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Lau NC, Macias VM. Transposon and Transgene Tribulations in Mosquitoes: A Perspective of piRNA Proportions. DNA 2024; 4:104-128. [PMID: 39076684 PMCID: PMC11286205 DOI: 10.3390/dna4020006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Mosquitoes, like Drosophila, are dipterans, the order of "true flies" characterized by a single set of two wings. Drosophila are prime model organisms for biomedical research, while mosquito researchers struggle to establish robust molecular biology in these that are arguably the most dangerous vectors of human pathogens. Both insects utilize the RNA interference (RNAi) pathway to generate small RNAs to silence transposons and viruses, yet details are emerging that several RNAi features are unique to each insect family, such as how culicine mosquitoes have evolved extreme genomic feature differences connected to their unique RNAi features. A major technical difference in the molecular genetic studies of these insects is that generating stable transgenic animals are routine in Drosophila but still variable in stability in mosquitoes, despite genomic DNA-editing advances. By comparing and contrasting the differences in the RNAi pathways of Drosophila and mosquitoes, in this review we propose a hypothesis that transgene DNAs are possibly more intensely targeted by mosquito RNAi pathways and chromatin regulatory pathways than in Drosophila. We review the latest findings on mosquito RNAi pathways, which are still much less well understood than in Drosophila, and we speculate that deeper study into how mosquitoes modulate transposons and viruses with Piwi-interacting RNAs (piRNAs) will yield clues to improving transgene DNA expression stability in transgenic mosquitoes.
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Affiliation(s)
- Nelson C. Lau
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- Genome Science Institute and National Emerging Infectious Disease Laboratory, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
| | - Vanessa M. Macias
- Department of Biology, University of North Texas, Denton, TX 76205, USA
- Advanced Environmental Research Institute, University of North Texas, Denton, TX 76205, USA
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2
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Palli SR. RNAi turns 25:contributions and challenges in insect science. FRONTIERS IN INSECT SCIENCE 2023; 3:1209478. [PMID: 38469536 PMCID: PMC10926446 DOI: 10.3389/finsc.2023.1209478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/26/2023] [Indexed: 03/13/2024]
Abstract
Since its discovery in 1998, RNA interference (RNAi), a Nobel prize-winning technology, made significant contributions to advances in biology because of its ability to mediate the knockdown of specific target genes. RNAi applications in medicine and agriculture have been explored with mixed success. The past 25 years of research on RNAi resulted in advances in our understanding of the mechanisms of its action, target specificity, and differential efficiency among animals and plants. RNAi played a major role in advances in insect biology. Did RNAi technology fully meet insect pest and disease vector management expectations? This review will discuss recent advances in the mechanisms of RNAi and its contributions to insect science. The remaining challenges, including delivery to the target site, differential efficiency, potential resistance development and possible solutions for the widespread use of this technology in insect management.
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Affiliation(s)
- Subba Reddy Palli
- Department of Entomology, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
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3
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Liu WT, Chen CC, Ji DD, Tu WC. The cecropin-prophenoloxidase regulatory mechanism is a cross-species physiological function in mosquitoes. iScience 2022; 25:104478. [PMID: 35712072 PMCID: PMC9194137 DOI: 10.1016/j.isci.2022.104478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 04/06/2022] [Accepted: 05/25/2022] [Indexed: 11/06/2022] Open
Abstract
This study's aim was to investigate whether the cecropin-prophenoloxidase regulatory mechanism is a cross-species physiological function among mosquitoes. BLAST and phylogenetic analysis revealed that three mosquito cecropin Bs, namely Aedes albopictus cecropin B (Aalcec B), Armigeres subalbatus cecropin B2 (Ascec B2), and Culex quinquefasciatus cecropin B1 (Cqcec B1), play crucial roles in cuticle formation during pupal development via the regulation of prophenoloxidase 3 (PPO 3). The effects of cecropin B knockdown were rescued in a cross-species manner by injecting synthetic cecropin B peptide into pupae. Further investigations showed that these three cecropin B peptides bind to TTGG(A/C)A motifs within each of the PPO 3 DNA fragments obtained from these three mosquitoes. These results suggest that Aalcec B, Ascec B2, and Cqcec B1 each play an important role as a transcription factor in cuticle formation and that similar cecropin-prophenoloxidase regulatory mechanisms exist in multiple mosquito species. Cecropin B is able to regulate PPO 3 expression in the pupae Cecropin B binds to TTGG(A/C)A motifs within the PPO 3 DNA The knockdown of cecropin B was rescued by sequence-similar cecropin B peptides The cecropin B-prophenoloxidase 3 regulatory mechanism is conserved in mosquitoes
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4
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Lee CW, Kwon YC, Lee Y, Park MY, Choe KM. cdc37 is essential for JNK pathway activation and wound closure in Drosophila. Mol Biol Cell 2019; 30:2651-2658. [PMID: 31483695 PMCID: PMC6761768 DOI: 10.1091/mbc.e18-12-0822] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Wound closure in the Drosophila larval epidermis mainly involves nonproliferative, endocyling epithelial cells. Consequently, it is largely mediated by cell growth and migration. We discovered that both cell growth and migration in Drosophila require the cochaperone-encoding gene cdc37. Larvae lacking cdc37 in the epidermis failed to close wounds, and the cells of the epidermis failed to change cell shape and polarize. Likewise, wound-induced cell growth was significantly reduced, and correlated with a reduction in the size of the cell nucleus. The c-Jun N-terminal kinase (JNK) pathway, which is essential for wound closure, was not typically activated in injured cdc37 knockdown larvae. In addition, JNK, Hep, Mkk4, and Tak1 protein levels were reduced, consistent with previous reports showing that Cdc37 is important for the stability of various client kinases. Protein levels of the integrin β subunit and its wound-induced protein expression were also reduced, reflecting the disruption of JNK activation, which is crucial for expression of integrin β during wound closure. These results are consistent with a role of Cdc37 in maintaining the stability of the JNK pathway kinases, thus mediating cell growth and migration during Drosophila wound healing.
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Affiliation(s)
- Chan-Wool Lee
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
| | - Young-Chang Kwon
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
| | - Youngbin Lee
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
| | - Min-Yoon Park
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
| | - Kwang-Min Choe
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
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5
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Lee KM, Mathies LD, Grotewiel M. Alcohol sedation in adult Drosophila is regulated by Cysteine proteinase-1 in cortex glia. Commun Biol 2019; 2:252. [PMID: 31286069 PMCID: PMC6610072 DOI: 10.1038/s42003-019-0492-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/30/2019] [Indexed: 02/06/2023] Open
Abstract
Although numerous studies have demonstrated that neuronal mechanisms regulate alcohol-related behaviors, very few have investigated the direct role of glia in behavioral responses to alcohol. The results described here begin to fill this gap in the alcohol behavior and gliobiology fields. Since Drosophila exhibit conserved behavioral responses to alcohol and their CNS glia are similar to mammalian CNS glia, we used Drosophila to begin exploring the role of glia in alcohol behavior. We found that knockdown of Cysteine proteinase-1 (Cp1) in glia increased Drosophila alcohol sedation and that this effect was specific to cortex glia and adulthood. These data implicate Cp1 and cortex glia in alcohol-related behaviors. Cortex glia are functionally homologous to mammalian astrocytes and Cp1 is orthologous to mammalian Cathepsin L. Our studies raise the possibility that cathepsins may influence behavioral responses to alcohol in mammals via roles in astrocytes.
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Affiliation(s)
- Kristen M. Lee
- Neuroscience Graduate Program, Virginia Commonwealth University, Richmond, VA 23298 USA
| | - Laura D. Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298 USA
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA 23298 USA
| | - Mike Grotewiel
- Neuroscience Graduate Program, Virginia Commonwealth University, Richmond, VA 23298 USA
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA 23298 USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298 USA
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6
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Luhur A, Klueg KM, Zelhof AC. Generating and working with Drosophila cell cultures: Current challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 8:e339. [PMID: 30561900 DOI: 10.1002/wdev.339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/30/2018] [Accepted: 11/21/2018] [Indexed: 12/26/2022]
Abstract
The use of Drosophila cell cultures has positively impacted both fundamental and biomedical research. The most widely used cell lines: Schneider, Kc, the CNS and imaginal disc lines continue to be the choice for many applications. Drosophila cell lines provide a homogenous source of cells suitable for biochemical experimentations, transcriptomics, functional genomics, and biomedical applications. They are amenable to RNA interference and serve as a platform for high-throughput screens to identify relevant candidate genes or drugs for any biological process. Currently, CRISPR-based functional genomics are also being developed for Drosophila cell lines. Even though many uniquely derived cell lines exist, cell genetic techniques such the transgenic UAS-GAL4-based RasV12 oncogene expression, CRISPR-Cas9 editing and recombination mediated cassette exchange are likely to drive the establishment of many more lines from specific tissues, cells, or genotypes. However, the pace of creating new lines is hindered by several factors inherent to working with Drosophila cell cultures: single cell cloning, optimal media formulations and culture conditions capable of supporting lines from novel tissue sources or genotypes. Moreover, even though many Drosophila cell lines are morphologically and transcriptionally distinct it may be necessary to implement a standard for Drosophila cell line authentication, ensuring the identity and purity of each cell line. Altogether, recent advances and a standardized authentication effort should improve the utility of Drosophila cell cultures as a relevant model for fundamental and biomedical research. This article is categorized under: Technologies > Analysis of Cell, Tissue, and Animal Phenotypes.
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Affiliation(s)
- Arthur Luhur
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Kristin M Klueg
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Andrew C Zelhof
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
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7
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Kanca O, Bellen HJ, Schnorrer F. Gene Tagging Strategies To Assess Protein Expression, Localization, and Function in Drosophila. Genetics 2017; 207:389-412. [PMID: 28978772 PMCID: PMC5629313 DOI: 10.1534/genetics.117.199968] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/13/2017] [Indexed: 01/15/2023] Open
Abstract
Analysis of gene function in complex organisms relies extensively on tools to detect the cellular and subcellular localization of gene products, especially proteins. Typically, immunostaining with antibodies provides these data. However, due to cost, time, and labor limitations, generating specific antibodies against all proteins of a complex organism is not feasible. Furthermore, antibodies do not enable live imaging studies of protein dynamics. Hence, tagging genes with standardized immunoepitopes or fluorescent tags that permit live imaging has become popular. Importantly, tagging genes present in large genomic clones or at their endogenous locus often reports proper expression, subcellular localization, and dynamics of the encoded protein. Moreover, these tagging approaches allow the generation of elegant protein removal strategies, standardization of visualization protocols, and permit protein interaction studies using mass spectrometry. Here, we summarize available genomic resources and techniques to tag genes and discuss relevant applications that are rarely, if at all, possible with antibodies.
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Affiliation(s)
- Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030
- Howard Hughes Medical Institute, Houston, Texas 77030
| | - Frank Schnorrer
- Developmental Biology Institute of Marseille (IBDM), UMR 7288, CNRS, Aix-Marseille Université, 13288, France
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8
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Genome-Wide RNAi Screens for RNA Processing Events in Drosophila melanogaster S2 Cells. Methods Mol Biol 2017. [PMID: 28766301 DOI: 10.1007/978-1-4939-7204-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Over the past 10 years, the design and application of genome-wide screening (GWS) has improved to the point that it can now be done at level of the individual laboratory. The advantages of GWSs compared to classical genetic screens include: immediate identification of a positive scoring gene, relatively short period of time necessary to conduct the screen (as little as 1 week), cell lines do not present developmental needs for gene expression that an organism normally would, and validation/confirmation of results is straightforward. Here, we describe a general protocol for GWS to be conducted in Drosophila melanogaster S2 cells. We provide specific details on what type of experiments must be done before initiating a screen, the materials that are required to conduct a screen, and make suggestions on methods to carry out secondary screening and counter-screening once the initial GWS is complete. Multiple considerations are also raised that focus on how to anticipate false positives/negatives and how to minimize their occurrence through intelligent design. Finally, we provide specific examples of data that our group has gathered from published genome-wide screens in order to exemplify how "hits" are scored and confirmed.
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9
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Crocker J, Stern DL. Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer. Development 2017; 144:3095-3101. [PMID: 28760812 DOI: 10.1242/dev.149427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/19/2017] [Indexed: 12/27/2022]
Abstract
Transcriptional enhancers are regions of DNA that drive precise patterns of gene expression. Although many studies have elucidated how individual enhancers can evolve, most of this work has focused on what are called 'minimal' enhancers, the smallest DNA regions that drive expression that approximates an aspect of native gene expression. Here, we explore how the Drosophila erecta even-skipped (eve) locus has evolved by testing its activity in the divergent D. melanogaster genome. We found, as has been reported previously, that the D. erecta eve stripe 2 enhancer (eveS2) fails to drive appreciable expression in D. melanogaster However, we found that a large transgene carrying the entire D. erecta eve locus drives normal eve expression, including in stripe 2. We performed a functional dissection of the region upstream of the D. erecta eveS2 region and found multiple Zelda motifs that are required for normal expression. Our results illustrate how sequences outside of minimal enhancer regions can evolve functionally through mechanisms other than changes in transcription factor-binding sites that drive patterning.
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Affiliation(s)
- Justin Crocker
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
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10
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Riechmann V. In vivo RNAi in the Drosophila Follicular Epithelium: Analysis of Stem Cell Maintenance, Proliferation, and Differentiation. Methods Mol Biol 2017; 1622:185-206. [PMID: 28674810 DOI: 10.1007/978-1-4939-7108-4_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In vivo RNAi in Drosophila facilitates simple and rapid analysis of gene functions in a cell- or tissue-specific manner. The versatility of the UAS-GAL4 system allows to control exactly where and when during development the function of a gene is depleted. The epithelium of the ovary is a particularly good model to study in a living animal how stem cells are maintained and how their descendants proliferate and differentiate. Here I provide basic information about the publicly available reagents for in vivo RNAi, and I describe how the oogenesis system can be applied to analyze stem cells and epithelial development at a histological level. Moreover, I give helpful hints to optimize the use of the UAS-GAL4 system for RNAi induction in the follicular epithelium. Finally, I provide detailed step-by-step protocols for ovary dissection, antibody stainings, and ovary mounting for microscopic analysis.
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Affiliation(s)
- Veit Riechmann
- Medical Faculty Mannheim, Department of Cell and Molecular Biology, Heidelberg University, Ludolf-Krehl-Strasse 13-17, D-68167, Mannheim, Germany.
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11
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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12
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Abstract
RNAi technologies enable the testing of gene function in a cell-type- and stage-specific manner in Drosophila. The development of genome-wide RNAi libraries has allowed expansion of this approach to the genome scale and supports identification of most genes required for a given process in a cell type of choice. However, a large-scale RNAi approach also harbors many potential pitfalls that can complicate interpretation of the results. Here, we summarize published screens and provide a guide on how to optimally plan and perform a large-scale, in vivo RNAi screen. We highlight the importance of assay design and give suggestions on how to optimize the assay conditions by testing positive and negative control genes. These genes are used to estimate false-negative and false-positive rates of the screen data. We discuss the planning and logistics of a large-scale screen in detail and suggest bioinformatics platforms to identify and select gene groups of interest for secondary assays. Finally, we review various options to confirm RNAi knock-down specificity and thus identify high confidence genes for more detailed case-by-case studies in the future.
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13
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Perkins LA, Holderbaum L, Tao R, Hu Y, Sopko R, McCall K, Yang-Zhou D, Flockhart I, Binari R, Shim HS, Miller A, Housden A, Foos M, Randkelv S, Kelley C, Namgyal P, Villalta C, Liu LP, Jiang X, Huan-Huan Q, Wang X, Fujiyama A, Toyoda A, Ayers K, Blum A, Czech B, Neumuller R, Yan D, Cavallaro A, Hibbard K, Hall D, Cooley L, Hannon GJ, Lehmann R, Parks A, Mohr SE, Ueda R, Kondo S, Ni JQ, Perrimon N. The Transgenic RNAi Project at Harvard Medical School: Resources and Validation. Genetics 2015; 201:843-52. [PMID: 26320097 PMCID: PMC4649654 DOI: 10.1534/genetics.115.180208] [Citation(s) in RCA: 368] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 08/24/2015] [Indexed: 01/30/2023] Open
Abstract
To facilitate large-scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome-scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently composed of 11,491 lines and covering 71% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated website, the RNAi Stock Validation and Phenotypes Project (RSVP, http://www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (United States), National Institute of Genetics (Japan), and TsingHua Fly Center (China).
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Affiliation(s)
- Lizabeth A Perkins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Laura Holderbaum
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Rong Tao
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Richelle Sopko
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Kim McCall
- Boston University, Boston, Massachusetts 02215
| | - Donghui Yang-Zhou
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Ian Flockhart
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Richard Binari
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 Howard Hughes Medical Institute, Boston, Massachusetts 02115
| | - Hye-Seok Shim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Audrey Miller
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Amy Housden
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Marianna Foos
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Sakara Randkelv
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Colleen Kelley
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Pema Namgyal
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Christians Villalta
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 Howard Hughes Medical Institute, Boston, Massachusetts 02115
| | - Lu-Ping Liu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 TsingHua Fly Center, Beijing, 100084, China
| | - Xia Jiang
- TsingHua Fly Center, Beijing, 100084, China
| | | | - Xia Wang
- TsingHua Fly Center, Beijing, 100084, China
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Kathleen Ayers
- Department of Genetics, Yale University, New Haven, Connecticut 06510
| | - Allison Blum
- Howard Hughes Medical Institute, Boston, Massachusetts 02115 Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, New York 10016
| | - Benjamin Czech
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 1TN, United Kingdom
| | - Ralph Neumuller
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Dong Yan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Amanda Cavallaro
- Howard Hughes Medical Institute, Boston, Massachusetts 02115 Janelia Farm Research Institute ,Asburn, Virginia, 20147
| | - Karen Hibbard
- Howard Hughes Medical Institute, Boston, Massachusetts 02115 Janelia Farm Research Institute ,Asburn, Virginia, 20147
| | - Don Hall
- Howard Hughes Medical Institute, Boston, Massachusetts 02115 Janelia Farm Research Institute ,Asburn, Virginia, 20147
| | - Lynn Cooley
- Department of Genetics, Yale University, New Haven, Connecticut 06510
| | - Gregory J Hannon
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 1TN, United Kingdom
| | - Ruth Lehmann
- Howard Hughes Medical Institute, Boston, Massachusetts 02115 Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, New York 10016
| | - Annette Parks
- Bloomington Drosophila Stock Center Bloomington, Indiana, 47405
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Ryu Ueda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Shu Kondo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 Invertebrate Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Jian-Quan Ni
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 TsingHua Fly Center, Beijing, 100084, China
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 Howard Hughes Medical Institute, Boston, Massachusetts 02115
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14
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Venken KJT, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. Genome engineering: Drosophila melanogaster and beyond. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:233-67. [PMID: 26447401 DOI: 10.1002/wdev.214] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 08/03/2015] [Accepted: 08/20/2015] [Indexed: 12/26/2022]
Abstract
A central challenge in investigating biological phenomena is the development of techniques to modify genomic DNA with nucleotide precision that can be transmitted through the germ line. Recent years have brought a boon in these technologies, now collectively known as genome engineering. Defined genomic manipulations at the nucleotide level enable a variety of reverse engineering paradigms, providing new opportunities to interrogate diverse biological functions. These genetic modifications include controlled removal, insertion, and substitution of genetic fragments, both small and large. Small fragments up to a few kilobases (e.g., single nucleotide mutations, small deletions, or gene tagging at single or multiple gene loci) to large fragments up to megabase resolution can be manipulated at single loci to create deletions, duplications, inversions, or translocations of substantial sections of whole chromosome arms. A specialized substitution of chromosomal portions that presumably are functionally orthologous between different organisms through syntenic replacement, can provide proof of evolutionary conservation between regulatory sequences. Large transgenes containing endogenous or synthetic DNA can be integrated at defined genomic locations, permitting an alternative proof of evolutionary conservation, and sophisticated transgenes can be used to interrogate biological phenomena. Precision engineering can additionally be used to manipulate the genomes of organelles (e.g., mitochondria). Novel genome engineering paradigms are often accelerated in existing, easily genetically tractable model organisms, primarily because these paradigms can be integrated in a rigorous, existing technology foundation. The Drosophila melanogaster fly model is ideal for these types of studies. Due to its small genome size, having just four chromosomes, the vast amount of cutting-edge genetic technologies, and its short life-cycle and inexpensive maintenance requirements, the fly is exceptionally amenable to complex genetic analysis using advanced genome engineering. Thus, highly sophisticated methods developed in the fly model can be used in nearly any sequenced organism. Here, we summarize different ways to perform precise inheritable genome engineering using integrases, recombinases, and DNA nucleases in the D. melanogaster. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Koen J T Venken
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Paul J Vandeventer
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Audrey E Christiansen
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Kristi L Hoffman
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
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15
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Mohr SE, Smith JA, Shamu CE, Neumüller RA, Perrimon N. RNAi screening comes of age: improved techniques and complementary approaches. Nat Rev Mol Cell Biol 2014; 15:591-600. [PMID: 25145850 PMCID: PMC4204798 DOI: 10.1038/nrm3860] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gene silencing through sequence-specific targeting of mRNAs by RNAi has enabled genome-wide functional screens in cultured cells and in vivo in model organisms. These screens have resulted in the identification of new cellular pathways and potential drug targets. Considerable progress has been made to improve the quality of RNAi screen data through the development of new experimental and bioinformatics approaches. The recent availability of genome-editing strategies, such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system, when combined with RNAi, could lead to further improvements in screen data quality and follow-up experiments, thus promoting our understanding of gene function and gene regulatory networks.
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Affiliation(s)
- Stephanie E Mohr
- 1] Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts MA 02115, USA. [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts MA 02115, USA
| | - Jennifer A Smith
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, Massachusetts MA 02115, USA
| | - Caroline E Shamu
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, Massachusetts MA 02115, USA
| | - Ralph A Neumüller
- Department of Genetics, Harvard Medical School, Boston, Massachusetts MA 02115, USA
| | - Norbert Perrimon
- 1] Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts MA 02115, USA. [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts MA 02115, USA. [3] Howard Hughes Medical Institute, Boston, Massachusetts MA 02115, USA
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16
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Ejsmont RK, Hassan BA. The Little Fly that Could: Wizardry and Artistry of Drosophila Genomics. Genes (Basel) 2014; 5:385-414. [PMID: 24827974 PMCID: PMC4094939 DOI: 10.3390/genes5020385] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/16/2014] [Accepted: 04/21/2014] [Indexed: 12/30/2022] Open
Abstract
For more than 100 years now, the fruit fly Drosophila melanogaster has been at the forefront of our endeavors to unlock the secrets of the genome. From the pioneering studies of chromosomes and heredity by Morgan and his colleagues, to the generation of fly models for human disease, Drosophila research has been at the forefront of genetics and genomics. We present a broad overview of some of the most powerful genomics tools that keep Drosophila research at the cutting edge of modern biomedical research.
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Affiliation(s)
| | - Bassem A Hassan
- VIB Center for the Biology of Disease, VIB, 3000 Leuven, Belgium.
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17
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Abstract
Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, "meta" information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally.
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18
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Venken KJT, Bellen HJ. Chemical mutagens, transposons, and transgenes to interrogate gene function in Drosophila melanogaster. Methods 2014; 68:15-28. [PMID: 24583113 DOI: 10.1016/j.ymeth.2014.02.025] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 12/22/2022] Open
Abstract
The study of genetics, genes, and chromosomal inheritance was initiated by Thomas Morgan in 1910, when the first visible mutations were identified in fruit flies. The field expanded upon the work initiated by Herman Muller in 1926 when he used X-rays to develop the first balancer chromosomes. Today, balancers are still invaluable to maintain mutations and transgenes but the arsenal of tools has expanded vastly and numerous new methods have been developed, many relying on the availability of the genome sequence and transposable elements. Forward genetic screens based on chemical mutagenesis or transposable elements have resulted in the unbiased identification of many novel players involved in processes probed by specific phenotypic assays. Reverse genetic approaches have relied on the availability of a carefully selected set of transposon insertions spread throughout the genome to allow the manipulation of the region in the vicinity of each insertion. Lastly, the ability to transform Drosophila with single copy transgenes using transposons or site-specific integration using the ΦC31 integrase has allowed numerous manipulations, including the ability to create and integrate genomic rescue constructs, generate duplications, RNAi knock-out technology, binary expression systems like the GAL4/UAS system as well as other methods. Here, we will discuss the most useful methodologies to interrogate the fruit fly genome in vivo focusing on chemical mutagenesis, transposons and transgenes. Genome engineering approaches based on nucleases and RNAi technology are discussed in following chapters.
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Affiliation(s)
- Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Program in Developmental Biology, Baylor College of Medicine, TX 77030, United States.
| | - Hugo J Bellen
- Program in Developmental Biology, Departments of Molecular and Human Genetics, Department of Neuroscience, Howard Hughes Medical Institute, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, United States.
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19
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Mohr SE. RNAi screening in Drosophila cells and in vivo. Methods 2014; 68:82-8. [PMID: 24576618 DOI: 10.1016/j.ymeth.2014.02.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/07/2014] [Accepted: 02/13/2014] [Indexed: 12/31/2022] Open
Abstract
Here, I discuss how RNAi screening can be used effectively to uncover gene function. Specifically, I discuss the types of high-throughput assays that can be done in Drosophila cells and in vivo, RNAi reagent design and available reagent collections, automated screen pipelines, analysis of screen results, and approaches to RNAi results verification.
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Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States.
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20
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In Vivo RNAi-Based Screens: Studies in Model Organisms. Genes (Basel) 2013; 4:646-65. [PMID: 24705267 PMCID: PMC3927573 DOI: 10.3390/genes4040646] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 10/29/2013] [Accepted: 11/14/2013] [Indexed: 11/23/2022] Open
Abstract
RNA interference (RNAi) is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA) and target mRNA molecules. Numerous cell-based genome-wide screens have successfully identified novel genes involved in various biological processes, including signal transduction, cell viability/death, and cell morphology. However, cell-based screens cannot address cellular processes such as development, behavior, and immunity. Drosophila and Caenorhabditis elegans are two model organisms whose whole bodies and individual body parts have been subjected to RNAi-based genome-wide screening. Moreover, Drosophila RNAi allows the manipulation of gene function in a spatiotemporal manner when it is implemented using the Gal4/UAS system. Using this inducible RNAi technique, various large-scale screens have been performed in Drosophila, demonstrating that the method is straightforward and valuable. However, accumulated results reveal that the results of RNAi-based screens have relatively high levels of error, such as false positives and negatives. Here, we review in vivo RNAi screens in Drosophila and the methods that could be used to remove ambiguity from screening results.
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21
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Validating RNAi phenotypes in Drosophila using a synthetic RNAi-resistant transgene. PLoS One 2013; 8:e70489. [PMID: 23950943 PMCID: PMC3738578 DOI: 10.1371/journal.pone.0070489] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022] Open
Abstract
RNA interference (RNAi) is a powerful and widely used approach to investigate gene function, but a major limitation of the approach is the high incidence of non-specific phenotypes that arise due to off-target effects. We previously showed that RNAi-mediated knock-down of pico, which encodes the only member of the MRL family of adapter proteins in Drosophila, resulted in reduction in cell number and size leading to reduced tissue growth. In contrast, a recent study reported that pico knockdown leads to tissue dysmorphology, pointing to an indirect role for pico in the control of wing size. To understand the cause of this disparity we have utilised a synthetic RNAi-resistant transgene, which bears minimal sequence homology to the predicted dsRNA but encodes wild type Pico protein, to reanalyse the RNAi lines used in the two studies. We find that the RNAi lines from different sources exhibit different effects, with one set of lines uniquely resulting in a tissue dysmorphology phenotype when expressed in the developing wing. Importantly, the loss of tissue morphology fails to be complemented by co-overexpression of RNAi-resistant pico suggesting that this phenotype is the result of an off-target effect. This highlights the importance of careful validation of RNAi-induced phenotypes, and shows the potential of synthetic transgenes for their experimental validation.
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22
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Wredenberg A, Lagouge M, Bratic A, Metodiev MD, Spåhr H, Mourier A, Freyer C, Ruzzenente B, Tain L, Grönke S, Baggio F, Kukat C, Kremmer E, Wibom R, Polosa PL, Habermann B, Partridge L, Park CB, Larsson NG. MTERF3 regulates mitochondrial ribosome biogenesis in invertebrates and mammals. PLoS Genet 2013; 9:e1003178. [PMID: 23300484 PMCID: PMC3536695 DOI: 10.1371/journal.pgen.1003178] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022] Open
Abstract
Regulation of mitochondrial DNA (mtDNA) expression is critical for the control of oxidative phosphorylation in response to physiological demand, and this regulation is often impaired in disease and aging. We have previously shown that mitochondrial transcription termination factor 3 (MTERF3) is a key regulator that represses mtDNA transcription in the mouse, but its molecular mode of action has remained elusive. Based on the hypothesis that key regulatory mechanisms for mtDNA expression are conserved in metazoans, we analyzed Mterf3 knockout and knockdown flies. We demonstrate here that decreased expression of MTERF3 not only leads to activation of mtDNA transcription, but also impairs assembly of the large mitochondrial ribosomal subunit. This novel function of MTERF3 in mitochondrial ribosomal biogenesis is conserved in the mouse, thus we identify a novel and unexpected role for MTERF3 in coordinating the crosstalk between transcription and translation for the regulation of mammalian mtDNA gene expression.
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Affiliation(s)
- Anna Wredenberg
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marie Lagouge
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Ana Bratic
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Henrik Spåhr
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Arnaud Mourier
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Christoph Freyer
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Luke Tain
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | | | | | | | - Elisabeth Kremmer
- Helmholtz Center, Institute for Molecular Immunology, Munich, Germany
| | - Rolf Wibom
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies, and Pharmacological Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | | | - Chan Bae Park
- Institute for Medical Sciences, Ajou University School of Medicine, Suwon, Korea
- Mitochondria Hub Regulation Center, Dong-A University College of Medicine, Busan, Republic of Korea
- * E-mail: (CBP); (N-GL)
| | - Nils-Göran Larsson
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (CBP); (N-GL)
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23
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St Johnston D. Using mutants, knockdowns, and transgenesis to investigate gene function in Drosophila. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:587-613. [PMID: 24014449 DOI: 10.1002/wdev.101] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The sophisticated genetic techniques available in Drosophila are largely responsible for its success as a model organism. One of the most important of these is the ability to disrupt gene function in vivo and observe the resulting phenotypes. This review considers the ever-increasing repertoire of approaches for perturbing the functions of specific genes in flies, ranging from classical and transposon-mediated mutageneses to newer techniques, such as homologous recombination and RNA interference. Since most genes are used over and over again in different contexts during development, many important advances have depended on being able to interfere with gene function at specific times or places in the developing animal, and a variety of approaches are now available to do this. Most of these techniques rely on being able to create genetically modified strains of Drosophila and the different methods for generating lines carrying single copy transgenic constructs will be described, along with the advantages and disadvantages of each approach.
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Affiliation(s)
- Daniel St Johnston
- The Gurdon Institute and the Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK.
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24
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Ahn J, Woo HN, Ko A, Khim M, Kim C, Park NH, Song HY, Kim SW, Lee H. Multispecies-compatible antitumor effects of a cross-species small-interfering RNA against mammalian target of rapamycin. Cell Mol Life Sci 2012; 69:3147-58. [PMID: 22562582 PMCID: PMC11115121 DOI: 10.1007/s00018-012-0998-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 12/11/2022]
Abstract
Successful development of sequence-specific siRNA (small interfering RNA)-based drugs requires an siRNA design that functions consistently in different organisms. Utilizing the CAPSID program previously developed by our group, we here designed siRNAs against mammalian target of rapamycin (mTOR) that are entirely complementary among various species and investigated their multispecies-compatible gene-silencing properties. The mTOR siRNAs markedly reduced mTOR expression at both the mRNA and protein levels in human, mouse, and monkey cell lines. The reduction in mTOR expression resulted in inactivation of both mTOR complex I and II signaling pathways, as confirmed by reduced phosphorylation of p70S6K (70-kDa ribosomal protein S6 kinase), 4EBP1 (eIF4E-binding protein 1), and AKT, and nuclear accumulation of FOXO1 (forkhead box O1), with consequent cell-cycle arrest, proliferation inhibition, and autophagy activation. Moreover, interfering with mTOR activity in vivo using mTOR small-hairpin RNA-expressing recombinant adeno-associated virus led to significant antitumor effects in xenograft and allograft models. Thus, the present study demonstrates that cross-species siRNA successfully silences its target and readily produces multispecies-compatible phenotypic alterations-antitumor effects in the case of mTOR siRNA. Application of cross-species siRNA should greatly facilitate the development of siRNA-based therapeutic agents.
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Affiliation(s)
- Jeonghyun Ahn
- Department of Microbiology, University of Ulsan College of Medicine, 86 Asanbyeongwon-Gil Songpa-Gu, Seoul, Korea
- Bio-Medical Research Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ha-Na Woo
- Department of Microbiology, University of Ulsan College of Medicine, 86 Asanbyeongwon-Gil Songpa-Gu, Seoul, Korea
- Bio-Medical Research Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ara Ko
- Department of Microbiology, University of Ulsan College of Medicine, 86 Asanbyeongwon-Gil Songpa-Gu, Seoul, Korea
| | - Maria Khim
- Department of Microbiology, University of Ulsan College of Medicine, 86 Asanbyeongwon-Gil Songpa-Gu, Seoul, Korea
| | - Catherine Kim
- Department of Microbiology, University of Ulsan College of Medicine, 86 Asanbyeongwon-Gil Songpa-Gu, Seoul, Korea
| | - Nung Hwa Park
- Bio-Medical Research Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Young Song
- Department of Radiology, University of Ulsan College of Medicine, Seoul, Korea
- Asan Medical Center, Seoul, Korea
| | - Seong Who Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
- Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Seoul, Korea
- Cellular Dysfunction Research Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Heuiran Lee
- Department of Microbiology, University of Ulsan College of Medicine, 86 Asanbyeongwon-Gil Songpa-Gu, Seoul, Korea
- Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Seoul, Korea
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25
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Abstract
Kinesin heavy chain (Khc) is crucially required for axonal transport and khc mutants show axonal swellings and paralysis. Here, we demonstrate that in Drosophila khc is equally important in glial cells. Glial-specific downregulation of khc by RNA interference suppresses neuronal excitability and results in spastic flies. The specificity of the phenotype was verified by interspecies rescue experiments and further mutant analyses. Khc is mostly required in the subperineurial glia forming the blood-brain barrier. Following glial-specific knockdown, peripheral nerves are swollen with maldistributed mitochondria. To better understand khc function, we determined Khc-dependent Rab proteins in glia and present evidence that Neurexin IV, a well known blood-brain barrier constituent, is one of the relevant cargo proteins. Our work shows that the role of Khc for neuronal excitability must be considered in the light of its necessity for directed transport in glia.
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26
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Venken KJT, Bellen HJ. Genome-wide manipulations of Drosophila melanogaster with transposons, Flp recombinase, and ΦC31 integrase. Methods Mol Biol 2012; 859:203-28. [PMID: 22367874 DOI: 10.1007/978-1-61779-603-6_12] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Transposable elements, the Flp recombinase, and the ΦC31 integrase are used in Drosophila melanogaster for numerous genome-wide manipulations. Often, their use is combined in a synergistic fashion to alter and engineer the fruit fly genome. Transposons are the foundation for all transgenic technologies in flies and hence almost all innovations in the fruit fly. They have been instrumental in the generation of genome-wide collections of insertions for gene disruption and manipulation. Many important transgenic strains of these collections are available from public repositories. The Flp protein is the most widely used recombinase to induce mitotic clones to study individual gene function. However, Flp has also been used to generate chromosome- and genome-wide collections of precise deletions, inversions, and duplications. Similarly, transposons that contain attP attachment sites for the ΦC31 integrase can be used for numerous applications. This integrase was incorporated into a transgenesis system that allows the integration of small to very large DNA fragments that can be easily manipulated through recombineering. This system allowed the creation of genomic DNA libraries for genome-wide gene manipulations and X chromosome duplications. Moreover, the attP sites are being used to create libraries of tens of thousands of RNAi constructs and tissue-specific GAL4 lines. This chapter focuses on genome-wide applications of transposons, Flp recombinase, and ΦC31 integrase that greatly facilitate experimental manipulation of Drosophila.
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Affiliation(s)
- Koen J T Venken
- Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA.
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27
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Meinertzhagen IA, Lee CH. The genetic analysis of functional connectomics in Drosophila. ADVANCES IN GENETICS 2012; 80:99-151. [PMID: 23084874 DOI: 10.1016/b978-0-12-404742-6.00003-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fly and vertebrate nervous systems share many organizational features, such as layers, columns and glomeruli, and utilize similar synaptic components, such as ion channels and receptors. Both also exhibit similar network features. Recent technological advances, especially in electron microscopy, now allow us to determine synaptic circuits and identify pathways cell-by-cell, as part of the fly's connectome. Genetic tools provide the means to identify synaptic components, as well as to record and manipulate neuronal activity, adding function to the connectome. This review discusses technical advances in these emerging areas of functional connectomics, offering prognoses in each and identifying the challenges in bridging structural connectomics to molecular biology and synaptic physiology, thereby determining fundamental mechanisms of neural computation that underlie behavior.
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Affiliation(s)
- Ian A Meinertzhagen
- Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2.
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28
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Flockhart IT, Booker M, Hu Y, McElvany B, Gilly Q, Mathey-Prevot B, Perrimon N, Mohr SE. FlyRNAi.org--the database of the Drosophila RNAi screening center: 2012 update. Nucleic Acids Res 2011; 40:D715-9. [PMID: 22067456 PMCID: PMC3245182 DOI: 10.1093/nar/gkr953] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
FlyRNAi (http://www.flyrnai.org), the database and website of the Drosophila RNAi Screening Center (DRSC) at Harvard Medical School, serves a dual role, tracking both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. The database and website is used as a platform for community availability of protocols, tools, and other resources useful to researchers planning, conducting, analyzing or interpreting the results of Drosophila RNAi screens. Based on our own experience and user feedback, we have made several changes. Specifically, we have restructured the database to accommodate new types of reagents; added information about new RNAi libraries and other reagents; updated the user interface and website; and added new tools of use to the Drosophila community and others. Overall, the result is a more useful, flexible and comprehensive website and database.
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Affiliation(s)
- Ian T Flockhart
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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29
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Venken KJ, Simpson JH, Bellen HJ. Genetic manipulation of genes and cells in the nervous system of the fruit fly. Neuron 2011; 72:202-30. [PMID: 22017985 PMCID: PMC3232021 DOI: 10.1016/j.neuron.2011.09.021] [Citation(s) in RCA: 301] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2011] [Indexed: 12/26/2022]
Abstract
Research in the fruit fly Drosophila melanogaster has led to insights in neural development, axon guidance, ion channel function, synaptic transmission, learning and memory, diurnal rhythmicity, and neural disease that have had broad implications for neuroscience. Drosophila is currently the eukaryotic model organism that permits the most sophisticated in vivo manipulations to address the function of neurons and neuronally expressed genes. Here, we summarize many of the techniques that help assess the role of specific neurons by labeling, removing, or altering their activity. We also survey genetic manipulations to identify and characterize neural genes by mutation, overexpression, and protein labeling. Here, we attempt to acquaint the reader with available options and contexts to apply these methods.
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Affiliation(s)
- Koen J.T. Venken
- Department of Molecular and Human Genetics, Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030
| | - Julie H. Simpson
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030
- Program in Developmental Biology, Department of Neuroscience, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, 77030
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30
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Mohr SE, Perrimon N. RNAi screening: new approaches, understandings, and organisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:145-58. [PMID: 21953743 DOI: 10.1002/wrna.110] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.
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Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA, USA
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31
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Abstract
Drosophila melanogaster has a long history as a model organism with several unique features that make it an ideal research tool for the study of the relationship between genotype and phenotype. Importantly fundamental genetic principles as well as key human disease genes have been uncovered through the use of Drosophila. The contribution of the fruit fly to science and medicine continues in the postgenomic era as cell-based Drosophila RNAi screens are a cost-effective and scalable enabling technology that can be used to quantify the contribution of different genes to diverse cellular processes. Drosophila high-throughput screens can also be used as integral part of systems-level approaches to describe the architecture and dynamics of cellular networks.
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Affiliation(s)
- Chris Bakal
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, The Institute of Cancer Research, London, UK.
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32
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Seinen E, Burgerhof JGM, Jansen RC, Sibon OCM. RNAi-induced off-target effects in Drosophila melanogaster: frequencies and solutions. Brief Funct Genomics 2011; 10:206-14. [PMID: 21596801 DOI: 10.1093/bfgp/elr017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genes can be silenced with short-interfering RNA molecules (siRNA). siRNAs are widely used to identify gene functions and have high potential for therapeutic treatments. It is critical that the siRNA specifically targets the expression of the gene of interest but has no off-target effects on other genes. Although siRNAs were initially considered to be exclusively active on mature mRNAs in the cytoplasm, additional studies have shown that siRNAs are present in the nucleus as well, suggesting that pre-mRNA sequences containing introns and other untranslated regions can also be targeted. In this study, we investigated the extent to which off-targets may occur in Drosophila melanogaster by looking at mature mRNA sequences and pre-mature RNA sequences separately. First, an in silico approach revealed that, based on sequence similarity, numerous off-targets are predicted to occur in RNAi experiments. Second, existing microarray data were used to investigate a possible effect of the predicted off-targets based on analysis of in vitro data. We found that the occurrence of off-targets in both mature and pre-mature RNA sequences in RNAi experiments can be extensive and significant. Possibilities are discussed how to minimize off-target effects.
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Affiliation(s)
- Erwin Seinen
- Section of Radiation & Stress Cell Biology, Department of Cell Biology, University Medical Center Groningen, The Netherlands
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Booker M, Samsonova AA, Kwon Y, Flockhart I, Mohr SE, Perrimon N. False negative rates in Drosophila cell-based RNAi screens: a case study. BMC Genomics 2011; 12:50. [PMID: 21251254 PMCID: PMC3036618 DOI: 10.1186/1471-2164-12-50] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 01/20/2011] [Indexed: 01/13/2023] Open
Abstract
Background High-throughput screening using RNAi is a powerful gene discovery method but is often complicated by false positive and false negative results. Whereas false positive results associated with RNAi reagents has been a matter of extensive study, the issue of false negatives has received less attention. Results We performed a meta-analysis of several genome-wide, cell-based Drosophila RNAi screens, together with a more focused RNAi screen, and conclude that the rate of false negative results is at least 8%. Further, we demonstrate how knowledge of the cell transcriptome can be used to resolve ambiguous results and how the number of false negative results can be reduced by using multiple, independently-tested RNAi reagents per gene. Conclusions RNAi reagents that target the same gene do not always yield consistent results due to false positives and weak or ineffective reagents. False positive results can be partially minimized by filtering with transcriptome data. RNAi libraries with multiple reagents per gene also reduce false positive and false negative outcomes when inconsistent results are disambiguated carefully.
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Affiliation(s)
- Matthew Booker
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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Ejsmont RK, Bogdanzaliewa M, Lipinski KA, Tomancak P. Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis. Methods Mol Biol 2011; 772:423-443. [PMID: 22065453 DOI: 10.1007/978-1-61779-228-1_25] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genomic DNA libraries are a valuable source of large constructs that can contain all the regulatory elements necessary for recapitulating wild-type gene expression when introduced into animal genomes as a transgene. Such clones can be directly used in complementation studies. In combination with recombineering manipulation, the tagged genomic clones can serve as faithful in vivo gene activity reporters that enable studies of tissue specificity of gene expression, subcellular protein localization, and affinity purification of complexes. We present a detailed protocol for generating an unbiased genomic library in a custom pFlyFos vector that is optimized for liquid culture recombineering manipulation and site-specific transgenesis of fosmid-size loci across different Drosophila species. The cross-species properties of the library can be used, for example, to establish the specificity of RNAi phenotypes or to selectively introgress specific genomic loci among different Drosophila species making it an ideal tool for experimental evolutionary studies. The FlyFos system can be easily adapted to other organisms.
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Neumüller RA, Perrimon N. Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 3:471-8. [PMID: 21197652 DOI: 10.1002/wsbm.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Systems biology aims to describe the complex interplays between cellular building blocks which, in their concurrence, give rise to the emergent properties observed in cellular behaviors and responses. This approach tries to determine the molecular players and the architectural principles of their interactions within the genetic networks that control certain biological processes. Large-scale loss-of-function screens, applicable in various different model systems, have begun to systematically interrogate entire genomes to identify the genes that contribute to a certain cellular response. In particular, RNA interference (RNAi)-based high-throughput screens have been instrumental in determining the composition of regulatory systems and paired with integrative data analyses have begun to delineate the genetic networks that control cell biological and developmental processes. Through the creation of tools for both, in vitro and in vivo genome-wide RNAi screens, Drosophila melanogaster has emerged as one of the key model organisms in systems biology research and over the last years has massively contributed to and hence shaped this discipline. WIREs Syst Biol Med 2011 3 471-478 DOI: 10.1002/wsbm.127
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Affiliation(s)
- Ralph A Neumüller
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA, USA
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Abstract
Reverse genetics consists in the modification of the activity of a target gene to analyse the phenotypic consequences. Four main approaches are used towards this goal and will be explained in this review. Two of them are centred on genome alterations. Mutations produced by random chemical or insertional mutagenesis can be screened to recover only mutants in a specific gene of interest. Alternatively, these alterations may be specifically targeted on a gene of interest by HR (homologous recombination). The other two approaches are centred on mRNA. RNA interference is a powerful method to reduce the level of gene products, while MO (morpholino) antisense oligonucleotides alter mRNA metabolism or translation. Some model species, such as Drosophila, are amenable to most of these approaches, whereas other model species are restricted to one of them. For example, in mice and yeasts, gene targeting by HR is prevalent, whereas in Xenopus and zebrafish MO oligonucleotides are mainly used. Genome-wide collections of mutants or inactivated models obtained in several species by these approaches have been made and will help decipher gene functions in the post-genomic era.
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Abstract
We describe a molecularly defined duplication kit for the X chromosome of Drosophila melanogaster. A set of 408 overlapping P[acman] BAC clones was used to create small duplications (average length 88 kb) covering the 22-Mb sequenced portion of the chromosome. The BAC clones were inserted into an attP docking site on chromosome 3L using ΦC31 integrase, allowing direct comparison of different transgenes. The insertions complement 92% of the essential and viable mutations and deletions tested, demonstrating that almost all Drosophila genes are compact and that the current annotations of the genome are reasonably accurate. Moreover, almost all genes are tolerated at twice the normal dosage. Finally, we more precisely mapped two regions at which duplications cause diplo-lethality in males. This collection comprises the first molecularly defined duplication set to cover a whole chromosome in a multicellular organism. The work presented removes a long-standing barrier to genetic analysis of the Drosophila X chromosome, will greatly facilitate functional assays of X-linked genes in vivo, and provides a model for functional analyses of entire chromosomes in other species.
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Abstract
RNA interference (RNAi) provides a powerful reverse genetics approach to analyze gene functions both in tissue culture and in vivo. Because of its widespread applicability and effectiveness it has become an essential part of the tool box kits of model organisms such as Caenorhabditis elegans, Drosophila, and the mouse. In addition, the use of RNAi in animals in which genetic tools are either poorly developed or nonexistent enables a myriad of fundamental questions to be asked. Here, we review the methods and applications of in vivo RNAi to characterize gene functions in model organisms and discuss their impact to the study of developmental as well as evolutionary questions. Further, we discuss the applications of RNAi technologies to crop improvement, pest control and RNAi therapeutics, thus providing an appreciation of the potential for phenomenal applications of RNAi to agriculture and medicine.
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Affiliation(s)
- Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Langer CCH, Ejsmont RK, Schönbauer C, Schnorrer F, Tomancak P. In vivo RNAi rescue in Drosophila melanogaster with genomic transgenes from Drosophila pseudoobscura. PLoS One 2010; 5:e8928. [PMID: 20126626 PMCID: PMC2812509 DOI: 10.1371/journal.pone.0008928] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 01/08/2010] [Indexed: 01/19/2023] Open
Abstract
Background Systematic, large-scale RNA interference (RNAi) approaches are very valuable to systematically investigate biological processes in cell culture or in tissues of organisms such as Drosophila. A notorious pitfall of all RNAi technologies are potential false positives caused by unspecific knock-down of genes other than the intended target gene. The ultimate proof for RNAi specificity is a rescue by a construct immune to RNAi, typically originating from a related species. Methodology/Principal Findings We show that primary sequence divergence in areas targeted by Drosophila melanogaster RNAi hairpins in five non-melanogaster species is sufficient to identify orthologs for 81% of the genes that are predicted to be RNAi refractory. We use clones from a genomic fosmid library of Drosophila pseudoobscura to demonstrate the rescue of RNAi phenotypes in Drosophila melanogaster muscles. Four out of five fosmid clones we tested harbour cross-species functionality for the gene assayed, and three out of the four rescue a RNAi phenotype in Drosophila melanogaster. Conclusions/Significance The Drosophila pseudoobscura fosmid library is designed for seamless cross-species transgenesis and can be readily used to demonstrate specificity of RNAi phenotypes in a systematic manner.
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Affiliation(s)
| | - Radoslaw K. Ejsmont
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Frank Schnorrer
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
- * E-mail: (FS); (PT)
| | - Pavel Tomancak
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- * E-mail: (FS); (PT)
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