Exp Cell Res 2014; 322:12-20. [PMID: 24440557 DOI: 10.1016/j.yexcr.2014.01.008] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 11/22/2022]
Abstract
Next-generation sequencing (NGS) has caused a revolution in biology. NGS requires the preparation of libraries in which (fragments of) DNA or RNA molecules are fused with adapters followed by PCR amplification and sequencing. It is evident that robust library preparation methods that produce a representative, non-biased source of nucleic acid material from the genome under investigation are of crucial importance. Nevertheless, it has become clear that NGS libraries for all types of applications contain biases that compromise the quality of NGS datasets and can lead to their erroneous interpretation. A detailed knowledge of the nature of these biases will be essential for a careful interpretation of NGS data on the one hand and will help to find ways to improve library quality or to develop bioinformatics tools to compensate for the bias on the other hand. In this review we discuss the literature on bias in the most common NGS library preparation protocols, both for DNA sequencing (DNA-seq) as well as for RNA sequencing (RNA-seq). Strikingly, almost all steps of the various protocols have been reported to introduce bias, especially in the case of RNA-seq, which is technically more challenging than DNA-seq. For each type of bias we discuss methods for improvement with a view to providing some useful advice to the researcher who wishes to convert any kind of raw nucleic acid into an NGS library.
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131
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Lakhotia N, Joshi G, Bhardwaj AR, Katiyar-Agarwal S, Agarwal M, Jagannath A, Goel S, Kumar A. Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing. BMC PLANT BIOLOGY 2014; 14:6. [PMID: 24397411 PMCID: PMC3913621 DOI: 10.1186/1471-2229-14-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/26/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. However, identification of miRNAs through deep sequencing approach was limited to a few tissue types and developmental stages. This study reports the identification and characterization of potato miRNAs in three different vegetative tissues and four stages of tuber development by high throughput sequencing. RESULTS Small RNA libraries were constructed from leaf, stem, root and four early developmental stages of tuberization and subjected to deep sequencing, followed by bioinformatics analysis. A total of 89 conserved miRNAs (belonging to 33 families), 147 potato-specific miRNAs (with star sequence) and 112 candidate potato-specific miRNAs (without star sequence) were identified. The digital expression profiling based on TPM (Transcripts Per Million) and qRT-PCR analysis of conserved and potato-specific miRNAs revealed that some of the miRNAs showed tissue specific expression (leaf, stem and root) while a few demonstrated tuberization stage-specific expressions. Targets were predicted for identified conserved and potato-specific miRNAs, and predicted targets of four conserved miRNAs, miR160, miR164, miR172 and miR171, which are ARF16 (Auxin Response Factor 16), NAM (NO APICAL MERISTEM), RAP1 (Relative to APETALA2 1) and HAM (HAIRY MERISTEM) respectively, were experimentally validated using 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). Gene ontology (GO) analysis for potato-specific miRNAs was also performed to predict their potential biological functions. CONCLUSIONS We report a comprehensive study of potato miRNAs at genome-wide level by high-throughput sequencing and demonstrate that these miRNAs have tissue and/or developmental stage-specific expression profile. Also, predicted targets of conserved miRNAs were experimentally confirmed for the first time in potato. Our findings indicate the existence of extensive and complex small RNA population in this crop and suggest their important role in pathways involved in diverse biological processes, including tuber development.
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Affiliation(s)
- Nisha Lakhotia
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Gopal Joshi
- Department of Botany, University of Delhi, Delhi 110007, India
| | | | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Arun Jagannath
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Amar Kumar
- Department of Botany, University of Delhi, Delhi 110007, India
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132
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Zheng D, Tian B. RNA-binding proteins in regulation of alternative cleavage and polyadenylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:97-127. [PMID: 25201104 DOI: 10.1007/978-1-4939-1221-6_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Almost all eukaryotic pre-mRNAs are processed at the 3' end by the cleavage and polyadenylation (C/P) reaction, which preludes termination of transcription and gives rise to the poly(A) tail of mature mRNA. Genomic studies in recent years have indicated that most eukaryotic mRNA genes have multiple cleavage and polyadenylation sites (pAs), leading to alternative cleavage and polyadenylation (APA) products. APA isoforms generally differ in their 3' untranslated regions (3' UTRs), but can also have different coding sequences (CDSs). APA expands the repertoire of transcripts expressed from the genome, and is highly regulated under various physiological and pathological conditions. Growing lines of evidence have shown that RNA-binding proteins (RBPs) play important roles in regulation of APA. Some RBPs are part of the machinery for C/P; others influence pA choice through binding to adjacent regions. In this chapter, we review cis elements and trans factors involved in C/P, the significance of APA, and increasingly elucidated roles of RBPs in APA regulation. We also discuss analysis of APA using transcriptome-wide techniques as well as molecular biology approaches.
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Affiliation(s)
- Dinghai Zheng
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, 185 South Orange Ave., Newark, NJ, 07103, USA
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133
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Chen X, El-Sagheer AH, Brown T. Reverse transcription through a bulky triazole linkage in RNA: implications for RNA sequencing. Chem Commun (Camb) 2014; 50:7597-600. [DOI: 10.1039/c4cc03027c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reverse-transcriptase reads through the bulky artificial triazole linkage with omission of one nucleotide with implications for RNA isolation and analysis.
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Affiliation(s)
- Xiong Chen
- School of Chemistry
- University of Southampton
- Southampton SO17 1BJ, UK
| | - Afaf H. El-Sagheer
- Chemistry Branch
- Dept. of Science and Mathematics
- Faculty of Petroleum and Mining Engineering
- Suez University
- Suez, Egypt
| | - Tom Brown
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford, UK
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134
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Abstract
The different RNA populations within the cell, or the 'RNAome', form a complex and integral layer of gene regulation. In particular, small non-coding RNAs such as microRNAs have been shown to regulate as much as half of all genes expressed in mammals. The recent discovery of novel small RNAs derived from tRNAs, snoRNAs and Y RNAs, as well as the development of techniques that can reduce sequencing bias of these molecules, is slowly helping us to unveil the secrets of the genome.
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135
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Identification of RNase L-dependent, 3'-end-modified, viral small RNAs in Sindbis virus-infected mammalian cells. mBio 2013; 4:e00698-13. [PMID: 24255120 PMCID: PMC3870239 DOI: 10.1128/mbio.00698-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Small RNAs play a critical role in host-pathogen interaction. Indeed, small RNA-mediated silencing or RNA interference (RNAi) is one of the earliest forms of antiviral immunity. Although it represents the main defense system against viruses in many organisms, the antiviral role of RNAi has not been clearly proven in higher vertebrates. However, it is well established that their response to viral infection relies on the recognition of viral RNAs by host pattern recognition receptors (PRRs) to trigger activation of the interferon pathway. In the present work, we report the existence of a novel small noncoding RNA population produced in mammalian cells upon RNA virus infection. Using Sindbis virus (SINV) as a prototypic arbovirus model, we profiled the small RNA population of infected cells in both human and African green monkey cell lines. Here, we provide evidence for the presence of discrete small RNAs of viral origin that are not associated with the RNA-induced silencing complex (RISC), that are highly expressed and detected by Northern blot analysis, and that accumulate as 21- to 28-nucleotide (nt) species during infection. We report that the cellular antiviral endoribonuclease RNase L cleaves the viral genome, producing in turn the small RNAs. Surprisingly, we uncovered the presence of a modification on the 3′-end nucleotide of SINV-derived viral small RNAs (SvsRNAs) that might be at the origin of their stability. Altogether, our findings show that stable modified small viral RNAs could represent a novel way to modulate host-virus interaction upon SINV infection. In a continuous arms race, viruses have to deal with host antiviral responses in order to successfully establish an infection. In mammalian cells, the host defense mechanism relies on the recognition of viral RNAs, resulting in the activation of type I interferons (IFNs). In turn, the expression of many interferon-stimulated genes (ISGs) is induced to inhibit viral replication. Here we report that the cytoplasmic, interferon-induced, cellular endoribonuclease RNase L is involved in the accumulation of a novel small RNA population of viral origin. These small RNAs are produced upon SINV infection of mammalian cells and are stabilized by a 3′-end modification. Altogether, our findings indicate that in our system RNA silencing is not active against Sindbis virus (SINV) and might open the way to a better understanding of the antiviral response mediated by a novel class of small RNAs.
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136
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Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS. Biases in small RNA deep sequencing data. Nucleic Acids Res 2013; 42:1414-26. [PMID: 24198247 PMCID: PMC3919602 DOI: 10.1093/nar/gkt1021] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
High-throughput RNA sequencing (RNA-seq) is considered a powerful tool for novel gene discovery and fine-tuned transcriptional profiling. The digital nature of RNA-seq is also believed to simplify meta-analysis and to reduce background noise associated with hybridization-based approaches. The development of multiplex sequencing enables efficient and economic parallel analysis of gene expression. In addition, RNA-seq is of particular value when low RNA expression or modest changes between samples are monitored. However, recent data uncovered severe bias in the sequencing of small non-protein coding RNA (small RNA-seq or sRNA-seq), such that the expression levels of some RNAs appeared to be artificially enhanced and others diminished or even undetectable. The use of different adapters and barcodes during ligation as well as complex RNA structures and modifications drastically influence cDNA synthesis efficacies and exemplify sources of bias in deep sequencing. In addition, variable specific RNA G/C-content is associated with unequal polymerase chain reaction amplification efficiencies. Given the central importance of RNA-seq to molecular biology and personalized medicine, we review recent findings that challenge small non-protein coding RNA-seq data and suggest approaches and precautions to overcome or minimize bias.
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Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Strasse 56, 48149 Muenster, Germany and Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Penang, Malaysia
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137
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Hébert SS, Wang WX, Zhu Q, Nelson PT. A study of small RNAs from cerebral neocortex of pathology-verified Alzheimer's disease, dementia with lewy bodies, hippocampal sclerosis, frontotemporal lobar dementia, and non-demented human controls. J Alzheimers Dis 2013; 35:335-48. [PMID: 23403535 DOI: 10.3233/jad-122350] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
MicroRNAs (miRNAs) are small (20-22 nucleotides) regulatory non-coding RNAs that strongly influence gene expression. Most prior studies addressing the role of miRNAs in neurodegenerative diseases (NDs) have focused on individual diseases such as Alzheimer's disease (AD), making disease-to-disease comparisons impossible. Using RNA deep sequencing, we sought to analyze in detail the small RNAs (including miRNAs) in the temporal neocortex gray matter from non-demented controls (n = 2), AD (n = 5), dementia with Lewy bodies (n = 4), hippocampal sclerosis of aging (n = 4), and frontotemporal lobar dementia (FTLD) (n = 5) cases, together accounting for the most prevalent ND subtypes. All cases had short postmortem intervals, relatively high-quality RNA, and state-of-the-art neuropathological diagnoses. The resulting data (over 113 million reads in total, averaging 5.6 million reads per sample) and secondary expression analyses constitute an unprecedented look into the human cerebral cortical miRNome at a nucleotide resolution. While we find no apparent changes in isomiR or miRNA editing patterns in correlation with ND pathology, our results validate and extend previous miRNA profiling studies with regard to quantitative changes in NDs. In agreement with this idea, we provide independent cohort validation for changes in miR-132 expression levels in AD (n = 8) and FTLD (n = 14) cases when compared to controls (n = 8). The identification of common and ND-specific putative novel brain miRNAs and/or short-hairpin molecules is also presented. The challenge now is to better understand the impact of these and other alterations on neuronal gene expression networks and neuropathologies.
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Affiliation(s)
- Sébastien S Hébert
- Axe Neurosciences, Centre de recherche du CHU de Québec, Québec, QC, Canada.
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138
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Chen CJ, Cox JE, Kincaid RP, Martinez A, Sullivan CS. Divergent MicroRNA targetomes of closely related circulating strains of a polyomavirus. J Virol 2013; 87:11135-47. [PMID: 23926342 PMCID: PMC3807300 DOI: 10.1128/jvi.01711-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/30/2013] [Indexed: 11/20/2022] Open
Abstract
Hundreds of virus-encoded microRNAs (miRNAs) have been uncovered, but an in-depth functional understanding is lacking for most. A major challenge for the field is separating those miRNA targets that are biologically relevant from those that are not advantageous to the virus. Here, we show that miRNAs from related variants of the polyomavirus simian vacuolating virus 40 (SV40) have differing host target repertoires (targetomes) while their direct autoregulatory activity on virus-encoded early gene products is completely preserved. These results underscore the importance of miRNA-mediated viral gene autoregulation in some polyomavirus life cycles. More broadly, these findings imply that some host targets of virus-encoded miRNAs are likely to be of little selective advantage to the virus, and our approach provides a strategy for prioritizing relevant targets.
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Affiliation(s)
- Chun Jung Chen
- The University of Texas at Austin, Molecular Genetics & Microbiology, Austin, Texas, USA
| | - Jennifer E. Cox
- The University of Texas at Austin, Molecular Genetics & Microbiology, Austin, Texas, USA
| | - Rodney P. Kincaid
- The University of Texas at Austin, Molecular Genetics & Microbiology, Austin, Texas, USA
| | - Angel Martinez
- American Chemical Society Project SEED Summer Internship Program, James Bowie High School, Austin, Texas, USA
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139
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Lin JS, Lin CC, Li YC, Wu MT, Tsai MH, Hsing YIC, Jeng ST. Interaction of small RNA-8105 and the intron of IbMYB1 RNA regulates IbMYB1 family genes through secondary siRNAs and DNA methylation after wounding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:781-794. [PMID: 23663233 DOI: 10.1111/tpj.12238] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 05/06/2013] [Accepted: 05/08/2013] [Indexed: 06/02/2023]
Abstract
Small RNAs (sRNAs) play important roles in plants under stress conditions. However, limited research has been performed on the sRNAs involved in plant wound responses. In the present study, a novel wounding-induced sRNA, sRNA8105, was identified in sweet potato (Ipomoea batatas cv. Tainung 57) using microarray analysis. It was found that expression of sRNA8105 increased after mechanical wounding. Furthermore, Dicer-like 1 (DCL1) is required for the sRNA8105 precursor (pre-sRNA8105) to generate 22 and 24 nt mature sRNA8105. sRNA8105 targeted the first intron of IbMYB1 (MYB domain protein 1) before RNA splicing, and mediated RNA cleavage and DNA methylation of IbMYB1. The interaction between sRNA8105 and IbMYB1 was confirmed by cleavage site mapping, agro-infiltration analyses, and use of a transgenic sweet potato over-expressing pre-sRNA8105 gene. Induction of IbMYB1-siRNA was observed in the wild-type upon wounding and in transgenic sweet potato over-expressing pre-sRNA8105 gene without wounding, resulting in decreased expression of the whole IbMYB1 gene family, i.e. IbMYB1 and the IbMYB2 genes, and thus directing metabolic flux toward biosynthesis of lignin in the phenylpropanoid pathway. In conclusion, sRNA8105 induced by wounding binds to the first intron of IbMYB1 RNA to methylate IbMYB1, cleave IbMYB1 RNA, and trigger production of secondary siRNAs, further repressing the expression of the IbMYB1 family genes and regulating the phenylpropanoid pathway.
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Affiliation(s)
- Jeng-Shane Lin
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Roosevelt Road, Taipei, 106, Taiwan
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140
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Marques JT, Wang JP, Wang X, de Oliveira KPV, Gao C, Aguiar ERGR, Jafari N, Carthew RW. Functional specialization of the small interfering RNA pathway in response to virus infection. PLoS Pathog 2013; 9:e1003579. [PMID: 24009507 PMCID: PMC3757037 DOI: 10.1371/journal.ppat.1003579] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/10/2013] [Indexed: 01/04/2023] Open
Abstract
In Drosophila, post-transcriptional gene silencing occurs when exogenous or endogenous double stranded RNA (dsRNA) is processed into small interfering RNAs (siRNAs) by Dicer-2 (Dcr-2) in association with a dsRNA-binding protein (dsRBP) cofactor called Loquacious (Loqs-PD). siRNAs are then loaded onto Argonaute-2 (Ago2) by the action of Dcr-2 with another dsRBP cofactor called R2D2. Loaded Ago2 executes the destruction of target RNAs that have sequence complementarity to siRNAs. Although Dcr-2, R2D2, and Ago2 are essential for innate antiviral defense, the mechanism of virus-derived siRNA (vsiRNA) biogenesis and viral target inhibition remains unclear. Here, we characterize the response mechanism mediated by siRNAs against two different RNA viruses that infect Drosophila. In both cases, we show that vsiRNAs are generated by Dcr-2 processing of dsRNA formed during viral genome replication and, to a lesser extent, viral transcription. These vsiRNAs seem to preferentially target viral polyadenylated RNA to inhibit viral replication. Loqs-PD is completely dispensable for silencing of the viruses, in contrast to its role in silencing endogenous targets. Biogenesis of vsiRNAs is independent of both Loqs-PD and R2D2. R2D2, however, is required for sorting and loading of vsiRNAs onto Ago2 and inhibition of viral RNA expression. Direct injection of viral RNA into Drosophila results in replication that is also independent of Loqs-PD. This suggests that triggering of the antiviral pathway is not related to viral mode of entry but recognition of intrinsic features of virus RNA. Our results indicate the existence of a vsiRNA pathway that is separate from the endogenous siRNA pathway and is specifically triggered by virus RNA. We speculate that this unique framework might be necessary for a prompt and efficient antiviral response. The RNA interference (RNAi) pathway utilizes small non-coding RNAs to silence gene expression. In insects, RNAi regulates endogenous genes and functions as an RNA-based immune system against viral infection. Here we have uncovered details of how RNAi is triggered by RNA viruses. Double-stranded RNA (dsRNA) generated as a replication intermediate or from transcription of the RNA virus can be used as substrate for the biogenesis of virus-derived small interfering RNAs (vsiRNAs). Unlike other dsRNAs, virus RNA processing involves Dicer but not its canonical partner protein Loqs-PD. Thus, vsiRNA biogenesis is mechanistically different from biogenesis of endogenous siRNAs or siRNAs derived from other exogenous RNA sources. Our results suggest a specialization of the pathway dedicated to silencing of RNA viruses versus other types of RNAi silencing. The understanding of RNAi mechanisms during viral infection could have implications for the control of insect-borne viruses and the use of siRNAs to treat viral infections in humans.
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Affiliation(s)
- Joao Trindade Marques
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail: (JTM); (RWC)
| | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, Illinois, United States of America
| | - Xiaohong Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Karla Pollyanna Vieira de Oliveira
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Catherine Gao
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Eric Roberto Guimaraes Rocha Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Nadereh Jafari
- Genomics Core, Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Richard W. Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail: (JTM); (RWC)
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141
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Bronkhorst AW, Miesen P, van Rij RP. Small RNAs tackle large viruses: RNA interference-based antiviral defense against DNA viruses in insects. Fly (Austin) 2013; 7:216-23. [PMID: 23974177 DOI: 10.4161/fly.25708] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The antiviral RNA interference (RNAi) pathway processes viral double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNA) that guide the recognition and cleavage of complementary viral target RNAs. In RNA virus infections, viral replication intermediates, dsRNA genomes or viral structured RNAs have been implicated as Dicer-2 substrates. In a recent publication, we demonstrated that a double-stranded DNA virus, Invertebrate iridescent virus 6, is a target of the Drosophila RNAi machinery, and we proposed that overlapping converging transcripts base pair to form the dsRNA substrates for vsiRNA biogenesis. Here, we discuss the role of RNAi in antiviral defense to DNA viruses in Drosophila and other invertebrate model systems.
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Affiliation(s)
- Alfred W Bronkhorst
- Department of Medical Microbiology; Radboud University Nijmegen Medical Centre; Nijmegen Centre for Molecular Life Sciences; Nijmegen Institute for Infection, Inflammation and Immunity; Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology; Radboud University Nijmegen Medical Centre; Nijmegen Centre for Molecular Life Sciences; Nijmegen Institute for Infection, Inflammation and Immunity; Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology; Radboud University Nijmegen Medical Centre; Nijmegen Centre for Molecular Life Sciences; Nijmegen Institute for Infection, Inflammation and Immunity; Nijmegen, The Netherlands
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142
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de Vanssay A, Bougé AL, Boivin A, Hermant C, Teysset L, Delmarre V, Ronsseray S, Antoniewski C. Profiles of piRNA abundances at emerging or established piRNA loci are determined by local DNA sequences. RNA Biol 2013; 10:1233-9. [PMID: 23880829 PMCID: PMC3817142 DOI: 10.4161/rna.25756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) ensure transposable element silencing in Drosophila, thereby preserving genome integrity across generations. Primary piRNAs arise from the processing of long RNA transcripts produced in the germ line by a limited number of telomeric and pericentromeric loci. Primary piRNAs bound to the Argonaute protein Aubergine then drive the production of secondary piRNAs through the "ping-pong" amplification mechanism that involves an interplay with piRNAs bound to the Argonaute protein Argonaute-3. We recently discovered that clusters of P-element-derived transgenes produce piRNAs and mediate silencing of homologous target transgenes in the female germ line. We also demonstrated that some clusters are able to convert other homologous inactive transgene clusters into piRNA-producing loci, which then transmit their acquired silencing capacity over generations. This paramutation phenomenon is mediated by maternal inheritance of piRNAs homologous to the transgenes. Here we further mined our piRNA sequencing data sets generated from various strains carrying transgenes with partial sequence homology at distinct genomic sites. This analysis revealed that same sequences in different genomic contexts generate highly similar profiles of piRNA abundances. The strong tendency of piRNAs for bearing a U at their 5' end has long been recognized. Our observations support the notion that, in addition, the relative frequencies of Drosophila piRNAs are locally determined by the DNA sequence of piRNA loci.
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Affiliation(s)
- Augustin de Vanssay
- Epigenetic Repression and Transposable Elements; Laboratoire Biologie du Développement; UMR7622; CNRS-Université Pierre et Marie Curie; Paris, France
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143
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McGahon MK, Yarham JM, Daly A, Guduric-Fuchs J, Ferguson LJ, Simpson DA, Collins A. Distinctive profile of IsomiR expression and novel microRNAs in rat heart left ventricle. PLoS One 2013; 8:e65809. [PMID: 23799049 PMCID: PMC3683050 DOI: 10.1371/journal.pone.0065809] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 05/03/2013] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are single-stranded non-coding RNAs that negatively regulate target gene expression through mRNA cleavage or translational repression. There is mounting evidence that they play critical roles in heart disease. The expression of known miRNAs in the heart has been studied at length by microarray and quantitative PCR but it is becoming evident that microRNA isoforms (isomiRs) are potentially physiologically important. It is well known that left ventricular (patho)physiology is influenced by transmural heterogeneity of cardiomyocyte phenotype, and this likely reflects underlying heterogeneity of gene expression. Given the significant role of miRNAs in regulating gene expression, knowledge of how the miRNA profile varies across the ventricular wall will be crucial to better understand the mechanisms governing transmural physiological heterogeneity. To determinine miRNA/isomiR expression profiles in the rat heart we investigated tissue from different locations across the left ventricular wall using deep sequencing. We detected significant quantities of 145 known rat miRNAs and 68 potential novel orthologs of known miRNAs, in mature, mature* and isomiR formation. Many isomiRs were detected at a higher frequency than their canonical sequence in miRBase and have different predicted targets. The most common miR-133a isomiR was more effective at targeting a construct containing a sequence from the gelsolin gene than was canonical miR-133a, as determined by dual-fluorescence assay. We identified a novel rat miR-1 homolog from a second miR-1 gene; and a novel rat miRNA similar to miR-676. We also cloned and sequenced the rat miR-486 gene which is not in miRBase (v18). Signalling pathways predicted to be targeted by the most highly detected miRNAs include Ubiquitin-mediated Proteolysis, Mitogen-Activated Protein Kinase, Regulation of Actin Cytoskeleton, Wnt signalling, Calcium Signalling, Gap junctions and Arrhythmogenic Right Ventricular Cardiomyopathy. Most miRNAs are not expressed in a gradient across the ventricular wall, with exceptions including miR-10b, miR-21, miR-99b and miR-486.
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Affiliation(s)
- Mary K. McGahon
- Centre for Vision and Vascular Science, Queen’s University Belfast, Belfast, County Antrim, United Kingdom
| | - Janet M. Yarham
- Centre for Vision and Vascular Science, Queen’s University Belfast, Belfast, County Antrim, United Kingdom
| | - Aideen Daly
- Centre for Vision and Vascular Science, Queen’s University Belfast, Belfast, County Antrim, United Kingdom
| | - Jasenka Guduric-Fuchs
- Centre for Vision and Vascular Science, Queen’s University Belfast, Belfast, County Antrim, United Kingdom
| | - Lyndsey J. Ferguson
- Centre for Vision and Vascular Science, Queen’s University Belfast, Belfast, County Antrim, United Kingdom
| | - David A. Simpson
- Centre for Vision and Vascular Science, Queen’s University Belfast, Belfast, County Antrim, United Kingdom
| | - Anthony Collins
- Centre for Vision and Vascular Science, Queen’s University Belfast, Belfast, County Antrim, United Kingdom
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Axtell MJ. ShortStack: comprehensive annotation and quantification of small RNA genes. RNA (NEW YORK, N.Y.) 2013; 19:740-51. [PMID: 23610128 PMCID: PMC3683909 DOI: 10.1261/rna.035279.112] [Citation(s) in RCA: 266] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Small RNA sequencing allows genome-wide discovery, categorization, and quantification of genes producing regulatory small RNAs. Many tools have been described for annotation and quantification of microRNA loci (MIRNAs) from small RNA-seq data. However, in many organisms and tissue types, MIRNA genes comprise only a small fraction of all small RNA-producing genes. ShortStack is a stand-alone application that analyzes reference-aligned small RNA-seq data and performs comprehensive de novo annotation and quantification of the inferred small RNA genes. ShortStack's output reports multiple parameters of direct relevance to small RNA gene annotation, including RNA size distributions, repetitiveness, strandedness, hairpin-association, MIRNA annotation, and phasing. In this study, ShortStack is demonstrated to perform accurate annotations and useful descriptions of diverse small RNA genes from four plants (Arabidopsis, tomato, rice, and maize) and three animals (Drosophila, mice, and humans). ShortStack efficiently processes very large small RNA-seq data sets using modest computational resources, and its performance compares favorably to previously described tools. Annotation of MIRNA loci by ShortStack is highly specific in both plants and animals. ShortStack is freely available under a GNU General Public License.
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Affiliation(s)
- Michael J Axtell
- Department of Biology, and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.
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Abstract
Arboviruses are transmitted to vertebrate hosts by biting arthropod vectors such as mosquitoes, ticks, and midges. These viruses replicate in both arthropods and vertebrates and are thus exposed to different antiviral responses in these organisms. RNA interference (RNAi) is a sequence-specific RNA degradation mechanism that has been shown to play a major role in the antiviral response against arboviruses in mosquitoes. Culicoides midges are important vectors of arboviruses, known to transmit pathogens of humans and livestock such as bluetongue virus (BTV) (Reoviridae), Oropouche virus (Bunyaviridae), and likely the recently discovered Schmallenberg virus (Bunyaviridae). In this study, we investigated whether Culicoides cells possess an antiviral RNAi response and whether this is effective against arboviruses, including those with double-stranded RNA (dsRNA) genomes, such as BTV. Using reporter gene-based assays, we established the presence of a functional RNAi response in Culicoides sonorensis-derived KC cells which is effective in inhibiting BTV infection. Sequencing of small RNAs from KC and Aedes aegypti-derived Aag2 cells infected with BTV or the unrelated Schmallenberg virus resulted in the production of virus-derived small interfering RNAs (viRNAs) of 21 nucleotides, similar to the viRNAs produced during arbovirus infections of mosquitoes. In addition, viRNA profiles strongly suggest that the BTV dsRNA genome is accessible to a Dicer-type nuclease. Thus, we show for the first time that midge cells target arbovirus replication by mounting an antiviral RNAi response mainly resembling that of other insect vectors of arboviruses.
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Aryal R, Yang X, Yu Q, Sunkar R, Li L, Ming R. Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya. BMC Genomics 2012; 13:682. [PMID: 23216749 PMCID: PMC3582581 DOI: 10.1186/1471-2164-13-682] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 11/29/2012] [Indexed: 11/10/2022] Open
Abstract
Background The small RNAs (sRNA) are a regulatory class of RNA mainly represented by the 21 and 24-nucleotide size classes. The cellular sRNAs are processed by RNase III family enzyme dicer (Dicer like in plant) from a self-complementary hairpin loop or other type of RNA duplexes. The papaya genome has been sequenced, but its microRNAs and other regulatory RNAs are yet to be analyzed. Results We analyzed the genomic features of the papaya sRNA population from three sRNA deep sequencing libraries made from leaves, flowers, and leaves infected with Papaya Ringspot Virus (PRSV). We also used the deep sequencing data to annotate the micro RNA (miRNA) in papaya. We identified 60 miRNAs, 24 of which were conserved in other species, and 36 of which were novel miRNAs specific to papaya. In contrast to the Chargaff’s purine-pyrimidine equilibrium, cellular sRNA was significantly biased towards a purine rich population. Of the two purine bases, higher frequency of adenine was present in 23nt or longer sRNAs, while 22nt or shorter sRNAs were over represented by guanine bases. However, this bias was not observed in the annotated miRNAs in plants. The 21nt species were expressed from fewer loci but expressed at higher levels relative to the 24nt species. The highly expressed 21nt species were clustered in a few isolated locations of the genome. The PRSV infected leaves showed higher accumulation of 21 and 22nt sRNA compared to uninfected leaves. We observed higher accumulation of miRNA* of seven annotated miRNAs in virus-infected tissue, indicating the potential function of miRNA* under stressed conditions. Conclusions We have identified 60 miRNAs in papaya. Our study revealed the asymmetric purine-pyrimidine distribution in cellular sRNA population. The 21nt species of sRNAs have higher expression levels than 24nt sRNA. The miRNA* of some miRNAs shows higher accumulation in PRSV infected tissues, suggesting that these strands are not totally functionally redundant. The findings open a new avenue for further investigation of the sRNA silencing pathway in plants.
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Affiliation(s)
- Rishi Aryal
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Grant-Downton R, Rodriguez-Enriquez J. Emerging Roles for Non-Coding RNAs in Male Reproductive Development in Flowering Plants. Biomolecules 2012; 2:608-21. [PMID: 24970151 PMCID: PMC4030863 DOI: 10.3390/biom2040608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 11/19/2012] [Accepted: 11/23/2012] [Indexed: 01/07/2023] Open
Abstract
Knowledge of sexual reproduction systems in flowering plants is essential to humankind, with crop fertility vitally important for food security. Here, we review rapidly emerging new evidence for the key importance of non-coding RNAs in male reproductive development in flowering plants. From the commitment of somatic cells to initiating reproductive development through to meiosis and the development of pollen—containing the male gametes (sperm cells)—in the anther, there is now overwhelming data for a diversity of non-coding RNAs and emerging evidence for crucial roles for them in regulating cellular events at these developmental stages. A particularly exciting development has been the association of one example of cytoplasmic male sterility, which has become an unparalleled breeding tool for producing new crop hybrids, with a non-coding RNA locus.
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Affiliation(s)
- Robert Grant-Downton
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Josefina Rodriguez-Enriquez
- Instituto de Bioorgánica Antonio González (IUBO) University of La Laguna, Avenida Astrofísico Francisco Sánchez, 38206 La Laguna Tenerife, Spain.
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Lopez-Gomollon S, Mohorianu I, Szittya G, Moulton V, Dalmay T. Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. PLANTA 2012; 236:1875-87. [PMID: 22922939 DOI: 10.1007/s00425-012-1734-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/27/2012] [Indexed: 05/03/2023]
Abstract
MicroRNAs negatively regulate the accumulation of mRNAs therefore when they are expressed in the same cells their expression profiles show an inverse correlation. We previously described one positively correlated miRNA/target pair, but it is not known how widespread this phenomenon is. Here, we investigated the correlation between the expression profiles of differentially expressed miRNAs and their targets during tomato fruit development using deep sequencing, Northern blot and RT-qPCR. We found an equal number of positively and negatively correlated miRNA/target pairs indicating that positive correlation is more frequent than previously thought. We also found that the correlation between microRNA and target expression profiles can vary between mRNAs belonging to the same gene family and even for the same target mRNA at different developmental stages. Since microRNAs always negatively regulate their targets, the high number of positively correlated microRNA/target pairs suggests that mutual exclusion could be as widespread as temporal regulation. The change of correlation during development suggests that the type of regulatory circuit directed by a microRNA can change over time and can be different for individual gene family members. Our results also highlight potential problems for expression profiling-based microRNA target identification/validation.
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Affiliation(s)
- Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Grimm D, Dalmay T, van Rij RP. Everybody wins! Poland hosts thrilling competitions of viruses, RNAi and football teams. EMBO Rep 2012; 13:874-6. [PMID: 22986551 PMCID: PMC3463971 DOI: 10.1038/embor.2012.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The ESF-EMBO conference on 'Antiviral RNAi: From Molecular Biology towards Applications' took place in June 2012 in Pultusk, Poland. It brought together scientists working at the interface of RNAi and virus infections in different organisms, covering the complete range from basic mechanisms of RNA silencing to RNAi-based antiviral therapy.
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Affiliation(s)
- Dirk Grimm
- Department of Infectious Diseases, Virology, Cluster of Excellence Cell Networks, Heidelberg University Hospital, Heidelberg, Germany.
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