1
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Rankin AE, Fox E, Chisholm T, Lantz N, Rajan A, Phillips W, Griffin E, Harper J, Suhr C, Tan M, Wang J, Yang A, Kim ES, Ankrah NKA, Chakraborty P, Lam ACK, Laws ME, Lee J, Park KK, Wesel E, Covert PH, Kockel L, Park S, Kim SK. Simplified homology-assisted CRISPR for gene editing in Drosophila. G3 (BETHESDA, MD.) 2024; 14:jkad277. [PMID: 38058125 PMCID: PMC10849607 DOI: 10.1093/g3journal/jkad277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 08/28/2023] [Accepted: 10/29/2023] [Indexed: 12/08/2023]
Abstract
In vivo genome editing with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 generates powerful tools to study gene regulation and function. We revised the homology-assisted CRISPR knock-in method to convert Drosophila GAL4 lines to LexA lines using a new universal knock-in donor strain. A balancer chromosome-linked donor strain with both body color (yellow) and eye red fluorescent protein (RFP) expression markers simplified the identification of LexA knock-in using light or fluorescence microscopy. A second balancer chromosome-linked donor strain readily converted the second chromosome-linked GAL4 lines regardless of target location in the cis-chromosome but showed limited success for the third chromosome-linked GAL4 lines. We observed a consistent and robust expression of the yellow transgene in progeny harboring a LexA knock-in at diverse genomic locations. Unexpectedly, the expression of the 3xP3-RFP transgene in the "dual transgene" cassette was significantly increased compared with that of the original single 3xP3-RFP transgene cassette in all tested genomic locations. Using this improved screening approach, we generated 16 novel LexA lines; tissue expression by the derived LexA and originating GAL4 lines was similar or indistinguishable. In collaboration with 2 secondary school classes, we also established a systematic workflow to generate a collection of LexA lines from frequently used GAL4 lines.
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Affiliation(s)
| | - Elizabeth Fox
- The Lawrenceville School, Lawrenceville, NJ 08648, USA
| | | | - Nicole Lantz
- The Lawrenceville School, Lawrenceville, NJ 08648, USA
| | - Arjun Rajan
- Phillips Exeter Academy, Exeter, NH 03833, USA
| | | | | | | | | | - Max Tan
- Phillips Exeter Academy, Exeter, NH 03833, USA
| | - Jason Wang
- Phillips Exeter Academy, Exeter, NH 03833, USA
| | - Alana Yang
- Phillips Exeter Academy, Exeter, NH 03833, USA
| | - Ella S Kim
- Phillips Exeter Academy, Exeter, NH 03833, USA
| | | | | | | | | | - Jackson Lee
- The Lawrenceville School, Lawrenceville, NJ 08648, USA
| | - Kyle K Park
- The Lawrenceville School, Lawrenceville, NJ 08648, USA
| | - Emily Wesel
- Stanford University, Stanford, CA 94305, USA
| | | | - Lutz Kockel
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sangbin Park
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Diabetes Research Center, Stanford, CA 94305, USA
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2
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Madan V, Albacete‐Albacete L, Jin L, Scaturro P, Watson JL, Muschalik N, Begum F, Boulanger J, Bauer K, Kiebler MA, Derivery E, Bullock SL. HEATR5B associates with dynein-dynactin and promotes motility of AP1-bound endosomal membranes. EMBO J 2023; 42:e114473. [PMID: 37872872 PMCID: PMC10690479 DOI: 10.15252/embj.2023114473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023] Open
Abstract
The microtubule motor dynein mediates polarised trafficking of a wide variety of organelles, vesicles and macromolecules. These functions are dependent on the dynactin complex, which helps recruit cargoes to dynein's tail and activates motor movement. How the dynein-dynactin complex orchestrates trafficking of diverse cargoes is unclear. Here, we identify HEATR5B, an interactor of the adaptor protein-1 (AP1) clathrin adaptor complex, as a novel player in dynein-dynactin function. HEATR5B was recovered in a biochemical screen for proteins whose association with the dynein tail is augmented by dynactin. We show that HEATR5B binds directly to the dynein tail and dynactin and stimulates motility of AP1-associated endosomal membranes in human cells. We also demonstrate that the Drosophila HEATR5B homologue is an essential gene that selectively promotes dynein-based transport of AP1-bound membranes to the Golgi apparatus. As HEATR5B lacks the coiled-coil architecture typical of dynein adaptors, our data point to a non-canonical process orchestrating motor function on a specific cargo. We additionally show that HEATR5B promotes association of AP1 with endosomal membranes independently of dynein. Thus, HEATR5B co-ordinates multiple events in AP1-based trafficking.
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Affiliation(s)
- Vanesa Madan
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
AbcamCambridgeUK
| | - Lucas Albacete‐Albacete
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Li Jin
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | | | - Joseph L Watson
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Nadine Muschalik
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Farida Begum
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Jérôme Boulanger
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Karl Bauer
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Emmanuel Derivery
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Simon L Bullock
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
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3
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Thakkar N, Hejzlarova A, Brabec V, Dolezel D. Germline Editing of Drosophila Using CRISPR-Cas9-Based Cytosine and Adenine Base Editors. CRISPR J 2023; 6:557-569. [PMID: 37917075 DOI: 10.1089/crispr.2023.0026] [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: 11/03/2023] Open
Abstract
Target-AID, BE3, and ABE7.10 base editors fused to the catalytically modified Cas9 and xCas9(3.7) were tested for germline editing of the fruit fly Drosophila melanogaster. We developed a guide RNA-expressing construct, white-4gRNA, targeting splice sites in the white gene, an X-chromosome located gene. Using white-4gRNA flies and transgenic lines expressing Target-AID, BE3, and ABE7.10 base editors, we tested the efficiency of stable germline gene editing at three different temperatures. Classical Cas9 generating insertions/deletions by non-homologous end joining served as a reference. Our data indicate that gene editing is most efficient at 28°C, the highest temperature suitable for fruit flies. Finally, we created a new allele of the core circadian clock gene timeless using Target-AID. This base edited mutant allele timSS308-9FL had a disrupted circadian clock with a period of ∼29 h. The white-4gRNA expressing fly can be used to test new generations of base editors for future applications in Drosophila.
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Affiliation(s)
- Nirav Thakkar
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Adela Hejzlarova
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Vaclav Brabec
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - David Dolezel
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
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4
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Son W, Chung KW. Targeted recombination of homologous chromosomes using CRISPR-Cas9. FEBS Open Bio 2023; 13:1658-1666. [PMID: 37462508 PMCID: PMC10476559 DOI: 10.1002/2211-5463.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/22/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
CRISPR mutagenesis is an efficient way to disrupt specific target genes in many model organisms. We previously devised a targeted CRISPR recombination method to generate intragenic recombinants of alleles in Drosophila. Here, we assessed the applicability of CRISPR targeting-induced recombination to different genetic loci. We compared the ectopic recombination rates in the male germline by CRISPR targeting at two neighboring genetic loci within the genomic region that consists of the repressed chromatin domain of the Lobe gene, and the transcriptionally active domain of PRAS40. Targeting around the transcription initiation of PRAS40 resulted in higher recombination rates of homologous chromosomes than targeting at the Lobe intron. Based on the efficient homologous recombination by CRISPR targeting observed around transcriptionally active loci, we further investigated targeted recombination between P-elements that are inserted at different genomic locations. Male recombination by CRISPR targeting of P-elements located proximally and distally to the ebony gene produced recombinants deficient for the intervening region of ebony transcription. Taken together, we suggest that targeted homologous recombination by CRISPR targeting may have specific genetic applications, such as generation of allelic combinations or chromosomal variations.
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Affiliation(s)
- Wonseok Son
- Department of Biological Sciences and BK21 Team for Field‐oriented BioCore Human Resources DevelopmentKongju National UniversityGongjuSouth Korea
| | - Ki Wha Chung
- Department of Biological Sciences and BK21 Team for Field‐oriented BioCore Human Resources DevelopmentKongju National UniversityGongjuSouth Korea
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5
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Rocha JJ, Jayaram SA, Stevens TJ, Muschalik N, Shah RD, Emran S, Robles C, Freeman M, Munro S. Functional unknomics: Systematic screening of conserved genes of unknown function. PLoS Biol 2023; 21:e3002222. [PMID: 37552676 PMCID: PMC10409296 DOI: 10.1371/journal.pbio.3002222] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023] Open
Abstract
The human genome encodes approximately 20,000 proteins, many still uncharacterised. It has become clear that scientific research tends to focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected. To address this, we have developed a publicly available and customisable "Unknome database" that ranks proteins based on how little is known about them. We applied RNA interference (RNAi) in Drosophila to 260 unknown genes that are conserved between flies and humans. Knockdown of some genes resulted in loss of viability, and functional screening of the rest revealed hits for fertility, development, locomotion, protein quality control, and resilience to stress. CRISPR/Cas9 gene disruption validated a component of Notch signalling and 2 genes contributing to male fertility. Our work illustrates the importance of poorly understood genes, provides a resource to accelerate future research, and highlights a need to support database curation to ensure that misannotation does not erode our awareness of our own ignorance.
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Affiliation(s)
- João J. Rocha
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Tim J. Stevens
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Rajen D. Shah
- Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sahar Emran
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Cristina Robles
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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6
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Schneider BK, Sun S, Lee M, Li W, Skvir N, Neretti N, Vijg J, Secombe J. Expression of retrotransposons contributes to aging in Drosophila. Genetics 2023; 224:iyad073. [PMID: 37084379 PMCID: PMC10213499 DOI: 10.1093/genetics/iyad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/12/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Retrotransposons are a class of transposable elements capable of self-replication and insertion into new genomic locations. Across species, the mobilization of retrotransposons in somatic cells has been suggested to contribute to the cell and tissue functional decline that occurs during aging. Retrotransposons are broadly expressed across cell types, and de novo insertions have been observed to correlate with tumorigenesis. However, the extent to which new retrotransposon insertions occur during normal aging and their effect on cellular and animal function remains understudied. Here, we use a single nucleus whole genome sequencing approach in Drosophila to directly test whether transposon insertions increase with age in somatic cells. Analyses of nuclei from thoraces and indirect flight muscles using a newly developed pipeline, Retrofind, revealed no significant increase in the number of transposon insertions with age. Despite this, reducing the expression of two different retrotransposons, 412 and Roo, extended lifespan, but did not alter indicators of health such as stress resistance. This suggests a key role for transposon expression and not insertion in regulating longevity. Transcriptomic analyses revealed similar changes to gene expression in 412 and Roo knockdown flies and highlighted changes to genes involved in proteolysis and immune function as potential contributors to the observed changes in longevity. Combined, our data show a clear link between retrotransposon expression and aging.
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Affiliation(s)
- Blair K Schneider
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 809 Bronx, NY 10461, USA
| | - Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
| | - Wenge Li
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 909 Bronx, NY 10461, USA
| | - Nicholas Skvir
- Department of Molecular biology, Cell biology and Biochemistry, Brown University, 70 Ship St., Providence 02903, USA
| | - Nicola Neretti
- Department of Molecular biology, Cell biology and Biochemistry, Brown University, 70 Ship St., Providence 02903, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 809 Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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7
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Ma M, Zhang X, Zheng Y, Lu S, Pan X, Mao X, Pan H, Chung HL, Wang H, Guo H, Bellen HJ. The fly homolog of SUPT16H, a gene associated with neurodevelopmental disorders, is required in a cell-autonomous fashion for cell survival. Hum Mol Genet 2023; 32:984-997. [PMID: 36255738 PMCID: PMC9991001 DOI: 10.1093/hmg/ddac259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/22/2022] [Accepted: 10/14/2022] [Indexed: 11/14/2022] Open
Abstract
SUPT16H encodes the large subunit of the FAcilitate Chromatin Transcription (FACT) complex, which functions as a nucleosome organizer during transcription. We identified two individuals from unrelated families carrying de novo missense variants in SUPT16H. The probands exhibit global developmental delay, intellectual disability, epilepsy, facial dysmorphism and brain structural abnormalities. We used Drosophila to characterize two variants: p.T171I and p.G808R. Loss of the fly ortholog, dre4, causes lethality at an early developmental stage. RNAi-mediated knockdown of dre4 in either glia or neurons causes severely reduced eclosion and longevity. Tissue-specific knockdown of dre4 in the eye or wing leads to the loss of these tissues, whereas overexpression of SUPT16H has no dominant effect. Moreover, expression of the reference SUPT16H significantly rescues the loss-of-function phenotypes in the nervous system as well as wing and eye. In contrast, expression of SUPT16H p.T171I or p.G808R rescues the phenotypes poorly, indicating that the variants are partial loss-of-function alleles. While previous studies argued that the developmental arrest caused by loss of dre4 is due to impaired ecdysone production in the prothoracic gland, our data show that dre4 is required for proper cell growth and survival in multiple tissues in a cell-autonomous manner. Altogether, our data indicate that the de novo loss-of-function variants in SUPT16H are indeed associated with developmental and neurological defects observed in the probands.
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Affiliation(s)
- Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xi Zhang
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yiming Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xiao Mao
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hyung-lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hua Wang
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Hunan Children’s Hospital, Changsha, Hunan 410007, China
| | - Hong Guo
- Department of Medical Genetics, Army Medical University, Chongqing 400038, China
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
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8
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Abstract
Intercellular communication by Wnt proteins governs many essential processes during development, tissue homeostasis and disease in all metazoans. Many context-dependent effects are initiated in the Wnt-producing cells and depend on the export of lipidated Wnt proteins. Although much focus has been on understanding intracellular Wnt signal transduction, the cellular machinery responsible for Wnt secretion became better understood only recently. After lipid modification by the acyl-transferase Porcupine, Wnt proteins bind their dedicated cargo protein Evi/Wntless for transport and secretion. Evi/Wntless and Porcupine are conserved transmembrane proteins, and their 3D structures were recently determined. In this Review, we summarise studies and structural data highlighting how Wnts are transported from the ER to the plasma membrane, and the role of SNX3-retromer during the recycling of its cargo receptor Evi/Wntless. We also describe the regulation of Wnt export through a post-translational mechanism and review the importance of Wnt secretion for organ development and cancer, and as a future biomarker.
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Affiliation(s)
- Lucie Wolf
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant and Department of Cell and Molecular Biology, 69120 Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant and Department of Cell and Molecular Biology, 69120 Heidelberg, Germany
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9
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CRISPR-Cas Genome Editing for Insect Pest Stress Management in Crop Plants. STRESSES 2022. [DOI: 10.3390/stresses2040034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Global crop yield and food security are being threatened by phytophagous insects. Innovative methods are required to increase agricultural output while reducing reliance on hazardous synthetic insecticides. Using the revolutionary CRISPR-Cas technology to develop insect-resistant plants appears to be highly efficient at lowering production costs and increasing farm profitability. The genomes of both a model insect, Drosophila melanogaster, and major phytophagous insect genera, viz. Spodoptera, Helicoverpa, Nilaparvata, Locusta, Tribolium, Agrotis, etc., were successfully edited by the CRISPR-Cas toolkits. This new method, however, has the ability to alter an insect’s DNA in order to either induce a gene drive or overcome an insect’s tolerance to certain insecticides. The rapid progress in the methodologies of CRISPR technology and their diverse applications show a high promise in the development of insect-resistant plant varieties or other strategies for the sustainable management of insect pests to ensure food security. This paper reviewed and critically discussed the use of CRISPR-Cas genome-editing technology in long-term insect pest management. The emphasis of this review was on the prospective uses of the CRISPR-Cas system for insect stress management in crop production through the creation of genome-edited crop plants or insects. The potential and the difficulties of using CRISPR-Cas technology to reduce pest stress in crop plants were critically examined and discussed.
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10
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Singh S, Rahangdale S, Pandita S, Saxena G, Upadhyay SK, Mishra G, Verma PC. CRISPR/Cas9 for Insect Pests Management: A Comprehensive Review of Advances and Applications. AGRICULTURE 2022; 12:1896. [DOI: 10.3390/agriculture12111896] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
Abstract
Insect pests impose a serious threat to agricultural productivity. Initially, for pest management, several breeding approaches were applied which have now been gradually replaced by genome editing (GE) strategies as they are more efficient and less laborious. CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated system) was discovered as an adaptive immune system of bacteria and with the scientific advancements, it has been improvised into a revolutionary genome editing technique. Due to its specificity and easy handling, CRISPR/Cas9-based genome editing has been applied to a wide range of organisms for various research purposes. For pest control, diverse approaches have been applied utilizing CRISPR/Cas9-like systems, thereby making the pests susceptible to various insecticides, compromising the reproductive fitness of the pest, hindering the metamorphosis of the pest, and there have been many other benefits. This article reviews the efficiency of CRISPR/Cas9 and proposes potential research ideas for CRISPR/Cas9-based integrated pest management. CRISPR/Cas9 technology has been successfully applied to several insect pest species. However, there is no review available which thoroughly summarizes the application of the technique in insect genome editing for pest control. Further, authors have highlighted the advancements in CRISPR/Cas9 research and have discussed its future possibilities in pest management.
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Affiliation(s)
- Sanchita Singh
- CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow 226001, UP, India
- Department of Botany, University of Lucknow, Lucknow 226007, UP, India
| | - Somnath Rahangdale
- CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow 226001, UP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, UP, India
| | - Shivali Pandita
- CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow 226001, UP, India
- Department of Zoology, University of Lucknow, Lucknow 226007, UP, India
| | - Gauri Saxena
- Department of Botany, University of Lucknow, Lucknow 226007, UP, India
| | | | - Geetanjali Mishra
- Department of Zoology, University of Lucknow, Lucknow 226007, UP, India
| | - Praveen C. Verma
- CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow 226001, UP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, UP, India
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11
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Steinacker TL, Wong SS, Novak ZA, Saurya S, Gartenmann L, van Houtum EJ, Sayers JR, Lagerholm BC, Raff JW. Centriole growth is limited by the Cdk/Cyclin-dependent phosphorylation of Ana2/STIL. J Cell Biol 2022; 221:e202205058. [PMID: 35861803 PMCID: PMC9442473 DOI: 10.1083/jcb.202205058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022] Open
Abstract
Centrioles duplicate once per cell cycle, but it is unclear how daughter centrioles assemble at the right time and place and grow to the right size. Here, we show that in Drosophila embryos the cytoplasmic concentrations of the key centriole assembly proteins Asl, Plk4, Ana2, Sas-6, and Sas-4 are low, but remain constant throughout the assembly process-indicating that none of them are limiting for centriole assembly. The cytoplasmic diffusion rate of Ana2/STIL, however, increased significantly toward the end of S-phase as Cdk/Cyclin activity in the embryo increased. A mutant form of Ana2 that cannot be phosphorylated by Cdk/Cyclins did not exhibit this diffusion change and allowed daughter centrioles to grow for an extended period. Thus, the Cdk/Cyclin-dependent phosphorylation of Ana2 seems to reduce the efficiency of daughter centriole assembly toward the end of S-phase. This helps to ensure that daughter centrioles stop growing at the correct time, and presumably also helps to explain why centrioles cannot duplicate during mitosis.
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Affiliation(s)
| | - Siu-Shing Wong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Zsofia A. Novak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Saroj Saurya
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lisa Gartenmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Judith R. Sayers
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Jordan W. Raff
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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12
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Wong S, Wilmott ZM, Saurya S, Alvarez‐Rodrigo I, Zhou FY, Chau K, Goriely A, Raff JW. Centrioles generate a local pulse of Polo/PLK1 activity to initiate mitotic centrosome assembly. EMBO J 2022; 41:e110891. [PMID: 35505659 PMCID: PMC9156973 DOI: 10.15252/embj.2022110891] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/03/2022] Open
Abstract
Mitotic centrosomes are formed when centrioles start to recruit large amounts of pericentriolar material (PCM) around themselves in preparation for mitosis. This centrosome "maturation" requires the centrioles and also Polo/PLK1 protein kinase. The PCM comprises several hundred proteins and, in Drosophila, Polo cooperates with the conserved centrosome proteins Spd-2/CEP192 and Cnn/CDK5RAP2 to assemble a PCM scaffold around the mother centriole that then recruits other PCM client proteins. We show here that in Drosophila syncytial blastoderm embryos, centrosomal Polo levels rise and fall during the assembly process-peaking, and then starting to decline, even as levels of the PCM scaffold continue to rise and plateau. Experiments and mathematical modelling indicate that a centriolar pulse of Polo activity, potentially generated by the interaction between Polo and its centriole receptor Ana1 (CEP295 in humans), could explain these unexpected scaffold assembly dynamics. We propose that centrioles generate a local pulse of Polo activity prior to mitotic entry to initiate centrosome maturation, explaining why centrioles and Polo/PLK1 are normally essential for this process.
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Affiliation(s)
- Siu‐Shing Wong
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Zachary M Wilmott
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
- Mathematical InstituteUniversity of OxfordOxfordUK
| | - Saroj Saurya
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | | | - Felix Y Zhou
- Ludwig Institute for Cancer ResearchNuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
- Present address:
Lyda Hill Department of BioinformaticsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Kwai‐Yin Chau
- Department of Computer ScienceUniversity of BathBathUK
| | | | - Jordan W Raff
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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13
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Wagner A, Seiler J, Beye M. Highly efficient site-specific integration of DNA fragments into the honeybee genome using CRISPR/Cas9. G3 (BETHESDA, MD.) 2022; 12:jkac098. [PMID: 35536186 PMCID: PMC9157169 DOI: 10.1093/g3journal/jkac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
Abstract
Functional genetic studies in honeybees have been limited to transposon mediated transformation and site directed mutagenesis tools. However, site- and sequence-specific manipulations that insert DNA fragments or replace sequences at specific target sites are lacking. Such tools would enable the tagging of proteins, the expression of reporters and site-specific amino acid changes, which are all gold standard manipulations for physiological, organismal, and genetic studies. However, such manipulations must be very efficient in honeybees since screening and crossing procedures are laborious due to their social organization. Here, we report an accurate and remarkably efficient site-specific integration of DNA-sequences into the honeybee genome using clustered regularly interspaced short palindromic repeat/clustered regularly interspaced short palindromic repeat-associated protein 9-mediated homology-directed repair. We employed early embryonic injections and selected a highly efficient sgRNA in order to insert 294 and 729 bp long DNA sequences into a specific locus at the dsx gene. These sequences were locus-specifically integrated in 57% and 59% of injected bees. Most importantly, 21% and 25% of the individuals lacked the wildtype sequence demonstrating that we generated homozygous mutants in which all cells are affected (no mosaicism). The highly efficient, locus-specific insertions of nucleotide sequences generating homozygous mutants demonstrate that systematic molecular studies for honeybees are in hand that allow somatic mutation approaches via workers or studies in the next generation using queens with their worker progeny. The employment of early embryonic injections and screenings of highly efficient sgRNAs may offer the prospect of highly successful sequence- and locus-specific mutations also in other organisms.
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Affiliation(s)
- Anna Wagner
- Department of Biology, Institute of Evolutionary Genetics, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Jana Seiler
- Department of Biology, Institute of Evolutionary Genetics, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Martin Beye
- Department of Biology, Institute of Evolutionary Genetics, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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14
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Zirin J, Bosch J, Viswanatha R, Mohr SE, Perrimon N. State-of-the-art CRISPR for in vivo and cell-based studies in Drosophila. Trends Genet 2022; 38:437-453. [PMID: 34933779 PMCID: PMC9007876 DOI: 10.1016/j.tig.2021.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/31/2022]
Abstract
For more than 100 years, the fruit fly, Drosophila melanogaster, has served as a powerful model organism for biological and biomedical research due to its many genetic and physiological similarities to humans and the availability of sophisticated technologies used to manipulate its genome and genes. The Drosophila research community quickly adopted CRISPR technologies and, in the 8 years since the first clustered regularly interspaced short palindromic repeats (CRISPR) publications in flies, has explored and innovated methods for mutagenesis, precise genome engineering, and beyond. Moreover, the short lifespan and ease of genetics have made Drosophila an ideal testing ground for in vivo applications and refinements of the rapidly evolving set of CRISPR-associated (CRISPR-Cas) tools. Here, we review innovations in delivery of CRISPR reagents, increased efficiency of cutting and homology-directed repair (HDR), and alternatives to standard Cas9-based approaches. While the focus is primarily on in vivo systems, we also describe the role of Drosophila cultured cells as both an indispensable first step in the process of assessing new CRISPR technologies and a platform for genome-wide CRISPR pooled screens.
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Affiliation(s)
- Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Justin Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Raghuvir Viswanatha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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15
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Port F, Boutros M. Tissue-Specific CRISPR-Cas9 Screening in Drosophila. Methods Mol Biol 2022; 2540:157-176. [PMID: 35980577 DOI: 10.1007/978-1-0716-2541-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last century research in Drosophila has resulted in many fundamental contributions to our understanding of the biology of multicellular organisms. Many of these breakthroughs have been based on the identification of novel gene functions in large-scale genetic screens. However, conventional forward-genetic screens have been limited by the random nature of mutagenesis and difficulties in mapping causal mutations, while reverse-genetic RNAi screens suffer from incomplete knockdown of gene expression. Recently developed large-scale CRISPR-Cas9 libraries promise to address these limitations by allowing the induction of targeted mutations in genes with spatial and temporal control. Here, we provide a guide for tissue-specific CRISPR screening in Drosophila, including the characterization of Gal4 UAS-Cas9 lines, selection of sgRNA libraries, and various quality control measures. We also discuss confounding factors that can give rise to false-positive and false-negative results in such experiments and suggest strategies on how to detect and avoid them. Conditional CRISPR screening represents an exciting new approach for functional genomics in vivo and is set to further expand our knowledge of the molecular underpinning of development, homeostasis, and disease.
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Affiliation(s)
- Fillip Port
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany.
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16
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Conditional CRISPR-Cas Genome Editing in Drosophila to Generate Intestinal Tumors. Cells 2021; 10:cells10113156. [PMID: 34831379 PMCID: PMC8620722 DOI: 10.3390/cells10113156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 01/19/2023] Open
Abstract
CRISPR-Cas has revolutionized genetics and extensive efforts have been made to enhance its editing efficiency by developing increasingly more elaborate tools. Here, we evaluate the CRISPR-Cas9 system in Drosophila melanogaster to assess its ability to induce stem cell-derived tumors in the intestine. We generated conditional tissue-specific CRISPR knockouts using different Cas9 expression vectors with guide RNAs targeting the BMP, Notch, and JNK pathways in intestinal progenitors such as stem cells (ISCs) and enteroblasts (EBs). Perturbing Notch and BMP signaling increased the proliferation of ISCs/EBs and resulted in the formation of intestinal tumors, albeit with different efficiencies. By assessing both the anterior and posterior regions of the midgut, we observed regional differences in ISC/EB proliferation and tumor formation upon mutagenesis. Surprisingly, high continuous expression of Cas9 in ISCs/EBs blocked age-dependent increase in ISCs/EBs proliferation and when combined with gRNAs targeting tumor suppressors, it prevented tumorigenesis. However, no such effects were seen when temporal parameters of Cas9 were adjusted to regulate its expression levels or with a genetically modified version, which expresses Cas9 at lower levels, suggesting that fine-tuning Cas9 expression is essential to avoid deleterious effects. Our findings suggest that modifications to Cas9 expression results in differences in editing efficiency and careful considerations are required when choosing reagents for CRISPR-Cas9 mutagenesis studies. In summary, Drosophila can serve as a powerful model for context-dependent CRISPR-Cas based perturbations and to test genome-editing systems in vivo.
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17
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Feng S, Lu S, Grueber WB, Mann RS. Scarless engineering of the Drosophila genome near any site-specific integration site. Genetics 2021; 217:6117239. [PMID: 33772309 DOI: 10.1093/genetics/iyab012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/13/2021] [Indexed: 11/14/2022] Open
Abstract
We describe a simple and efficient technique that allows scarless engineering of Drosophila genomic sequences near any landing site containing an inverted attP cassette, such as a MiMIC insertion. This two-step method combines phiC31 integrase-mediated site-specific integration and homing nuclease-mediated resolution of local duplications, efficiently converting the original landing site allele to modified alleles that only have the desired change(s). Dominant markers incorporated into this method allow correct individual flies to be efficiently identified at each step. In principle, single attP sites and FRT sites are also valid landing sites. Given the large and increasing number of landing site lines available in the fly community, this method provides an easy and fast way to efficiently edit the majority of the Drosophila genome in a scarless manner. This technique should also be applicable to other species.
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Affiliation(s)
- Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Shan Lu
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Wesley B Grueber
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.,Department of Neuroscience, Columbia University, New York, NY 10027, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.,Department of Systems Biology, Columbia University, New York, NY 10032, USA
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18
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López Del Amo V, Leger BS, Cox KJ, Gill S, Bishop AL, Scanlon GD, Walker JA, Gantz VM, Choudhary A. Small-Molecule Control of Super-Mendelian Inheritance in Gene Drives. Cell Rep 2021; 31:107841. [PMID: 32610142 PMCID: PMC7587219 DOI: 10.1016/j.celrep.2020.107841] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/20/2020] [Accepted: 06/09/2020] [Indexed: 11/29/2022] Open
Abstract
Synthetic CRISPR-based gene-drive systems have tremendous potential in public health and agriculture, such as for fighting vector-borne diseases or suppressing crop pest populations. These elements can rapidly spread in a population by breaching the inheritance limit of 50% dictated by Mendel's law of gene segregation, making them a promising tool for population engineering. However, current technologies lack control over their propagation capacity, and there are important concerns about potential unchecked spreading. Here, we describe a gene-drive system in Drosophila that generates an analog inheritance output that can be tightly and conditionally controlled to between 50% and 100%. This technology uses a modified SpCas9 that responds to a synthetic, orally available small molecule, fine-tuning the inheritance probability. This system opens a new avenue to feasibility studies for spatial and temporal control of gene drives using small molecules.
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Affiliation(s)
- Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Brittany S Leger
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kurt J Cox
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Shubhroz Gill
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Garrett D Scanlon
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA.
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19
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Abstract
CRISPR-Cas9 genome editing has transformed biology by enabling site-specific genome modifications to be simply engineered. Here, we describe two CRISPR-Cas9 approaches to introduce MS2 stem-loop sequences into endogenous gene loci in Drosophila. This can facilitate live imaging of nascent transcription in Drosophila. For complete details on the use and execution of this protocol, please refer to Hoppe et al. (2020).
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Affiliation(s)
- Caroline Hoppe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Hilary L. Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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20
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Rigon L, De Filippis C, Napoli B, Tomanin R, Orso G. Exploiting the Potential of Drosophila Models in Lysosomal Storage Disorders: Pathological Mechanisms and Drug Discovery. Biomedicines 2021; 9:biomedicines9030268. [PMID: 33800050 PMCID: PMC8000850 DOI: 10.3390/biomedicines9030268] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/12/2022] Open
Abstract
Lysosomal storage disorders (LSDs) represent a complex and heterogeneous group of rare genetic diseases due to mutations in genes coding for lysosomal enzymes, membrane proteins or transporters. This leads to the accumulation of undegraded materials within lysosomes and a broad range of severe clinical features, often including the impairment of central nervous system (CNS). When available, enzyme replacement therapy slows the disease progression although it is not curative; also, most recombinant enzymes cannot cross the blood-brain barrier, leaving the CNS untreated. The inefficient degradative capability of the lysosomes has a negative impact on the flux through the endolysosomal and autophagic pathways; therefore, dysregulation of these pathways is increasingly emerging as a relevant disease mechanism in LSDs. In the last twenty years, different LSD Drosophila models have been generated, mainly for diseases presenting with neurological involvement. The fruit fly provides a large selection of tools to investigate lysosomes, autophagy and endocytic pathways in vivo, as well as to analyse neuronal and glial cells. The possibility to use Drosophila in drug repurposing and discovery makes it an attractive model for LSDs lacking effective therapies. Here, ee describe the major cellular pathways implicated in LSDs pathogenesis, the approaches available for their study and the Drosophila models developed for these diseases. Finally, we highlight a possible use of LSDs Drosophila models for drug screening studies.
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Affiliation(s)
- Laura Rigon
- Fondazione Istituto di Ricerca Pediatrica “Città della Speranza”, Corso Stati Uniti 4, 35127 Padova, Italy; (C.D.F.); (R.T.)
- Correspondence:
| | - Concetta De Filippis
- Fondazione Istituto di Ricerca Pediatrica “Città della Speranza”, Corso Stati Uniti 4, 35127 Padova, Italy; (C.D.F.); (R.T.)
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women’s and Children’s Health, University of Padova, Via Giustiniani 3, 35128 Padova, Italy
| | - Barbara Napoli
- Laboratory of Molecular Biology, Scientific Institute, IRCCS Eugenio Medea, Via Don Luigi Monza 20, Bosisio Parini, 23842 Lecco, Italy;
| | - Rosella Tomanin
- Fondazione Istituto di Ricerca Pediatrica “Città della Speranza”, Corso Stati Uniti 4, 35127 Padova, Italy; (C.D.F.); (R.T.)
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women’s and Children’s Health, University of Padova, Via Giustiniani 3, 35128 Padova, Italy
| | - Genny Orso
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy;
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21
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Bosch JA, Birchak G, Perrimon N. Precise genome engineering in Drosophila using prime editing. Proc Natl Acad Sci U S A 2021; 118:e2021996118. [PMID: 33443210 PMCID: PMC7817132 DOI: 10.1073/pnas.2021996118] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Precise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double-strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organism Drosophila melanogaster and developed conditions for optimal editing. By expressing prime editing components in cultured cells or somatic cells of transgenic flies, we precisely introduce premature stop codons in three classical visible marker genes, ebony, white, and forked Furthermore, by restricting editing to germ cells, we demonstrate efficient germ-line transmission of a precise edit in ebony to 36% of progeny. Our results suggest that prime editing is a useful system in Drosophila to study gene function, such as engineering precise point mutations, deletions, or epitope tags.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
| | - Gabriel Birchak
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
- HHMI, Harvard Medical School, Boston, MA 02115
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22
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Huynh N, Depner N, Larson R, King-Jones K. A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila. Genome Biol 2020; 21:279. [PMID: 33203452 PMCID: PMC7670108 DOI: 10.1186/s13059-020-02193-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/04/2020] [Indexed: 02/08/2023] Open
Abstract
Advances in CRISPR technology have immensely improved our ability to manipulate nucleic acids, and the recent discovery of the RNA-targeting endonuclease Cas13 adds even further functionality. Here, we show that Cas13 works efficiently in Drosophila, both ex vivo and in vivo. We test 44 different Cas13 variants to identify enzymes with the best overall performance and show that Cas13 could target endogenous Drosophila transcripts in vivo with high efficiency and specificity. We also develop Cas13 applications to edit mRNAs and target mitochondrial transcripts. Our vector collection represents a versatile tool collection to manipulate gene expression at the post-transcriptional level.
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Affiliation(s)
- Nhan Huynh
- Department of Biological Sciences, University of Alberta, G-504 Biological Sciences Bldg., Edmonton, Alberta, T6G 2E9, Canada
| | - Noah Depner
- Department of Biological Sciences, University of Alberta, G-504 Biological Sciences Bldg., Edmonton, Alberta, T6G 2E9, Canada
| | - Raegan Larson
- Department of Biological Sciences, University of Alberta, G-504 Biological Sciences Bldg., Edmonton, Alberta, T6G 2E9, Canada
| | - Kirst King-Jones
- Department of Biological Sciences, University of Alberta, G-504 Biological Sciences Bldg., Edmonton, Alberta, T6G 2E9, Canada.
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23
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Yan Y, Ziemek J, Schetelig MF. CRISPR/Cas9 mediated disruption of the white gene leads to pigmentation deficiency and copulation failure in Drosophila suzukii. JOURNAL OF INSECT PHYSIOLOGY 2020; 126:104091. [PMID: 32745561 DOI: 10.1016/j.jinsphys.2020.104091] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/11/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
The Spotted-wing Drosophila (Drosophila suzukii) is a devastating invasive pest of fruit crops. In D. melanogaster, the white (w) gene was associated with pigmentation and mating behavior, which are also important aspects to understand the invasion biology as well as to develop control strategies for D. suzukii. Here, we show that the generation of D. suzukii white-eyed mutants by CRISPR/Cas9 mutagenesis of the w gene resulted in the complete failure of copulation when w- males were individually paired with w- females in small circular arenas (diameter 0.7 cm) for 24 h. Further analysis showed that the mating defect was associated with w- males and could not be rectified by two years of inbreeding by crossing sibling w- females with w+ males, dim red illumination, male-female sexual training, changing to large arenas (diameter 3.5 cm), or different sex ratios. Profound pigmentation deficiency was detected in the compound eyes, ocelli, Malpighian tubules and testis sheaths in the w- flies. Specifically, testis imaging showed that w- males failed to deposit any pigments into pigment cells of the testis sheath, and produced smaller sperms and less seminal fluid compared to those from wildtype males. Together these observations suggest that the w gene plays an essential role in the regulation of sexual behavior and reproduction in D. suzukii. The similarities and differences in w gene function between D. suzukii and D. melanogaster in the context of pigmentation and mating behavior are discussed.
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Affiliation(s)
- Ying Yan
- Justus-Liebig-University Giessen, Institute for Insect Biotechnology, Insect Biotechnology in Plant Protection, Winchesterstr. 2, 35394 Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Winchesterstr. 2, 35394 Giessen, Germany.
| | - Judith Ziemek
- Justus-Liebig-University Giessen, Institute for Insect Biotechnology, Insect Biotechnology in Plant Protection, Winchesterstr. 2, 35394 Giessen, Germany
| | - Marc F Schetelig
- Justus-Liebig-University Giessen, Institute for Insect Biotechnology, Insect Biotechnology in Plant Protection, Winchesterstr. 2, 35394 Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Winchesterstr. 2, 35394 Giessen, Germany.
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24
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Ewen-Campen B, Perrimon N. Expanding the horizons of genome editing in the fruit fly with Cas12a. Proc Natl Acad Sci U S A 2020; 117:24019-24021. [PMID: 32883881 PMCID: PMC7533843 DOI: 10.1073/pnas.2016446117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ben Ewen-Campen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Boston, MA 02115
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25
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Port F, Starostecka M, Boutros M. Multiplexed conditional genome editing with Cas12a in Drosophila. Proc Natl Acad Sci U S A 2020; 117:22890-22899. [PMID: 32843348 PMCID: PMC7502738 DOI: 10.1073/pnas.2004655117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas genome engineering has revolutionized biomedical research by enabling targeted genome modification with unprecedented ease. In the popular model organism Drosophila melanogaster, gene editing has so far relied exclusively on the prototypical CRISPR nuclease Cas9. Additional CRISPR systems could expand the genomic target space, offer additional modes of regulation, and enable the independent manipulation of genes in different cells of the same animal. Here we describe a platform for efficient Cas12a gene editing in Drosophila We show that Cas12a from Lachnospiraceae bacterium, but not Acidaminococcus spec., can mediate robust gene editing in vivo. In combination with most CRISPR RNAs (crRNAs), LbCas12a activity is high at 29 °C, but low at 18 °C, enabling modulation of gene editing by temperature. LbCas12a can directly utilize compact crRNA arrays that are substantially easier to construct than Cas9 single-guide RNA arrays, facilitating multiplex genome engineering. Furthermore, we show that conditional expression of LbCas12a is sufficient to mediate tightly controlled gene editing in a variety of tissues, allowing detailed analysis of gene function in a multicellular organism. We also test a variant of LbCas12a with a D156R point mutation and show that it has substantially higher activity and outperforms a state-of-the-art Cas9 system in identifying essential genes. Cas12a gene editing expands the genome-engineering toolbox in Drosophila and will be a powerful method for the functional annotation of the genome. This work also presents a fully genetically encoded Cas12a system in an animal, laying out principles for the development of similar systems in other genetically tractable organisms for multiplexed conditional genome engineering.
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Affiliation(s)
- Fillip Port
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Department for Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, D-69120 Heidelberg, Germany
| | - Maja Starostecka
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Department for Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, D-69120 Heidelberg, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Department for Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, D-69120 Heidelberg, Germany
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26
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Son W, Choi KW. The Classic Lobe Eye Phenotype of Drosophila Is Caused by Transposon Insertion-Induced Misexpression of a Zinc-Finger Transcription Factor. Genetics 2020; 216:117-134. [PMID: 32641295 PMCID: PMC7463288 DOI: 10.1534/genetics.120.303486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 07/06/2020] [Indexed: 11/18/2022] Open
Abstract
Drosophila Lobe (L) alleles were first discovered ∼100 years ago as spontaneous dominant mutants with characteristic developmental eye defects. However, the molecular basis for L dominant eye phenotypes has not been clearly understood. A previous work reported identification of CG10109/PRAS40 as the L gene, but subsequent analyses suggested that PRAS40 may not be related to L Here, we revisited the L gene to clarify this discrepancy and understand the basis for the dominance of L mutations. Genetic analysis localized the L gene to Oaz, which encodes a homolog of the vertebrate zinc finger protein 423 (Zfp423) family transcriptional regulators. We demonstrate that RNAi knockdown of Oaz almost completely restores all L dominant alleles tested. Lrev6-3 , a revertant allele of the L2 dominant eye phenotype, has an inframe deletion in the Oaz coding sequence. Molecular analysis of L dominant mutants identified allele-specific insertions of natural transposons (roo[ ]L1 , hopper[ ]L5 , and roo[ ]Lr ) or alterations of a preexisting transposon (L2 -specific mutations in roo[ ]Mohr) in the Oaz region. In addition, we generated additional L2 -reversion alleles by CRISPR targeting at Oaz These new loss-of-function Oaz mutations suppress the dominant L eye phenotype. Oaz protein is not expressed in wild-type eye disc but is expressed ectopically in L2/+ mutant eye disc. We induced male recombination between Oaz-GAL4 insertions and the L2 mutation through homologous recombination. By using the L2 -recombined GAL4 reporters, we show that Oaz-GAL4 is expressed ectopically in L2 eye imaginal disc. Taken together, our data suggest that neomorphic L eye phenotypes are likely due to misregulation of Oaz by spontaneous transposon insertions.
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Affiliation(s)
- Wonseok Son
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Kwang-Wook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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27
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Kleinschnitz K, Vießmann N, Jordan M, Heidmann SK. Condensin I is required for faithful meiosis in Drosophila males. Chromosoma 2020; 129:141-160. [PMID: 32314039 PMCID: PMC7260282 DOI: 10.1007/s00412-020-00733-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 01/03/2023]
Abstract
The heteropentameric condensin complexes play vital roles in the formation and faithful segregation of mitotic chromosomes in eukaryotes. While the different contributions of the two common condensin complexes, condensin I and condensin II, to chromosome morphology and behavior in mitosis have been thoroughly investigated, much less is known about the specific roles of the two complexes during meiotic divisions. In Drosophila melanogaster, faithful mitotic divisions depend on functional condensin I, but not on condensin II. However, meiotic divisions in Drosophila males require functional condensin II subunits. The role of condensin I during male meiosis in Drosophila has been unresolved. Here, we show that condensin I-specific subunits localize to meiotic chromatin in both meiosis I and II during Drosophila spermatogenesis. Live cell imaging reveals defects during meiotic divisions after RNAi-mediated knockdown of condensin I-specific mRNAs. This phenotype correlates with reduced male fertility and an increase in nondisjunction events both in meiosis I and meiosis II. Consistently, a reduction in male fertility was also observed after proteasome-mediated degradation of the condensin I subunit Barren. Taken together, our results demonstrate an essential role of condensin I during male meiosis in Drosophila melanogaster.
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Affiliation(s)
| | - Nina Vießmann
- Lehrstuhl für Genetik, University of Bayreuth, Bayreuth, Germany
| | - Mareike Jordan
- Lehrstuhl für Genetik, University of Bayreuth, Bayreuth, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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28
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Port F, Strein C, Stricker M, Rauscher B, Heigwer F, Zhou J, Beyersdörffer C, Frei J, Hess A, Kern K, Lange L, Langner N, Malamud R, Pavlović B, Rädecke K, Schmitt L, Voos L, Valentini E, Boutros M. A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila. eLife 2020; 9:e53865. [PMID: 32053108 PMCID: PMC7062466 DOI: 10.7554/elife.53865] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/01/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic screens are powerful tools for the functional annotation of genomes. In the context of multicellular organisms, interrogation of gene function is greatly facilitated by methods that allow spatial and temporal control of gene abrogation. Here, we describe a large-scale transgenic short guide (sg) RNA library for efficient CRISPR-based disruption of specific target genes in a constitutive or conditional manner. The library consists currently of more than 2600 plasmids and 1700 fly lines with a focus on targeting kinases, phosphatases and transcription factors, each expressing two sgRNAs under control of the Gal4/UAS system. We show that conditional CRISPR mutagenesis is robust across many target genes and can be efficiently employed in various somatic tissues, as well as the germline. In order to prevent artefacts commonly associated with excessive amounts of Cas9 protein, we have developed a series of novel UAS-Cas9 transgenes, which allow fine tuning of Cas9 expression to achieve high gene editing activity without detectable toxicity. Functional assays, as well as direct sequencing of genomic sgRNA target sites, indicates that the vast majority of transgenic sgRNA lines mediate efficient gene disruption. Furthermore, we conducted the so far largest fully transgenic CRISPR screen in any metazoan organism, which further supported the high efficiency and accuracy of our library and revealed many so far uncharacterized genes essential for development.
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Affiliation(s)
- Fillip Port
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Claudia Strein
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Mona Stricker
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Benedikt Rauscher
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Florian Heigwer
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Jun Zhou
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Celine Beyersdörffer
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Jana Frei
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Amy Hess
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Katharina Kern
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Laura Lange
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Nora Langner
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Roberta Malamud
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Bojana Pavlović
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Kristin Rädecke
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Lukas Schmitt
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Lukas Voos
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Erica Valentini
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg UniversityHeidelbergGermany
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29
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Bosch JA, Colbeth R, Zirin J, Perrimon N. Gene Knock-Ins in Drosophila Using Homology-Independent Insertion of Universal Donor Plasmids. Genetics 2020; 214:75-89. [PMID: 31685521 PMCID: PMC6944404 DOI: 10.1534/genetics.119.302819] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/25/2019] [Indexed: 11/18/2022] Open
Abstract
Targeted genomic knock-ins are a valuable tool to probe gene function. However, knock-in methods involving homology-directed repair (HDR) can be laborious. Here, we adapt the mammalian CRISPaint [clustered regularly interspaced short palindromic repeat (CRISPR)-assisted insertion tagging] homology-independent knock-in method for Drosophila melanogaster, which uses CRISPR/Cas9 and nonhomologous end joining to insert "universal" donor plasmids into the genome. Using this method in cultured S2R+ cells, we efficiently tagged four endogenous proteins with the bright fluorescent protein mNeonGreen, thereby demonstrating that an existing collection of CRISPaint universal donor plasmids is compatible with insect cells. In addition, we inserted the transgenesis marker 3xP3-red fluorescent protein into seven genes in the fly germ line, producing heritable loss-of-function alleles that were isolated by simple fluorescence screening. Unlike in cultured cells, insertions/deletions always occurred at the genomic insertion site, which prevents predictably matching the insert coding frame to the target gene. Despite this effect, we were able to isolate T2A-Gal4 insertions in four genes that serve as in vivo expression reporters. Therefore, homology-independent insertion in Drosophila is a fast and simple alternative to HDR that will enable researchers to dissect gene function.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Ryan Colbeth
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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30
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Paré AC, Naik P, Shi J, Mirman Z, Palmquist KH, Zallen JA. An LRR Receptor-Teneurin System Directs Planar Polarity at Compartment Boundaries. Dev Cell 2019; 51:208-221.e6. [PMID: 31495696 DOI: 10.1016/j.devcel.2019.08.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/25/2019] [Accepted: 08/02/2019] [Indexed: 12/28/2022]
Abstract
Epithelial cells dynamically self-organize in response to extracellular spatial cues relayed by cell-surface receptors. During convergent extension in Drosophila, Toll-related receptors direct planar polarized cell rearrangements that elongate the head-to-tail axis. However, many cells establish polarity in the absence of Toll receptor activity, indicating the presence of additional spatial cues. Here we demonstrate that the leucine-rich-repeat receptor Tartan and the teneurin Ten-m provide critical polarity signals at epithelial compartment boundaries. The Tartan and Ten-m extracellular domains interact in vitro, and Tartan promotes Ten-m localization to compartment boundaries in vivo. We show that Tartan and Ten-m are necessary for the planar polarity and organization of compartment boundary cells. Moreover, ectopic stripes of Tartan and Ten-m are sufficient to induce myosin accumulation at stripe boundaries. These results demonstrate that the Tartan/Ten-m and Toll receptor systems together create a high-resolution network of spatial cues that guides cell behavior during convergent extension.
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Affiliation(s)
- Adam C Paré
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Pooja Naik
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Jay Shi
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Zachary Mirman
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Karl H Palmquist
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Jennifer A Zallen
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
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31
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Paulo DF, Williamson ME, Arp AP, Li F, Sagel A, Skoda SR, Sanchez-Gallego J, Vasquez M, Quintero G, Pérez de León AA, Belikoff EJ, Azeredo-Espin AML, McMillan WO, Concha C, Scott MJ. Specific Gene Disruption in the Major Livestock Pests Cochliomyia hominivorax and Lucilia cuprina Using CRISPR/Cas9. G3 (BETHESDA, MD.) 2019; 9:3045-3055. [PMID: 31340950 PMCID: PMC6723136 DOI: 10.1534/g3.119.400544] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
Cochliomyia hominivorax and Lucilia cuprina are major pests of livestock. Their larvae infest warm-blooded vertebrates and feed on host's tissues, resulting in severe industry losses. As they are serious pests, considerable effort has been made to develop genomic resources and functional tools aiming to improve their management and control. Here, we report a significant addition to the pool of genome manipulation tools through the establishment of efficient CRISPR/Cas9 protocols for the generation of directed and inheritable modifications in the genome of these flies. Site-directed mutations were introduced in the C hominivorax and L cuprina yellow genes (ChY and LcY) producing lightly pigmented adults. High rates of somatic mosaicism were induced when embryos were injected with Cas9 ribonucleoprotein complexes (RNPs) pre-assembled with guide RNAs (sgRNAs) at high concentrations. Adult flies carrying disrupted yellow alleles lacked normal pigmentation (brown body phenotype) and efficiently transmitted the mutated alleles to the subsequent generation, allowing the rapid creation of homozygous strains for reverse genetics of candidate loci. We next used our established CRISPR protocol to disrupt the C hominivorax transformer gene (Chtra). Surviving females carrying mutations in the Chtra locus developed mosaic phenotypes of transformed ovipositors with characteristics of male genitalia while exhibiting abnormal reproductive tissues. The CRISPR protocol described here is a significant improvement on the existing toolkit of molecular methods in calliphorids. Our results also suggest that Cas9-based systems targeting Chtra and Lctra could be an effective means for controlling natural populations of these important pests.
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Affiliation(s)
- Daniel F Paulo
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas
- Laboratory of Ecological and Evolutionary Genomics, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Megan E Williamson
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC
| | - Alex P Arp
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville TX, and
| | - Fang Li
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC
| | - Agustin Sagel
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Steven R Skoda
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Joel Sanchez-Gallego
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Mario Vasquez
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Gladys Quintero
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
| | - Adalberto A Pérez de León
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville TX, and
| | - Esther J Belikoff
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC
| | - Ana M L Azeredo-Espin
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas
| | - W Owen McMillan
- Laboratory of Ecological and Evolutionary Genomics, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Carolina Concha
- Laboratory of Ecological and Evolutionary Genomics, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Maxwell J Scott
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC
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32
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Ramaekers A, Claeys A, Kapun M, Mouchel-Vielh E, Potier D, Weinberger S, Grillenzoni N, Dardalhon-Cuménal D, Yan J, Wolf R, Flatt T, Buchner E, Hassan BA. Altering the Temporal Regulation of One Transcription Factor Drives Evolutionary Trade-Offs between Head Sensory Organs. Dev Cell 2019; 50:780-792.e7. [PMID: 31447264 DOI: 10.1016/j.devcel.2019.07.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 04/24/2019] [Accepted: 07/25/2019] [Indexed: 12/30/2022]
Abstract
Size trade-offs of visual versus olfactory organs is a pervasive feature of animal evolution. This could result from genetic or functional constraints. We demonstrate that head sensory organ size trade-offs in Drosophila are genetically encoded and arise through differential subdivision of the head primordium into visual versus non-visual fields. We discover that changes in the temporal regulation of the highly conserved eyeless/Pax6 gene expression during development is a conserved mechanism for sensory trade-offs within and between Drosophila species. We identify a natural single nucleotide polymorphism in the cis-regulatory region of eyeless in a binding site of its repressor Cut that is sufficient to alter its temporal regulation and eye size. Because eyeless/Pax6 is a conserved regulator of head sensory placode subdivision, we propose that its temporal regulation is key to define the relative size of head sensory organs.
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Affiliation(s)
- Ariane Ramaekers
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France.
| | - Annelies Claeys
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Martin Kapun
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Emmanuèle Mouchel-Vielh
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine, LBD-IBPS), Paris, France
| | - Delphine Potier
- Aix-Marseille Université, CNRS, INSERM, CIML, Marseille, France
| | - Simon Weinberger
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Nicola Grillenzoni
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France
| | - Delphine Dardalhon-Cuménal
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine, LBD-IBPS), Paris, France
| | - Jiekun Yan
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Reinhard Wolf
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Erich Buchner
- Institute for Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Bassem A Hassan
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France.
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33
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Meltzer H, Marom E, Alyagor I, Mayseless O, Berkun V, Segal-Gilboa N, Unger T, Luginbuhl D, Schuldiner O. Tissue-specific (ts)CRISPR as an efficient strategy for in vivo screening in Drosophila. Nat Commun 2019; 10:2113. [PMID: 31068592 PMCID: PMC6506539 DOI: 10.1038/s41467-019-10140-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/17/2019] [Indexed: 12/22/2022] Open
Abstract
Gene editing by CRISPR/Cas9 is commonly used to generate germline mutations or perform in vitro screens, but applicability for in vivo screening has so far been limited. Recently, it was shown that in Drosophila, Cas9 expression could be limited to a desired group of cells, allowing tissue-specific mutagenesis. Here, we thoroughly characterize tissue-specific (ts)CRISPR within the complex neuronal system of the Drosophila mushroom body. We report the generation of a library of gRNA-expressing plasmids and fly lines using optimized tools, which provides a valuable resource to the fly community. We demonstrate the application of our library in a large-scale in vivo screen, which reveals insights into developmental neuronal remodeling.
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Affiliation(s)
- Hagar Meltzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Efrat Marom
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Idan Alyagor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oded Mayseless
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Victoria Berkun
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Netta Segal-Gilboa
- Structural Proteomics Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Structural Proteomics Unit, Weizmann Institute of Science, Rehovot, Israel
| | - David Luginbuhl
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, USA
| | - Oren Schuldiner
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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34
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Erdmann RS, Baguley SW, Richens JH, Wissner RF, Xi Z, Allgeyer ES, Zhong S, Thompson AD, Lowe N, Butler R, Bewersdorf J, Rothman JE, St Johnston D, Schepartz A, Toomre D. Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tags. Cell Chem Biol 2019; 26:584-592.e6. [PMID: 30745239 PMCID: PMC6474801 DOI: 10.1016/j.chembiol.2019.01.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 07/13/2018] [Accepted: 01/07/2019] [Indexed: 12/22/2022]
Abstract
Super-resolution microscopy requires that subcellular structures are labeled with bright and photostable fluorophores, especially for live-cell imaging. Organic fluorophores may help here as they can yield more photons-by orders of magnitude-than fluorescent proteins. To achieve molecular specificity with organic fluorophores in live cells, self-labeling proteins are often used, with HaloTags and SNAP-tags being the most common. However, how these two different tagging systems compare with each other is unclear, especially for stimulated emission depletion (STED) microscopy, which is limited to a small repertoire of fluorophores in living cells. Herein, we compare the two labeling approaches in confocal and STED imaging using various proteins and two model systems. Strikingly, we find that the fluorescent signal can be up to 9-fold higher with HaloTags than with SNAP-tags when using far-red rhodamine derivatives. This result demonstrates that the labeling strategy matters and can greatly influence the duration of super-resolution imaging.
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Affiliation(s)
- Roman S. Erdmann
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, USA
| | - Stephanie Wood Baguley
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Jennifer H. Richens
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Rebecca F. Wissner
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, USA
| | - Zhiqun Xi
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Edward S. Allgeyer
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sheng Zhong
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | | | - Nicholas Lowe
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Richard Butler
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA,Department of Biomedical Engineering, Yale University, 55 Prospect Street, New Haven, CT, USA
| | - James E. Rothman
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Daniel St Johnston
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Alanna Schepartz
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, USA
| | - Derek Toomre
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA.
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35
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Neuert H, Deing P, Krukkert K, Naffin E, Steffes G, Risse B, Silies M, Klämbt C. The Drosophila NCAM homolog Fas2 signals independent of adhesion. Development 2019; 147:dev.181479. [DOI: 10.1242/dev.181479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/09/2019] [Indexed: 12/22/2022]
Abstract
The development of tissues and organs requires close interaction of cells. To do so, cells express adhesion proteins such as the neural cell adhesion molecule (NCAM) or its Drosophila orthologue Fasciclin 2 (Fas2). Both are members of the Ig-domain superfamily of proteins that mediate homophilic adhesion. These proteins are expressed as different isoforms differing in their membrane anchorage and their cytoplasmic domains. To study the function of single isoforms we have conducted a comprehensive genetic analysis of fas2. We reveal the expression pattern of all major Fas2 isoforms, two of which are GPI-anchored. The remaining five isoforms carry transmembrane domains with variable cytoplasmic tails. We generated fas2 mutants expressing only single isoforms. In contrast to the null mutation which causes embryonic lethality, these mutants are viable, indicating redundancy among the different isoforms. Cell type specific rescue experiments showed that glial secreted Fas2 can rescue the fas2 mutant phenotype to viability. This demonstrates cytoplasmic Fas2 domains have no apparent essential functions and indicate that Fas2 has function(s) other than homophilic adhesion. In conclusion, our data propose novel mechanistic aspects of a long studied adhesion protein.
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Affiliation(s)
- Helen Neuert
- University of Münster, Institute for Neuro- and Behavioral Biology, Badestr. 9, 48149 Münster, Germany
| | - Petra Deing
- University of Münster, Institute for Neuro- and Behavioral Biology, Badestr. 9, 48149 Münster, Germany
| | - Karin Krukkert
- University of Münster, Institute for Neuro- and Behavioral Biology, Badestr. 9, 48149 Münster, Germany
| | - Elke Naffin
- University of Münster, Institute for Neuro- and Behavioral Biology, Badestr. 9, 48149 Münster, Germany
| | - Georg Steffes
- University of Münster, Institute for Neuro- and Behavioral Biology, Badestr. 9, 48149 Münster, Germany
| | - Benjamin Risse
- University of Münster, Institute for Neuro- and Behavioral Biology, Badestr. 9, 48149 Münster, Germany
| | - Marion Silies
- University of Münster, Institute for Neuro- and Behavioral Biology, Badestr. 9, 48149 Münster, Germany
| | - Christian Klämbt
- University of Münster, Institute for Neuro- and Behavioral Biology, Badestr. 9, 48149 Münster, Germany
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36
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Facultative dosage compensation of developmental genes on autosomes in Drosophila and mouse embryonic stem cells. Nat Commun 2018; 9:3626. [PMID: 30194291 PMCID: PMC6128902 DOI: 10.1038/s41467-018-05642-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/04/2018] [Indexed: 12/25/2022] Open
Abstract
Haploinsufficiency and aneuploidy are two phenomena, where gene dosage alterations cause severe defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between sexes are buffered by dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. The evolutionary origin and conservation of this process orchestrated by MSL2, the only male-specific protein within the fly MSLc, have remained unclear. Here, we report that MSL2, in addition to regulating the X chromosome, targets autosomal genes involved in patterning and morphogenesis. Precise regulation of these genes by MSL2 is required for proper development. This set of dosage-sensitive genes maintains such regulation during evolution, as MSL2 binds and similarly regulates mouse orthologues via Histone H4 lysine 16 acetylation. We propose that this gene-by-gene dosage compensation mechanism was co-opted during evolution for chromosome-wide regulation of the Drosophila male X. In Drosophila the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. Here the authors provide evidence that MSL2 also targets autosomal genes required for proper development and that MSL2 binds and similarly regulates mouse orthologues.
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37
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ovoD Co-selection: A Method for Enriching CRISPR/Cas9-Edited Alleles in Drosophila. G3-GENES GENOMES GENETICS 2018; 8:2749-2756. [PMID: 29934375 PMCID: PMC6071590 DOI: 10.1534/g3.118.200498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Screening for successful CRISPR/Cas9 editing events remains a time consuming technical bottleneck in the field of Drosophila genome editing. This step can be particularly laborious for events that do not cause a visible phenotype, or those which occur at relatively low frequency. A promising strategy to enrich for desired CRISPR events is to co-select for an independent CRISPR event that produces an easily detectable phenotype. Here, we describe a simple negative co-selection strategy involving CRISPR-editing of a dominant female sterile allele, ovoD1 In this system ("ovoD co-selection"), the only functional germ cells in injected females are those that have been edited at the ovoD1 locus, and thus all offspring of these flies have undergone editing of at least one locus. We demonstrate that ovoD co-selection can be used to enrich for knock-out mutagenesis via nonhomologous end-joining (NHEJ), and for knock-in alleles via homology-directed repair (HDR). Altogether, our results demonstrate that ovoD co-selection reduces the amount of screening necessary to isolate desired CRISPR events in Drosophila.
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38
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Roy B, Zhao J, Yang C, Luo W, Xiong T, Li Y, Fang X, Gao G, Singh CO, Madsen L, Zhou Y, Kristiansen K. CRISPR/Cascade 9-Mediated Genome Editing-Challenges and Opportunities. Front Genet 2018; 9:240. [PMID: 30026755 PMCID: PMC6042012 DOI: 10.3389/fgene.2018.00240] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/18/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and Cascade 9 (also known as Cas9, CRISPR associated protein 9) confer protection against invading viruses or plasmids. The CRISPR/Cascade 9 system constitutes one of the most powerful genome technologies available to researchers today. So far, this technology has enabled efficient genome editing and modification in several model organisms and has successfully been used in biomedicine and biomedical engineering. However, challenges for efficient and safe genetic manipulation in several organisms persist. Here, we review functional approaches and future challenges associated with the use of the CRISPR/Cascade 9 genome editing system and discuss opportunities, ethical issues and future directions within this field.
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Affiliation(s)
| | - Jing Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Chao Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wen Luo
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Teng Xiong
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Guanjun Gao
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Chabungbam O Singh
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Lise Madsen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Institute of Marine Research, Bergen, Norway
| | - Yong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Karsten Kristiansen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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39
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Volkenhoff A, Hirrlinger J, Kappel JM, Klämbt C, Schirmeier S. Live imaging using a FRET glucose sensor reveals glucose delivery to all cell types in the Drosophila brain. JOURNAL OF INSECT PHYSIOLOGY 2018; 106:55-64. [PMID: 28733241 DOI: 10.1016/j.jinsphys.2017.07.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/13/2017] [Accepted: 07/17/2017] [Indexed: 05/26/2023]
Abstract
All complex nervous systems are metabolically separated from circulation by a blood-brain barrier (BBB) that prevents uncontrolled leakage of solutes into the brain. Thus, all metabolites needed to sustain energy homeostasis must be transported across this BBB. In invertebrates, such as Drosophila, the major carbohydrate in circulation is the disaccharide trehalose and specific trehalose transporters are expressed by the glial BBB. Here we analyzed whether glucose is able to contribute to energy homeostasis in Drosophila. To study glucose influx into the brain we utilized a genetically encoded, FRET-based glucose sensor expressed in a cell type specific manner. When confronted with glucose all brain cells take up glucose within two minutes. In order to characterize the glucose transporter involved, we studied Drosophila Glut1, the homologue of which is primarily expressed by the BBB-forming endothelial cells and astrocytes in the mammalian nervous system. In Drosophila, however, Glut1 is expressed in neurons and is not found at the BBB. Thus, Glut1 cannot contribute to initial glucose uptake from the hemolymph. To test whether gap junctional coupling between the BBB forming cells and other neural cells contributes to glucose distribution we assayed these junctions using RNAi experiments and only found a minor contribution of gap junctions to glucose metabolism. Our results provide the entry point to further dissect the mechanisms underlying glucose distribution and offer new opportunities to understand brain metabolism.
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Affiliation(s)
- Anne Volkenhoff
- Institut für Neuro- und Verhaltensbiologie, Badestr. 9, 48149 Münster, Germany
| | - Johannes Hirrlinger
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany; Department of Neurogenetics, Max-Planck-Institute for Experimental Medicine, Hermann-Rein-Str. 3, D-37075 Göttingen, Germany
| | - Johannes M Kappel
- Institut für Neuro- und Verhaltensbiologie, Badestr. 9, 48149 Münster, Germany
| | - Christian Klämbt
- Institut für Neuro- und Verhaltensbiologie, Badestr. 9, 48149 Münster, Germany
| | - Stefanie Schirmeier
- Institut für Neuro- und Verhaltensbiologie, Badestr. 9, 48149 Münster, Germany.
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40
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Sun D, Guo Z, Liu Y, Zhang Y. Progress and Prospects of CRISPR/Cas Systems in Insects and Other Arthropods. Front Physiol 2017; 8:608. [PMID: 28932198 PMCID: PMC5592444 DOI: 10.3389/fphys.2017.00608] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/07/2017] [Indexed: 01/03/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated gene Cas9 represent an invaluable system for the precise editing of genes in diverse species. The CRISPR/Cas9 system is an adaptive mechanism that enables bacteria and archaeal species to resist invading viruses and phages or plasmids. Compared with zinc finger nucleases and transcription activator-like effector nucleases, the CRISPR/Cas9 system has the advantage of requiring less time and effort. This efficient technology has been used in many species, including diverse arthropods that are relevant to agriculture, forestry, fisheries, and public health; however, there is no review that systematically summarizes its successful application in the editing of both insect and non-insect arthropod genomes. Thus, this paper seeks to provide a comprehensive and impartial overview of the progress of the CRISPR/Cas9 system in different arthropods, reviewing not only fundamental studies related to gene function exploration and experimental optimization but also applied studies in areas such as insect modification and pest control. In addition, we also describe the latest research advances regarding two novel CRISPR/Cas systems (CRISPR/Cpf1 and CRISPR/C2c2) and discuss their future prospects for becoming crucial technologies in arthropods.
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Affiliation(s)
- Dan Sun
- Longping Branch, Graduate School of Hunan UniversityChangsha, China.,Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yong Liu
- Longping Branch, Graduate School of Hunan UniversityChangsha, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
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41
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Kudumala SR, Penserga T, Börner J, Slipchuk O, Kakad P, Lee LH, Qureshi A, Pielage J, Godenschwege TA. Lissencephaly-1 dependent axonal retrograde transport of L1-type CAM Neuroglian in the adult drosophila central nervous system. PLoS One 2017; 12:e0183605. [PMID: 28837701 PMCID: PMC5570280 DOI: 10.1371/journal.pone.0183605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 08/08/2017] [Indexed: 11/25/2022] Open
Abstract
Here, we established the Drosophila Giant Fiber neurons (GF) as a novel model to study axonal trafficking of L1-type Cell Adhesion Molecules (CAM) Neuroglian (Nrg) in the adult CNS using live imaging. L1-type CAMs are well known for their importance in nervous system development and we previously demonstrated a role for Nrg in GF synapse formation. However, in the adult they have also been implicated in synaptic plasticity and regeneration. In addition, to its canonical role in organizing cytoskeletal elements at the plasma membrane, vertebrate L1CAM has also been shown to regulate transcription indirectly as well as directly via its import to the nucleus. Here, we intend to determine if the sole L1CAM homolog Nrg is retrogradley transported and thus has the potential to relay signals from the synapse to the soma. Live imaging of c-terminally tagged Nrg in the GF revealed that there are at least two populations of retrograde vesicles that differ in speed, and either move with consistent or varying velocity. To determine if endogenous Nrg is retrogradely transported, we inhibited two key regulators, Lissencephaly-1 (Lis1) and Dynactin, of the retrograde motor protein Dynein. Similar to previously described phenotypes for expression of poisonous subunits of Dynactin, we found that developmental knock down of Lis1 disrupted GF synaptic terminal growth and that Nrg vesicles accumulated inside the stunted terminals in both mutant backgrounds. Moreover, post mitotic Lis1 knock down in mature GFs by either RNAi or Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) induced mutations, resulted in normal length terminals with fully functional GF synapses which also exhibited severe accumulation of endogenous Nrg vesicles. Thus, our data suggests that accumulation of Nrg vesicles is due to failure of retrograde transport rather than a failure of terminal development. Together with the finding that post mitotic knock down of Lis1 also disrupted retrograde transport of tagged Nrg vesicles in GF axons, it demonstrates that endogenous Nrg protein is transported from the synapse to the soma in the adult central nervous system in a Lis1-dependent manner.
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Affiliation(s)
- Sirisha R. Kudumala
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Tyrone Penserga
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Jana Börner
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Olesya Slipchuk
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Priyanka Kakad
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
| | - LaTasha H. Lee
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Aater Qureshi
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Jan Pielage
- Department of Biology, Division of Zoology/Neurobiology, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Tanja A. Godenschwege
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
- * E-mail:
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42
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Shi Z, Tian D, Xin H, Lian J, Guo X, Chen Y. Targeted integration of genes in Xenopus tropicalis. Genesis 2017; 55. [PMID: 28095621 DOI: 10.1002/dvg.23006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 11/17/2016] [Accepted: 11/19/2016] [Indexed: 11/06/2022]
Abstract
With the successful establishment of both targeted gene disruption and integration methods in the true diploid frog Xenopus tropicalis, this excellent vertebrate genetic model now is making a unique contribution to modelling human diseases. Here, we summarize our efforts on establishing homologous recombination-mediated targeted integration in Xenopus tropicalis, the usefulness, and limitation of targeted integration via the homology-independent strategy, and future directions on how to further improve targeted gene integration in Xenopus tropicalis.
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Affiliation(s)
- Zhaoying Shi
- Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Dandan Tian
- Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Huhu Xin
- Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Jingru Lian
- Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Xiaogang Guo
- DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen N, Denmark
| | - Yonglong Chen
- Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
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43
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van Tienen LM, Mieszczanek J, Fiedler M, Rutherford TJ, Bienz M. Constitutive scaffolding of multiple Wnt enhanceosome components by Legless/BCL9. eLife 2017; 6:e20882. [PMID: 28296634 PMCID: PMC5352222 DOI: 10.7554/elife.20882] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/07/2017] [Indexed: 12/30/2022] Open
Abstract
Wnt/β-catenin signaling elicits context-dependent transcription switches that determine normal development and oncogenesis. These are mediated by the Wnt enhanceosome, a multiprotein complex binding to the Pygo chromatin reader and acting through TCF/LEF-responsive enhancers. Pygo renders this complex Wnt-responsive, by capturing β-catenin via the Legless/BCL9 adaptor. We used CRISPR/Cas9 genome engineering of Drosophila legless (lgs) and human BCL9 and B9L to show that the C-terminus downstream of their adaptor elements is crucial for Wnt responses. BioID proximity labeling revealed that BCL9 and B9L, like PYGO2, are constitutive components of the Wnt enhanceosome. Wnt-dependent docking of β-catenin to the enhanceosome apparently causes a rearrangement that apposes the BCL9/B9L C-terminus to TCF. This C-terminus binds to the Groucho/TLE co-repressor, and also to the Chip/LDB1-SSDP enhanceosome core complex via an evolutionary conserved element. An unexpected link between BCL9/B9L, PYGO2 and nuclear co-receptor complexes suggests that these β-catenin co-factors may coordinate Wnt and nuclear hormone responses.
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Affiliation(s)
| | | | - Marc Fiedler
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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44
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Efficient Screening of CRISPR/Cas9-Induced Events in Drosophila Using a Co-CRISPR Strategy. G3-GENES GENOMES GENETICS 2017; 7:87-93. [PMID: 27793971 PMCID: PMC5217126 DOI: 10.1534/g3.116.036723] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genome editing using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated nuclease (Cas9) enables specific genetic modifications, including deletions, insertions, and substitutions in numerous organisms, such as the fruit fly Drosophila melanogaster. One challenge of the CRISPR/Cas9 system can be the laborious and time-consuming screening required to find CRISPR-induced modifications due to a lack of an obvious phenotype and low frequency after editing. Here we apply the successful co-CRISPR technique in Drosophila to simultaneously target a gene of interest and a marker gene, ebony, which is a recessive gene that produces dark body color and has the further advantage of not being a commonly used transgenic marker. We found that Drosophila broods containing higher numbers of CRISPR-induced ebony mutations (“jackpot” lines) are significantly enriched for indel events in a separate gene of interest, while broods with few or no ebony offspring showed few mutations in the gene of interest. Using two different PAM sites in our gene of interest, we report that ∼61% (52–70%) of flies from the ebony-enriched broods had an indel in DNA near either PAM site. Furthermore, this marker mutation system may be useful in detecting the less frequent homology-directed repair events, all of which occurred in the ebony-enriched broods. By focusing on the broods with a significant number of ebony flies, successful identification of CRISPR-induced events is much faster and more efficient. The co-CRISPR technique we present significantly improves the screening efficiency in identification of genome-editing events in Drosophila.
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45
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Lamb AM, Walker EA, Wittkopp PJ. Tools and strategies for scarless allele replacement in Drosophila using CRISPR/Cas9. Fly (Austin) 2017; 11:53-64. [PMID: 27494619 PMCID: PMC5354236 DOI: 10.1080/19336934.2016.1220463] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/30/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022] Open
Abstract
Genome editing via the CRISPR/Cas9 RNA-guided nuclease system has opened up exciting possibilities for genetic analysis. However, technical challenges associated with homology-directed repair have proven to be roadblocks for producing changes in the absence of unwanted, secondary mutations commonly known as "scars." To address these issues, we developed a 2-stage, marker-assisted strategy to facilitate precise, "scarless" edits in Drosophila with a minimal requirement for molecular screening. Using this method, we modified 2 base pairs in a gene of interest without altering the final sequence of the CRISPR cut sites. We executed this 2-stage allele swap using a novel transformation marker that drives expression in the pupal wings, which can be screened for in the presence of common eye-expressing reporters. The tools we developed can be used to make a single change or a series of allelic substitutions in a region of interest in any D. melanogaster genetic background as well as in other Drosophila species.
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Affiliation(s)
- Abigail M. Lamb
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth A. Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Patricia J. Wittkopp
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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46
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Vigoder FM, Parker DJ, Cook N, Tournière O, Sneddon T, Ritchie MG. Inducing Cold-Sensitivity in the Frigophilic Fly Drosophila montana by RNAi. PLoS One 2016; 11:e0165724. [PMID: 27832122 PMCID: PMC5104470 DOI: 10.1371/journal.pone.0165724] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022] Open
Abstract
Cold acclimation is a critical physiological adaptation for coping with seasonal cold. By increasing their cold tolerance individuals can remain active for longer at the onset of winter and can recover more quickly from a cold shock. In insects, despite many physiological studies, little is known about the genetic basis of cold acclimation. Recently, transcriptomic analyses in Drosophila virilis and D. montana revealed candidate genes for cold acclimation by identifying genes upregulated during exposure to cold. Here, we test the role of myo-inositol-1-phosphate synthase (Inos), in cold tolerance in D. montana using an RNAi approach. D. montana has a circumpolar distribution and overwinters as an adult in northern latitudes with extreme cold. We assessed cold tolerance of dsRNA knock-down flies using two metrics: chill-coma recovery time (CCRT) and mortality rate after cold acclimation. Injection of dsRNAInos did not alter CCRT, either overall or in interaction with the cold treatment, however it did induced cold-specific mortality, with high levels of mortality observed in injected flies acclimated at 5°C but not at 19°C. Overall, injection with dsRNAInos induced a temperature-sensitive mortality rate of over 60% in this normally cold-tolerant species. qPCR analysis confirmed that dsRNA injection successfully reduced gene expression of Inos. Thus, our results demonstrate the involvement of Inos in increasing cold tolerance in D. montana. The potential mechanisms involved by which Inos increases cold tolerance are also discussed.
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Affiliation(s)
- Felipe M. Vigoder
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, United Kingdom
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Darren J. Parker
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, United Kingdom
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Nicola Cook
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, United Kingdom
| | - Océane Tournière
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, United Kingdom
- Sars International Centre for Marine Molecular Biology, Thormøhlensgt, Bergen, Norway
| | - Tanya Sneddon
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, United Kingdom
| | - Michael G. Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, United Kingdom
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47
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Ge DT, Tipping C, Brodsky MH, Zamore PD. Rapid Screening for CRISPR-Directed Editing of the Drosophila Genome Using white Coconversion. G3 (BETHESDA, MD.) 2016; 6:3197-3206. [PMID: 27543296 PMCID: PMC5068941 DOI: 10.1534/g3.116.032557] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/04/2016] [Indexed: 11/20/2022]
Abstract
Adoption of a streamlined version of the bacterial clustered regular interspersed short palindromic repeat (CRISPR)/Cas9 defense system has accelerated targeted genome engineering. The Streptococcus pyogenes Cas9 protein, directed by a simplified, CRISPR-like single-guide RNA, catalyzes a double-stranded DNA break at a specific genomic site; subsequent repair by end joining can introduce mutagenic insertions or deletions, while repair by homologous recombination using an exogenous DNA template can incorporate new sequences at the target locus. However, the efficiency of Cas9-directed mutagenesis is low in Drosophila melanogaster Here, we describe a strategy that reduces the time and effort required to identify flies with targeted genomic changes. The strategy uses editing of the white gene, evidenced by altered eye color, to predict successful editing of an unrelated gene-of-interest. The red eyes of wild-type flies are readily distinguished from white-eyed (end-joining-mediated loss of White function) or brown-eyed (recombination-mediated conversion to the whitecoffee allele) mutant flies. When single injected G0 flies produce individual G1 broods, flies carrying edits at a gene-of-interest were readily found in broods in which all G1 offspring carried white mutations. Thus, visual assessment of eye color substitutes for wholesale PCR screening of large numbers of G1 offspring. We find that end-joining-mediated mutations often show signatures of microhomology-mediated repair and that recombination-based mutations frequently involve donor plasmid integration at the target locus. Finally, we show that gap repair induced by two guide RNAs more reliably converts the intervening target sequence, whereas the use of Lig4169 mutants to suppress end joining does not improve recombination efficacy.
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Affiliation(s)
- Daniel Tianfang Ge
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605 Interdisciplinary Graduate Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Cindy Tipping
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605 Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Michael H Brodsky
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605 Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605 Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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48
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Port F, Bullock SL. Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs. Nat Methods 2016; 13:852-4. [PMID: 27595403 PMCID: PMC5215823 DOI: 10.1038/nmeth.3972] [Citation(s) in RCA: 275] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/02/2016] [Indexed: 12/25/2022]
Abstract
We present tRNA-based vectors for producing multiple clustered regularly interspaced short palindromic repeats (CRISPR) single guide RNAs (sgRNAs) from a single RNA polymerase II or III transcript in Drosophila. The system, which is based on liberation of sgRNAs by processing flanking tRNAs, permits highly efficient multiplexing of Cas9-based mutagenesis. We also demonstrate that the tRNA-sgRNA system markedly increases the efficacy of conditional gene disruption by Cas9 and can promote editing by the recently discovered RNA-guided endonuclease Cpf1.
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Affiliation(s)
- Fillip Port
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Simon L Bullock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
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Perkin LC, Adrianos SL, Oppert B. Gene Disruption Technologies Have the Potential to Transform Stored Product Insect Pest Control. INSECTS 2016; 7:insects7030046. [PMID: 27657138 PMCID: PMC5039559 DOI: 10.3390/insects7030046] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/01/2016] [Accepted: 09/09/2016] [Indexed: 12/26/2022]
Abstract
Stored product insects feed on grains and processed commodities manufactured from grain post-harvest, reducing the nutritional value and contaminating food. Currently, the main defense against stored product insect pests is the pesticide fumigant phosphine. Phosphine is highly toxic to all animals, but is the most effective and economical control method, and thus is used extensively worldwide. However, many insect populations have become resistant to phosphine, in some cases to very high levels. New, environmentally benign and more effective control strategies are needed for stored product pests. RNA interference (RNAi) may overcome pesticide resistance by targeting the expression of genes that contribute to resistance in insects. Most data on RNAi in stored product insects is from the coleopteran genetic model, Tribolium castaneum, since it has a strong RNAi response via injection of double stranded RNA (dsRNA) in any life stage. Additionally, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology has been suggested as a potential resource for new pest control strategies. In this review we discuss background information on both gene disruption technologies and summarize the advances made in terms of molecular pest management in stored product insects, mainly T. castaneum, as well as complications and future needs.
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Affiliation(s)
- Lindsey C Perkin
- Center for Grain and Animal Health Research, Agricultural Research Service, USDA, 1515 College Avenue, Manhattan, KS 66502, USA.
| | - Sherry L Adrianos
- Center for Grain and Animal Health Research, Agricultural Research Service, USDA, 1515 College Avenue, Manhattan, KS 66502, USA.
| | - Brenda Oppert
- Center for Grain and Animal Health Research, Agricultural Research Service, USDA, 1515 College Avenue, Manhattan, KS 66502, USA.
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Ceasar SA, Rajan V, Prykhozhij SV, Berman JN, Ignacimuthu S. Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:2333-44. [PMID: 27350235 DOI: 10.1016/j.bbamcr.2016.06.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 12/26/2022]
Abstract
The clustered, regularly interspaced, short palindromic repeat (CRISPR) and CRISPR associated protein 9 (Cas9) system discovered as an adaptive immunity mechanism in prokaryotes has emerged as the most popular tool for the precise alterations of the genomes of diverse species. CRISPR/Cas9 system has taken the world of genome editing by storm in recent years. Its popularity as a tool for altering genomes is due to the ability of Cas9 protein to cause double-stranded breaks in DNA after binding with short guide RNA molecules, which can be produced with dramatically less effort and expense than required for production of transcription-activator like effector nucleases (TALEN) and zinc-finger nucleases (ZFN). This system has been exploited in many species from prokaryotes to higher animals including human cells as evidenced by the literature showing increasing sophistication and ease of CRISPR/Cas9 as well as increasing species variety where it is applicable. This technology is poised to solve several complex molecular biology problems faced in life science research including cancer research. In this review, we highlight the recent advancements in CRISPR/Cas9 system in editing genomes of prokaryotes, fungi, plants and animals and provide details on software tools available for convenient design of CRISPR/Cas9 targeting plasmids. We also discuss the future prospects of this advanced molecular technology.
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Affiliation(s)
- S Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India; Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Vinothkumar Rajan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason N Berman
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - S Ignacimuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India; International Scientific Partnership Program, Deanship of Scientific Research, College of Science, King Saud University, Riyadh, Saudi Arabia.
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