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Mao R, Yu J, Deng B, Dai X, Du Y, Du S, Zhang W, Rao Y. Conditional chemoconnectomics (cCCTomics) as a strategy for efficient and conditional targeting of chemical transmission. eLife 2024; 12:RP91927. [PMID: 38686992 PMCID: PMC11060718 DOI: 10.7554/elife.91927] [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] [Indexed: 05/02/2024] Open
Abstract
Dissection of neural circuitry underlying behaviors is a central theme in neurobiology. We have previously proposed the concept of chemoconnectome (CCT) to cover the entire chemical transmission between neurons and target cells in an organism and created tools for studying it (CCTomics) by targeting all genes related to the CCT in Drosophila. Here we have created lines targeting the CCT in a conditional manner after modifying GFP RNA interference, Flp-out, and CRISPR/Cas9 technologies. All three strategies have been validated to be highly effective, with the best using chromatin-peptide fused Cas9 variants and scaffold optimized sgRNAs. As a proof of principle, we conducted a comprehensive intersection analysis of CCT genes expression profiles in the clock neurons, uncovering 43 CCT genes present in clock neurons. Specific elimination of each from clock neurons revealed that loss of the neuropeptide CNMa in two posterior dorsal clock neurons (DN1ps) or its receptor (CNMaR) caused advanced morning activity, indicating a suppressive role of CNMa-CNMaR on morning anticipation, opposite to the promoting role of PDF-PDFR on morning anticipation. These results demonstrate the effectiveness of conditional CCTomics and its tools created here and establish an antagonistic relationship between CNMa-CNMaR and PDF-PDFR signaling in regulating morning anticipation.
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Affiliation(s)
- Renbo Mao
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
- National Institute of Biological Sciences, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Jianjun Yu
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Bowen Deng
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Xihuimin Dai
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Yuyao Du
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Sujie Du
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Wenxia Zhang
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Yi Rao
- Laboratory of Neurochemical Biology, Chinese Institute for Brain ResearchBeijingChina
- PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Pharmaceutical Sciences, Peking UniversityBeijingChina
- Chinese Institutes for Medical Research, Capital Medical University; Changping LaboratoryChangpingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
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Bouzidi A, Krouma A. Impact of lead and zinc heavy metal pollution on the growth and phytoremediation potential of Sulla carnosa in Sebkha el Kalbia, Tunisia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-32350-w. [PMID: 38424244 DOI: 10.1007/s11356-024-32350-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Heavy metal pollution from human and natural activities poses significant environmental and health concerns for wildlife and humans, with lead and zinc being particularly threatening. This study focuses on Sebkha el Kalbia in Tunisia, highlighting the challenges faced by local communities in addressing heavy metal pollution. The area is prone to contamination through rivers and streams that transport pollutants from industrial zones and rural areas into the salt pan. The recent establishment of an industrial zone has worsened pollution levels, calling for strict regulatory measures and clean technologies to limit heavy metal pollution and protect human health and the environment. The study assesses the impact of lead and zinc pollution on the growth of Sulla carnosa and its potential for phytoremediation. Soil and plant samples from contaminated areas were analyzed, revealing high levels of heavy metal contamination. The growth parameters of Sulla carnosa, such as plant height, weight, and enzymatic activity, were examined, showing a significant reduction in plant growth when exposed to high metal concentrations. Specifically, in the presence of 100 ppm of lead (Pb), net photosynthetic assimilation (An) decreased by 52%, while the amount of Pb increased by 78%. At 800 ppm of Pb, An decreased by 87%, and the amount of Pb increased by over 800%. Furthermore, the relationship between net photosynthetic assimilation and lead (Pb) content remained significant but negative. At high doses (800 ppm), the biomass produced decreases by 64%, while the amount of Zn increases 2.7 times. These results suggest that at low doses, zinc is not toxic. These findings highlight Sulla carnosa as a potential candidate for phytoremediation with preferential metal accumulation in the roots and improved enzymatic activity, underscoring the urgency of addressing heavy metal pollution in Sebkha el Kalbia.
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Affiliation(s)
- Amal Bouzidi
- Laboratory of Ecosystems and Biodiversity in Arid Land of Tunisia, Faculty of Sciences, University of Sfax, Sfax, Tunisia.
| | - Abdelmajid Krouma
- Faculty of Sciences and Techniques of Sidi Bouzid, University of Kairouan, Sidi Bouzid, Tunisia
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Chen X, Perry S, Wang B, Wang S, Hu J, Loxterkamp E, Dickman D, Han C. Tissue-specific knockout in Drosophila neuromuscular system reveals ESCRT's role in formation of synapse-derived extracellular vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559303. [PMID: 37808853 PMCID: PMC10557614 DOI: 10.1101/2023.09.25.559303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Tissue-specific gene knockout by CRISPR/Cas9 is a powerful approach for characterizing gene functions in animal development. However, this approach has been successfully applied in only a small number of Drosophila tissues. The Drosophila motor nervous system is an excellent model system for studying the biology of neuromuscular junction (NMJ). To expand tissue-specific CRISPR to the Drosophila motor system, here we present a CRISPR-mediated tissue-restricted mutagenesis (CRISPR-TRiM) toolkit for knocking out genes in motoneurons, muscles, and glial cells. We validated the efficacy of this toolkit by knocking out known genes in each tissue, demonstrated its orthogonal use with the Gal4/UAS binary expression system, and showed simultaneous knockout of multiple redundant genes. Using these tools, we discovered an essential role for SNARE pathways in NMJ maintenance. Furthermore, we demonstrate that the canonical ESCRT pathway suppresses NMJ bouton growth by downregulating the retrograde Gbb signaling. Lastly, we found that axon termini of motoneurons rely on ESCRT-mediated intra-axonal membrane trafficking to lease extracellular vesicles at the NMJ.
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Affiliation(s)
- Xinchen Chen
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sarah Perry
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Shuran Wang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jiayi Hu
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth Loxterkamp
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Chun Han
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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Currier TA, Pang MM, Clandinin TR. Visual processing in the fly, from photoreceptors to behavior. Genetics 2023; 224:iyad064. [PMID: 37128740 PMCID: PMC10213501 DOI: 10.1093/genetics/iyad064] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023] Open
Abstract
Originally a genetic model organism, the experimental use of Drosophila melanogaster has grown to include quantitative behavioral analyses, sophisticated perturbations of neuronal function, and detailed sensory physiology. A highlight of these developments can be seen in the context of vision, where pioneering studies have uncovered fundamental and generalizable principles of sensory processing. Here we begin with an overview of vision-guided behaviors and common methods for probing visual circuits. We then outline the anatomy and physiology of brain regions involved in visual processing, beginning at the sensory periphery and ending with descending motor control. Areas of focus include contrast and motion detection in the optic lobe, circuits for visual feature selectivity, computations in support of spatial navigation, and contextual associative learning. Finally, we look to the future of fly visual neuroscience and discuss promising topics for further study.
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Affiliation(s)
- Timothy A Currier
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michelle M Pang
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
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5
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Allen D, Kalter N, Rosenberg M, Hendel A. Homology-Directed-Repair-Based Genome Editing in HSPCs for the Treatment of Inborn Errors of Immunity and Blood Disorders. Pharmaceutics 2023; 15:pharmaceutics15051329. [PMID: 37242571 DOI: 10.3390/pharmaceutics15051329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Genome engineering via targeted nucleases, specifically CRISPR-Cas9, has revolutionized the field of gene therapy research, providing a potential treatment for diseases of the blood and immune system. While numerous genome editing techniques have been used, CRISPR-Cas9 homology-directed repair (HDR)-mediated editing represents a promising method for the site-specific insertion of large transgenes for gene knock-in or gene correction. Alternative methods, such as lentiviral/gammaretroviral gene addition, gene knock-out via non-homologous end joining (NHEJ)-mediated editing, and base or prime editing, have shown great promise for clinical applications, yet all possess significant drawbacks when applied in the treatment of patients suffering from inborn errors of immunity or blood system disorders. This review aims to highlight the transformational benefits of HDR-mediated gene therapy and possible solutions for the existing problems holding the methodology back. Together, we aim to help bring HDR-based gene therapy in CD34+ hematopoietic stem progenitor cells (HSPCs) from the lab bench to the bedside.
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Affiliation(s)
- Daniel Allen
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Nechama Kalter
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Liu CQ, Qu XC, He MF, Liang DH, Xie SM, Zhang XX, Lin YM, Zhang WJ, Wu KC, Qiao JD. Efficient strategies based on behavioral and electrophysiological methods for epilepsy-related gene screening in the Drosophila model. Front Mol Neurosci 2023; 16:1121877. [PMID: 37152436 PMCID: PMC10157486 DOI: 10.3389/fnmol.2023.1121877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction With the advent of trio-based whole-exome sequencing, the identification of epilepsy candidate genes has become easier, resulting in a large number of potential genes that need to be validated in a whole-organism context. However, conducting animal experiments systematically and efficiently remains a challenge due to their laborious and time-consuming nature. This study aims to develop optimized strategies for validating epilepsy candidate genes using the Drosophila model. Methods This study incorporate behavior, morphology, and electrophysiology for genetic manipulation and phenotypic examination. We utilized the Gal4/UAS system in combination with RNAi techniques to generate loss-of-function models. We performed a range of behavioral tests, including two previously unreported seizure phenotypes, to evaluate the seizure behavior of mutant and wild-type flies. We used Gal4/UAS-mGFP flies to observe the morphological alterations in the brain under a confocal microscope. We also implemented patch-clamp recordings, including a novel electrophysiological method for studying synapse function and improved methods for recording action potential currents and spontaneous EPSCs on targeted neurons. Results We applied different techniques or methods mentioned above to investigate four epilepsy-associated genes, namely Tango14, Klp3A, Cac, and Sbf, based on their genotype-phenotype correlation. Our findings showcase the feasibility and efficiency of our screening system for confirming epilepsy candidate genes in the Drosophila model. Discussion This efficient screening system holds the potential to significantly accelerate and optimize the process of identifying epilepsy candidate genes, particularly in conjunction with trio-based whole-exome sequencing.
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Affiliation(s)
- Chu-Qiao Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Chong Qu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ming-Feng He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - De-Hai Liang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shi-Ming Xie
- The First Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Xi-Xing Zhang
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Yong-Miao Lin
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Wen-Jun Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ka-Chun Wu
- School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jing-Da Qiao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jing-Da Qiao, ; orcid.org/0000-0002-4693-8390
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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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Schulz C. Employing the CRISPR Technology for Studying Notch Signaling in the Male Gonad of Drosophila melanogaster. Methods Mol Biol 2022; 2472:159-172. [PMID: 35674899 DOI: 10.1007/978-1-0716-2201-8_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The Notch (N) signaling pathway plays versatile roles in development and disease of many model organisms (Andersson et al., Development 138, 3593-3612, 2011; Hori et al., J Cell Sci, 126, 2135-2140, 2013). However, studying a role for N in adult tissue of Drosophila melanogaster is challenging, because the gene is located on the X-chromosome. To reduce the expression of N specifically in either the germline or the somatic cells of the adult gonad, we used the CRISPR technology in combination with the UAS/Gal4 expression system. After generation of the flies, gonads were investigated for germline survival. Here, we outline our detailed protocol.
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Affiliation(s)
- Cordula Schulz
- Department of Cellular Biology, Univeristy of Georgia, Athens, GA, USA.
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9
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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 2021; 38:437-453. [PMID: 34933779 PMCID: PMC9007876 DOI: 10.1016/j.tig.2021.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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10
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Javaid N, Choi S. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency. Front Cell Dev Biol 2021; 9:761709. [PMID: 34901007 PMCID: PMC8652214 DOI: 10.3389/fcell.2021.761709] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The diverse applications of genetically modified cells and organisms require more precise and efficient genome-editing tool such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas). The CRISPR/Cas system was originally discovered in bacteria as a part of adaptive-immune system with multiple types. Its engineered versions involve multiple host DNA-repair pathways in order to perform genome editing in host cells. However, it is still challenging to get maximum genome-editing efficiency with fewer or no off-targets. Here, we focused on factors affecting the genome-editing efficiency and precision of CRISPR/Cas system along with its defense-mechanism, orthologues, and applications.
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Affiliation(s)
- Nasir Javaid
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, South Korea
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11
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Nunes C, Koyama T, Sucena É. Co-option of immune effectors by the hormonal signalling system triggering metamorphosis in Drosophila melanogaster. PLoS Genet 2021; 17:e1009916. [PMID: 34843450 PMCID: PMC8659296 DOI: 10.1371/journal.pgen.1009916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/09/2021] [Accepted: 10/29/2021] [Indexed: 11/24/2022] Open
Abstract
Insect metamorphosis is triggered by the production, secretion and degradation of 20-hydroxyecdysone (ecdysone). In addition to its role in developmental regulation, increasing evidence suggests that ecdysone is involved in innate immunity processes, such as phagocytosis and the induction of antimicrobial peptide (AMP) production. AMP regulation includes systemic responses as well as local responses at surface epithelia that contact with the external environment. At pupariation, Drosophila melanogaster increases dramatically the expression of three AMP genes, drosomycin (drs), drosomycin-like 2 (drsl2) and drosomycin-like 5 (drsl5). We show that the systemic action of drs at pupariation is dependent on ecdysone signalling in the fat body and operates via the ecdysone downstream target, Broad. In parallel, ecdysone also regulates local responses, specifically through the activation of drsl2 expression in the gut. Finally, we confirm the relevance of this ecdysone dependent AMP expression for the control of bacterial load by showing that flies lacking drs expression in the fat body have higher bacterial persistence over metamorphosis. In contrast, local responses may be redundant with the systemic effect of drs since reduction of ecdysone signalling or of drsl2 expression has no measurable negative effect on bacterial load control in the pupa. Together, our data emphasize the importance of the association between ecdysone signalling and immunity using in vivo studies and establish a new role for ecdysone at pupariation, which impacts developmental success by regulating the immune system in a stage-dependent manner. We speculate that this co-option of immune effectors by the hormonal system may constitute an anticipatory mechanism to control bacterial numbers in the pupa, at the core of metamorphosis evolution.
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Affiliation(s)
- Catarina Nunes
- Evolution and Development Laboratory, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Takashi Koyama
- Section for Cell and Neurobiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Élio Sucena
- Evolution and Development Laboratory, Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Yin J, Spillman E, Cheng ES, Short J, Chen Y, Lei J, Gibbs M, Rosenthal JS, Sheng C, Chen YX, Veerasammy K, Choetso T, Abzalimov R, Wang B, Han C, He Y, Yuan Q. Brain-specific lipoprotein receptors interact with astrocyte derived apolipoprotein and mediate neuron-glia lipid shuttling. Nat Commun 2021; 12:2408. [PMID: 33893307 PMCID: PMC8065144 DOI: 10.1038/s41467-021-22751-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/29/2021] [Indexed: 02/08/2023] Open
Abstract
Lipid shuttling between neurons and glia contributes to the development, function, and stress responses of the nervous system. To understand how a neuron acquires its lipid supply from specific lipoproteins and their receptors, we perform combined genetic, transcriptome, and biochemical analyses in the developing Drosophila larval brain. Here we report, the astrocyte-derived secreted lipocalin Glial Lazarillo (GLaz), a homolog of human Apolipoprotein D (APOD), and its neuronal receptor, the brain-specific short isoforms of Drosophila lipophorin receptor 1 (LpR1-short), cooperatively mediate neuron-glia lipid shuttling and support dendrite morphogenesis. The isoform specificity of LpR1 defines its distribution, binding partners, and ability to support proper dendrite growth and synaptic connectivity. By demonstrating physical and functional interactions between GLaz/APOD and LpR1, we elucidate molecular pathways mediating lipid trafficking in the fly brain, and provide in vivo evidence indicating isoform-specific expression of lipoprotein receptors as a key mechanism for regulating cell-type specific lipid recruitment.
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Affiliation(s)
- Jun Yin
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Emma Spillman
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Ethan S Cheng
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jacob Short
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yang Chen
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jingce Lei
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mary Gibbs
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Justin S Rosenthal
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Sheng
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Pharmacology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuki X Chen
- The City University of New York, Graduate Center-Advanced Science Research Center, New York, NY, USA
- The City College of New York, CUNY, New York, NY, USA
| | - Kelly Veerasammy
- The City University of New York, Graduate Center-Advanced Science Research Center, New York, NY, USA
- The City College of New York, CUNY, New York, NY, USA
| | - Tenzin Choetso
- The City University of New York, Graduate Center-Advanced Science Research Center, New York, NY, USA
- The City College of New York, CUNY, New York, NY, USA
| | - Rinat Abzalimov
- The City University of New York, Graduate Center-Advanced Science Research Center, New York, NY, USA
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Chun Han
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Ye He
- The City University of New York, Graduate Center-Advanced Science Research Center, New York, NY, USA
| | - Quan Yuan
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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13
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Koreman GT, Xu Y, Hu Q, Zhang Z, Allen SE, Wolfner MF, Wang B, Han C. Upgraded CRISPR/Cas9 tools for tissue-specific mutagenesis in Drosophila. Proc Natl Acad Sci U S A 2021; 118:e2014255118. [PMID: 33782117 PMCID: PMC8040800 DOI: 10.1073/pnas.2014255118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
CRISPR/Cas9 has emerged as a powerful technology for tissue-specific mutagenesis. However, tissue-specific CRISPR/Cas9 tools currently available in Drosophila remain deficient in three significant ways. First, many existing gRNAs are inefficient, such that further improvements of gRNA expression constructs are needed for more efficient and predictable mutagenesis in both somatic and germline tissues. Second, it has been difficult to label mutant cells in target tissues with current methods. Lastly, application of tissue-specific mutagenesis at present often relies on Gal4-driven Cas9, which hampers the flexibility and effectiveness of the system. Here, we tackle these deficiencies by building upon our previous CRISPR-mediated tissue-restricted mutagenesis (CRISPR-TRiM) tools. First, we significantly improved gRNA efficiency in somatic tissues by optimizing multiplexed gRNA design. Similarly, we also designed efficient dual-gRNA vectors for the germline. Second, we developed methods to positively and negatively label mutant cells in tissue-specific mutagenesis by incorporating co-CRISPR reporters into gRNA expression vectors. Lastly, we generated genetic reagents for convenient conversion of existing Gal4 drivers into tissue-specific Cas9 lines based on homology-assisted CRISPR knock-in. In this way, we expand the choices of Cas9 for CRISPR-TRiM analysis to broader tissues and developmental stages. Overall, our upgraded CRISPR/Cas9 tools make tissue-specific mutagenesis more versatile, reliable, and effective in Drosophila These improvements may be also applied to other model systems.
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Affiliation(s)
- Gabriel T Koreman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Yineng Xu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Qinan Hu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Zijing Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Sarah E Allen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Bei Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Chun Han
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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14
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Ryvkin J, Bentzur A, Shmueli A, Tannenbaum M, Shallom O, Dokarker S, Benichou JIC, Levi M, Shohat-Ophir G. Transcriptome Analysis of NPFR Neurons Reveals a Connection Between Proteome Diversity and Social Behavior. Front Behav Neurosci 2021; 15:628662. [PMID: 33867948 PMCID: PMC8044454 DOI: 10.3389/fnbeh.2021.628662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
Social behaviors are mediated by the activity of highly complex neuronal networks, the function of which is shaped by their transcriptomic and proteomic content. Contemporary advances in neurogenetics, genomics, and tools for automated behavior analysis make it possible to functionally connect the transcriptome profile of candidate neurons to their role in regulating behavior. In this study we used Drosophila melanogaster to explore the molecular signature of neurons expressing receptor for neuropeptide F (NPF), the fly homolog of neuropeptide Y (NPY). By comparing the transcription profile of NPFR neurons to those of nine other populations of neurons, we discovered that NPFR neurons exhibit a unique transcriptome, enriched with receptors for various neuropeptides and neuromodulators, as well as with genes known to regulate behavioral processes, such as learning and memory. By manipulating RNA editing and protein ubiquitination programs specifically in NPFR neurons, we demonstrate that the proper expression of their unique transcriptome and proteome is required to suppress male courtship and certain features of social group interaction. Our results highlight the importance of transcriptome and proteome diversity in the regulation of complex behaviors and pave the path for future dissection of the spatiotemporal regulation of genes within highly complex tissues, such as the brain.
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Affiliation(s)
- Julia Ryvkin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Assa Bentzur
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Anat Shmueli
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Miriam Tannenbaum
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Omri Shallom
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shiran Dokarker
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Jennifer I. C. Benichou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Mali Levi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Galit Shohat-Ophir
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
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15
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Efficient expression of multiple guide RNAs for CRISPR/Cas genome editing. ABIOTECH 2020; 1:123-134. [PMID: 36304720 PMCID: PMC9590505 DOI: 10.1007/s42994-019-00014-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/21/2019] [Indexed: 01/16/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein system (CRISPR/Cas) has recently become the most powerful tool available for genome engineering in various organisms. With efficient and proper expression of multiple guide RNAs (gRNAs), the CRISPR/Cas system is particularly suitable for multiplex genome editing. During the past several years, different CRISPR/Cas expression strategies, such as two-component transcriptional unit, single transcriptional unit, and bidirectional promoter systems, have been developed to efficiently express gRNAs as well as Cas nucleases. Significant progress has been made to optimize gRNA production using different types of promoters and RNA processing strategies such as ribozymes, endogenous RNases, and exogenous endoribonuclease (Csy4). Besides being constitutively and ubiquitously expressed, inducible and spatiotemporal regulations of gRNA expression have been demonstrated using inducible, tissue-specific, and/or synthetic promoters for specific research purposes. Most recently, the emergence of CRISPR/Cas ribonucleoprotein delivery methods, such as engineered nanoparticles, further revolutionized transgene-free and multiplex genome editing. In this review, we discuss current strategies and future perspectives for efficient expression and engineering of gRNAs with a goal to facilitate CRISPR/Cas-based multiplex genome editing.
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16
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Pauls D, Hamarat Y, Trufasu L, Schendzielorz TM, Gramlich G, Kahnt J, Vanselow JT, Schlosser A, Wegener C. Drosophila carboxypeptidase D (SILVER) is a key enzyme in neuropeptide processing required to maintain locomotor activity levels and survival rate. Eur J Neurosci 2019; 50:3502-3519. [PMID: 31309630 DOI: 10.1111/ejn.14516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/19/2019] [Accepted: 07/05/2019] [Indexed: 11/27/2022]
Abstract
Neuropeptides are processed from larger preproproteins by a dedicated set of enzymes. The molecular and biochemical mechanisms underlying preproprotein processing and the functional importance of processing enzymes are well-characterised in mammals, but little studied outside this group. In contrast to mammals, Drosophila melanogaster lacks a gene for carboxypeptidase E (CPE), a key enzyme for mammalian peptide processing. By combining peptidomics and neurogenetics, we addressed the role of carboxypeptidase D (dCPD) in global neuropeptide processing and selected peptide-regulated behaviours in Drosophila. We found that a deficiency in dCPD results in C-terminally extended peptides across the peptidome, suggesting that dCPD took over CPE function in the fruit fly. dCPD is widely expressed throughout the nervous system, including peptidergic neurons in the mushroom body and neuroendocrine cells expressing adipokinetic hormone. Conditional hypomorphic mutation in the dCPD-encoding gene silver in the larva causes lethality, and leads to deficits in starvation-induced hyperactivity and appetitive gustatory preference, as well as to reduced viability and activity levels in adults. A phylogenomic analysis suggests that loss of CPE is not common to insects, but only occurred in Hymenoptera and Diptera. Our results show that dCPD is a key enzyme for neuropeptide processing and peptide-regulated behaviour in Drosophila. dCPD thus appears as a suitable target to genetically shut down total neuropeptide production in peptidergic neurons. The persistent occurrence of CPD in insect genomes may point to important further CPD functions beyond neuropeptide processing which cannot be fulfilled by CPE.
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Affiliation(s)
- Dennis Pauls
- Neurobiology and Genetics, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Yasin Hamarat
- Neurobiology and Genetics, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany.,'Santaka' Valley I Health Telematics Science Institute, Kaunas University of Technology, Kaunas, Lithuania
| | - Luisa Trufasu
- Neurobiology and Genetics, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Tim M Schendzielorz
- Neurobiology and Genetics, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Gertrud Gramlich
- Neurobiology and Genetics, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jörg Kahnt
- Max-Planck-Institute of Terrestrial Microbiology, Marburg, Germany
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Christian Wegener
- Neurobiology and Genetics, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
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17
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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: 53] [Impact Index Per Article: 10.6] [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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18
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Perspectives on gene expression regulation techniques in Drosophila. J Genet Genomics 2019; 46:213-220. [DOI: 10.1016/j.jgg.2019.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/27/2019] [Accepted: 03/12/2019] [Indexed: 12/26/2022]
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19
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Poe AR, Wang B, Sapar ML, Ji H, Li K, Onabajo T, Fazliyeva R, Gibbs M, Qiu Y, Hu Y, Han C. Robust CRISPR/Cas9-Mediated Tissue-Specific Mutagenesis Reveals Gene Redundancy and Perdurance in Drosophila. Genetics 2019; 211:459-472. [PMID: 30504366 PMCID: PMC6366929 DOI: 10.1534/genetics.118.301736] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
Tissue-specific loss-of-function (LOF) analysis is essential for characterizing gene function. Here, we present a simple, yet highly efficient, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated tissue-restricted mutagenesis (CRISPR-TRiM) method for ablating gene function in Drosophila This binary system consists of a tissue-specific Cas9 and a ubiquitously expressed multi-guide RNA (gRNA) transgene. We describe convenient toolkits for making enhancer-driven Cas9 lines and multi-gRNAs that are optimized for mutagenizing somatic cells. We demonstrate that insertions or deletions in coding sequences more reliably cause somatic mutations than DNA excisions induced by two gRNAs. We further show that enhancer-driven Cas9 is less cytotoxic yet results in more complete LOF than Gal4-driven Cas9 in larval sensory neurons. Finally, CRISPR-TRiM efficiently unmasks redundant soluble N-ethylmaleimide-sensitive factor attachment protein receptor gene functions in neurons and epidermal cells. Importantly, Cas9 transgenes expressed at different times in the neuronal lineage reveal the extent to which gene products persist in cells after tissue-specific gene knockout. These CRISPR tools can be applied to analyze tissue-specific gene function in many biological processes.
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Affiliation(s)
- Amy R Poe
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Maria L Sapar
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Hui Ji
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Kailyn Li
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Tireniolu Onabajo
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Rushaniya Fazliyeva
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Mary Gibbs
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Yue Qiu
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Yuzhao Hu
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Chun Han
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
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20
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A Drosophila CRISPR/Cas9 Toolkit for Conditionally Manipulating Gene Expression in the Prothoracic Gland as a Test Case for Polytene Tissues. G3-GENES GENOMES GENETICS 2018; 8:3593-3605. [PMID: 30213867 PMCID: PMC6222582 DOI: 10.1534/g3.118.200539] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Targeting gene function with spatial or temporal specificity is a key goal in molecular genetics. CRISPR-Cas9 has greatly facilitated this strategy, but some standard approaches are problematic. For instance, simple tissue-specific or global overexpression of Cas9 can cause significant lethality or developmental delays even in the absence of gRNAs. In particular, we found that Gal4-mediated expression of UAS-Cas9 in the Drosophila prothoracic gland (PG) was not a suitable strategy to disrupt gene expression, since Cas9 alone caused widespread lethality. The PG is widely used for studying endocrine gland function during animal development, but tools validating PG-specific RNAi phenotypes are lacking. Here, we present a collection of modular gateway-compatible CRISPR-Cas9 tools that allow precise modulation of target gene activity with temporal and spatial specificity. We also demonstrate that Cas9 fused to the progesterone ligand-binding domain can be used to activate gene expression via RU486. Using these approaches, we were able to avoid the lethality associated with simple GAL4-mediated overexpression of Cas9 in the PG. Given that the PG is a polytene tissue, we conclude that these tools work effectively in endoreplicating cells where Cas9 has to target multiple copies of the same locus. Our toolkit can be easily adapted for other tissues and can be used both for gain- and loss-of-function studies.
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21
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Abstract
Motion in the visual world provides critical information to guide the behavior of sighted animals. Furthermore, as visual motion estimation requires comparisons of signals across inputs and over time, it represents a paradigmatic and generalizable neural computation. Focusing on the Drosophila visual system, where an explosion of technological advances has recently accelerated experimental progress, we review our understanding of how, algorithmically and mechanistically, motion signals are first computed.
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Affiliation(s)
- Helen H Yang
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA; .,Current affiliation: Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA;
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22
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Şentürk M, Bellen HJ. Genetic strategies to tackle neurological diseases in fruit flies. Curr Opin Neurobiol 2018; 50:24-32. [PMID: 29128849 PMCID: PMC5940587 DOI: 10.1016/j.conb.2017.10.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
Abstract
Drosophila melanogaster is a genetic model organism that has contributed to the discovery of numerous genes whose human homologues are associated with diseases. The development of sophisticated genetic tools to manipulate its genome accelerates the discovery of the genetic basis of undiagnosed human diseases and the elucidation of molecular pathogenic events of known and novel diseases. Here, we discuss various approaches used in flies to assess the function of the fly homologues of disease-associated genes. We highlight how systematic and combinatorial approaches based on recently established methods provide us with integrated tool sets that can be applied to the study of neurodevelopmental and neurodegenerative disorders.
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Affiliation(s)
- Mümine Şentürk
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston TX 77030, USA; Department of Neuroscience, BCM, Houston TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston TX 77030, USA; Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA.
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23
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Dong Y, Simões ML, Marois E, Dimopoulos G. CRISPR/Cas9 -mediated gene knockout of Anopheles gambiae FREP1 suppresses malaria parasite infection. PLoS Pathog 2018. [PMID: 29518156 PMCID: PMC5843335 DOI: 10.1371/journal.ppat.1006898] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Plasmodium relies on numerous agonists during its journey through the mosquito vector, and these agonists represent potent targets for transmission-blocking by either inhibiting or interfering with them pre- or post-transcriptionally. The recently developed CRISPR/Cas9-based genome editing tools for Anopheles mosquitoes provide new and promising opportunities for the study of agonist function and for developing malaria control strategies through gene deletion to achieve complete agonist inactivation. Here we have established a modified CRISPR/Cas9 gene editing procedure for the malaria vector Anopheles gambiae, and studied the effect of inactivating the fibrinogen-related protein 1 (FREP1) gene on the mosquito’s susceptibility to Plasmodium and on mosquito fitness. FREP1 knockout mutants developed into adult mosquitoes that showed profound suppression of infection with both human and rodent malaria parasites at the oocyst and sporozoite stages. FREP1 inactivation, however, resulted in fitness costs including a significantly lower blood-feeding propensity, fecundity and egg hatching rate, a retarded pupation time, and reduced longevity after a blood meal. The causative agent of malaria, Plasmodium, has to complete a complex infection cycle in the Anopheles gambiae mosquito vector in order to reach the salivary gland from where it can be transmitted to a human host. The parasite’s development in the mosquito relies on numerous host factors (agonists), and their inhibition or inactivation can thereby result in suppression of infection and consequently malaria transmission. The recently developed CRISPR/Cas9-based genome editing tools for Anopheles mosquitoes provide new and promising opportunities to delete (inactivate) Plasmodium agonists to better understand their function and for blocking malaria transmission. Here we have established a modified CRISPR/Cas9 genome editing technique for malaria vector A. gambiae mosquitoes. Through this approach we have inactivated the fibrinogen-related protein 1 (FREP1) gene, via CRISPR/Cas9 genome editing, and the impact of this manipulation on the mosquito’s susceptibility to Plasmodium and on mosquito fitness. FREP1 knockout mutants showed a profound suppression of infection with both human and rodent malaria parasites, while it also resulted in fitness costs: a significantly lower blood-feeding propensity, fecundity and egg hatching rate, and a retarded larval development and pupation time, and reduced longevity after a blood meal.
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Affiliation(s)
- Yuemei Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Malaria Research Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Maria L. Simões
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Malaria Research Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Eric Marois
- Inserm, CNRS, Université de Strasbourg, Strasbourg, France
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Malaria Research Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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24
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Korona D, Koestler SA, Russell S. Engineering the Drosophila Genome for Developmental Biology. J Dev Biol 2017; 5:jdb5040016. [PMID: 29615571 PMCID: PMC5831791 DOI: 10.3390/jdb5040016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 02/07/2023] Open
Abstract
The recent development of transposon and CRISPR-Cas9-based tools for manipulating the fly genome in vivo promises tremendous progress in our ability to study developmental processes. Tools for introducing tags into genes at their endogenous genomic loci facilitate imaging or biochemistry approaches at the cellular or subcellular levels. Similarly, the ability to make specific alterations to the genome sequence allows much more precise genetic control to address questions of gene function.
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Affiliation(s)
- Dagmara Korona
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Stefan A Koestler
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
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25
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Abstract
With a century-old history of fundamental discoveries, the fruit fly has long been a favored experimental organism for a wide range of scientific inquiries. But Drosophila is not a “legacy” model organism; technical and intellectual innovations continue to revitalize fly research and drive advances in our understanding of conserved mechanisms of animal biology. Here, we provide an overview of this “ecosystem” and discuss how to address emerging challenges to ensure its continued productivity. Drosophila researchers are fortunate to have a sophisticated and ever-growing toolkit for the analysis of gene function. Access to these tools depends upon continued support for both physical and informational resources. Uncertainty regarding stable support for bioinformatic databases is a particular concern, at a time when there is the need to make the vast knowledge of functional biology provided by this model animal accessible to scientists studying other organisms. Communication and advocacy efforts will promote appreciation of the value of the fly in delivering biomedically important insights. Well-tended traditions of large-scale tool development, open sharing of reagents, and community engagement provide a strong basis for coordinated and proactive initiatives to improve the fly research ecosystem. Overall, there has never been a better time to be a fly pusher.
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26
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Qian Y, Cao Y, Deng B, Yang G, Li J, Xu R, Zhang D, Huang J, Rao Y. Sleep homeostasis regulated by 5HT2b receptor in a small subset of neurons in the dorsal fan-shaped body of drosophila. eLife 2017; 6:26519. [PMID: 28984573 PMCID: PMC5648528 DOI: 10.7554/elife.26519] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 10/05/2017] [Indexed: 12/14/2022] Open
Abstract
Our understanding of the molecular mechanisms underlying sleep homeostasis is limited. We have taken a systematic approach to study neural signaling by the transmitter 5-hydroxytryptamine (5-HT) in drosophila. We have generated knockout and knockin lines for Trh, the 5-HT synthesizing enzyme and all five 5-HT receptors, making it possible for us to determine their expression patterns and to investigate their functional roles. Loss of the Trh, 5HT1a or 5HT2b gene decreased sleep time whereas loss of the Trh or 5HT2b gene diminished sleep rebound after sleep deprivation. 5HT2b expression in a small subset of, probably a single pair of, neurons in the dorsal fan-shaped body (dFB) is functionally essential: elimination of the 5HT2b gene from these neurons led to loss of sleep homeostasis. Genetic ablation of 5HT2b neurons in the dFB decreased sleep and impaired sleep homeostasis. Our results have shown that serotonergic signaling in specific neurons is required for the regulation of sleep homeostasis.
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Affiliation(s)
- Yongjun Qian
- Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Biomembrane and Membrane Biology, PKU-IDG/McGovern Institute For Brain Research, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Yue Cao
- Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Biomembrane and Membrane Biology, PKU-IDG/McGovern Institute For Brain Research, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China
| | - Bowen Deng
- Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Biomembrane and Membrane Biology, PKU-IDG/McGovern Institute For Brain Research, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Guang Yang
- Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Biomembrane and Membrane Biology, PKU-IDG/McGovern Institute For Brain Research, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China
| | - Jiayun Li
- Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Biomembrane and Membrane Biology, PKU-IDG/McGovern Institute For Brain Research, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China
| | - Rui Xu
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Dandan Zhang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Juan Huang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yi Rao
- Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Biomembrane and Membrane Biology, PKU-IDG/McGovern Institute For Brain Research, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
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27
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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: 87] [Impact Index Per Article: 12.4] [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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28
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Nagarkar-Jaiswal S, Manivannan SN, Zuo Z, Bellen HJ. A cell cycle-independent, conditional gene inactivation strategy for differentially tagging wild-type and mutant cells. eLife 2017; 6. [PMID: 28561736 PMCID: PMC5493436 DOI: 10.7554/elife.26420] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/25/2017] [Indexed: 12/14/2022] Open
Abstract
Here, we describe a novel method based on intronic MiMIC insertions described in Nagarkar-Jaiswal et al. (2015) to perform conditional gene inactivation in Drosophila. Mosaic analysis in Drosophila cannot be easily performed in post-mitotic cells. We therefore, therefore, developed Flip-Flop, a flippase-dependent in vivo cassette-inversion method that marks wild-type cells with the endogenous EGFP-tagged protein, whereas mutant cells are marked with mCherry upon inversion. We document the ease and usefulness of this strategy in differential tagging of wild-type and mutant cells in mosaics. We use this approach to phenotypically characterize the loss of SNF4Aγ, encoding the γ subunit of the AMP Kinase complex. The Flip-Flop method is efficient and reliable, and permits conditional gene inactivation based on both spatial and temporal cues, in a cell cycle-, and developmental stage-independent fashion, creating a platform for systematic screens of gene function in developing and adult flies with unprecedented detail. DOI:http://dx.doi.org/10.7554/eLife.26420.001 The instructions needed to build and maintain cells in an organism are encoded in their DNA. There are many different cell types, and each type only needs a small portion of the information found in the DNA to do its job. Hence, only some of the instructions, in the form of genes, need to be active or ‘expressed’ in any given cell type. To understand how a gene works, it is necessary to know in which cell the gene is expressed and where in the cell the gene product – normally a protein – is located. Researchers may study a gene by deleting it, which prevents the protein from being made, or by attaching a new instruction into the gene, which generates a fluorescent tag on the protein to determine where and when it is expressed. Until now, it was not possible to selectively inactivate a gene and simultaneously mark both normal cells containing the protein and mutant cells lacking the protein. Based on an existing tagging approach, Nagarkar-Jaiswal et al. have now developed a method in which normal and mutant cells of fruit flies are marked differently. A gene of interest is tagged with a fluorescent marker called green fluorescent protein (or GFP). The same gene is then inactivated in some of the cells, which are tagged with a red marker called mCherry. Nagarkar-Jaiswal et al. compared normal and mutant cells, and were able to determine how long it takes before the mutant cells become abnormal. With this new method, the role of numerous genes in any tissue of adult flies can be reassessed. This will allow to investigate what happens when a protein is removed in specific cells in adult flies. A future goal will be to apply this method to other animals that are more closely related to humans, such as mice, to gain a clearer picture of the role of genes in different cell types and how faulty genes may cause disease. DOI:http://dx.doi.org/10.7554/eLife.26420.002
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Affiliation(s)
| | - Sathiya N Manivannan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Hugo J Bellen
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, United States.,Program in Developmental Biology, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States
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29
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Ren X, Holsteens K, Li H, Sun J, Zhang Y, Liu LP, Liu Q, Ni JQ. Genome editing in Drosophila melanogaster: from basic genome engineering to the multipurpose CRISPR-Cas9 system. SCIENCE CHINA-LIFE SCIENCES 2017; 60:476-489. [PMID: 28527116 DOI: 10.1007/s11427-017-9029-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/05/2017] [Indexed: 12/16/2022]
Abstract
Nowadays, genome editing tools are indispensable for studying gene function in order to increase our knowledge of biochemical processes and disease mechanisms. The extensive availability of mutagenesis and transgenesis tools make Drosophila melanogaster an excellent model organism for geneticists. Early mutagenesis tools relied on chemical or physical methods, ethyl methane sulfonate (EMS) and X-rays respectively, to randomly alter DNA at a nucleotide or chromosomal level. Since the discovery of transposable elements and the availability of the complete fly genome, specific genome editing tools, such as P-elements, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have undergone rapid development. Currently, one of the leading and most effective contemporary tools is the CRISPR-cas9 system made popular because of its low cost, effectiveness, specificity and simplicity of use. This review briefly addresses the most commonly used mutagenesis and transgenesis tools in Drosophila, followed by an in-depth review of the multipurpose CRISPR-Cas9 system and its current applications.
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Affiliation(s)
- Xingjie Ren
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Kristof Holsteens
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Haiyi Li
- French International School of Hong Kong, Hong Kong SAR, 999000, China
| | - Jin Sun
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yifan Zhang
- Department of Biology, University of California, San Diego, 92093, USA
| | - Lu-Ping Liu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Qingfei Liu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China.
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30
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Taning CNT, Van Eynde B, Yu N, Ma S, Smagghe G. CRISPR/Cas9 in insects: Applications, best practices and biosafety concerns. JOURNAL OF INSECT PHYSIOLOGY 2017; 98:245-257. [PMID: 28108316 DOI: 10.1016/j.jinsphys.2017.01.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/28/2016] [Accepted: 01/12/2017] [Indexed: 05/13/2023]
Abstract
Discovered as a bacterial adaptive immune system, CRISPR/Cas9 (clustered, regularly interspaced, short palindromic repeat/CRISPR associated) is being developed as an attractive tool in genome editing. Due to its high specificity and applicability, CRISPR/Cas9-mediated gene editing has been employed in a multitude of organisms and cells, including insects, for not only fundamental research such as gene function studies, but also applied research such as modification of organisms of economic importance. Despite the rapid increase in the use of CRISPR in insect genome editing, results still differ from each study, principally due to existing differences in experimental parameters, such as the Cas9 and guide RNA form, the delivery method, the target gene and off-target effects. Here, we review current reports on the successes of CRISPR/Cas9 applications in diverse insects and insect cells. We furthermore summarize several best practices to give a useful checklist of CRISPR/Cas9 experimental setup in insects for beginners. Lastly, we discuss the biosafety concerns related to the release of CRISPR/Cas9-edited insects into the environment.
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Affiliation(s)
- Clauvis Nji Tizi Taning
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Benigna Van Eynde
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Na Yu
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
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31
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CRISPR-Cas-Induced Mutants Identify a Requirement for dSTIM in Larval Dopaminergic Cells of Drosophila melanogaster. G3-GENES GENOMES GENETICS 2017; 7:923-933. [PMID: 28131984 PMCID: PMC5345722 DOI: 10.1534/g3.116.038539] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular components of store-operated calcium entry have been identified in the recent past and consist of the endoplasmic reticulum (ER) membrane-resident calcium sensor STIM and the plasma membrane-localized calcium channel Orai. The physiological function of STIM and Orai is best defined in vertebrate immune cells. However, genetic studies with RNAi strains in Drosophila suggest a role in neuronal development and function. We generated a CRISPR-Cas-mediated deletion for the gene encoding STIM in Drosophila (dSTIM), which we demonstrate is larval lethal. To study STIM function in neurons, we merged the CRISPR-Cas9 method with the UAS-GAL4 system to generate either tissue- or cell type-specific inducible STIM knockouts (KOs). Our data identify an essential role for STIM in larval dopaminergic cells. The molecular basis for this cell-specific requirement needs further investigation.
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32
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Fisher YE, Yang HH, Isaacman-Beck J, Xie M, Gohl DM, Clandinin TR. FlpStop, a tool for conditional gene control in Drosophila. eLife 2017; 6. [PMID: 28211790 PMCID: PMC5342825 DOI: 10.7554/elife.22279] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/13/2017] [Indexed: 12/15/2022] Open
Abstract
Manipulating gene function cell type-specifically is a common experimental goal in Drosophila research and has been central to studies of neural development, circuit computation, and behavior. However, current cell type-specific gene disruption techniques in flies often reduce gene activity incompletely or rely on cell division. Here we describe FlpStop, a generalizable tool for conditional gene disruption and rescue in post-mitotic cells. In proof-of-principle experiments, we manipulated apterous, a regulator of wing development. Next, we produced conditional null alleles of Glutamic acid decarboxylase 1 (Gad1) and Resistant to dieldrin (Rdl), genes vital for GABAergic neurotransmission, as well as cacophony (cac) and paralytic (para), voltage-gated ion channels central to neuronal excitability. To demonstrate the utility of this approach, we manipulated cac in a specific visual interneuron type and discovered differential regulation of calcium signals across subcellular compartments. Thus, FlpStop will facilitate investigations into the interactions between genes, circuits, and computation. DOI:http://dx.doi.org/10.7554/eLife.22279.001
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Affiliation(s)
- Yvette E Fisher
- Department of Neurobiology, Stanford University, Stanford, United States
| | - Helen H Yang
- Department of Neurobiology, Stanford University, Stanford, United States
| | | | - Marjorie Xie
- Department of Neurobiology, Stanford University, Stanford, United States
| | - Daryl M Gohl
- Department of Neurobiology, Stanford University, Stanford, United States
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University, Stanford, United States
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33
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Exploring the potential of genome editing CRISPR-Cas9 technology. Gene 2017; 599:1-18. [DOI: 10.1016/j.gene.2016.11.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/18/2016] [Accepted: 11/06/2016] [Indexed: 12/26/2022]
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34
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Lv YH, Li XQ, Yue CW, Wang M. Application of genome editing technologies in gastrointestinal cancers. Shijie Huaren Xiaohua Zazhi 2016; 24:4772-4780. [DOI: 10.11569/wcjd.v24.i36.4772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome editing is a site-directed modification technology for gene targeting and a powerful tool to edit the target DNA by site-specific DNA knockout or knockin. Genome editing has achieved a considerable success from lower microbes to human in the past years and may play a very important role in tumor staging, precision medicine as well as prognosis evaluation in gastrointestinal cancers. This review discusses the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including transcription activator-like effector nucleases, zinc finger nucleases and the CRISPR/Cas9 system. We also summarize the progress made in applying genome editing to the research of gastrointestinal cancers.
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35
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Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DYR, Seydoux G, Mohr SE, Zuber J, Perrimon N. Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet 2016; 18:24-40. [PMID: 27795562 DOI: 10.1038/nrg.2016.118] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Our understanding of the genetic mechanisms that underlie biological processes has relied extensively on loss-of-function (LOF) analyses. LOF methods target DNA, RNA or protein to reduce or to ablate gene function. By analysing the phenotypes that are caused by these perturbations the wild-type function of genes can be elucidated. Although all LOF methods reduce gene activity, the choice of approach (for example, mutagenesis, CRISPR-based gene editing, RNA interference, morpholinos or pharmacological inhibition) can have a major effect on phenotypic outcomes. Interpretation of the LOF phenotype must take into account the biological process that is targeted by each method. The practicality and efficiency of LOF methods also vary considerably between model systems. We describe parameters for choosing the optimal combination of method and system, and for interpreting phenotypes within the constraints of each method.
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Affiliation(s)
- Benjamin E Housden
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Matthew Gemberling
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 43 Ludwigstrasse, Bad Nauheim 61231, Germany
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21218, USA.,Howard Hughes Medical Institute, 725 North Wolfe Street, Baltimore, Maryland 21218, USA
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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36
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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: 257] [Impact Index Per Article: 32.1] [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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37
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Housden BE, Hu Y, Perrimon N. Design and Generation of Drosophila Single Guide RNA Expression Constructs. Cold Spring Harb Protoc 2016; 2016:2016/9/pdb.prot090779. [PMID: 27587779 DOI: 10.1101/pdb.prot090779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The recent advances in CRISPR-based genome engineering have enabled a plethora of new experiments to study a wide range of biological questions. The major attraction of this system over previous methods is its high efficiency and simplicity of use. For example, whereas previous genome engineering technologies required the generation of new proteins to target each new locus, CRISPR requires only the expression of a different single guide RNA (sgRNA). This sgRNA binds to the Cas9 endonuclease protein and directs the generation of a double-strand break to a highly specific genomic site determined by the sgRNA sequence. In addition, the relative simplicity of the Drosophila genome is a particular advantage, as possible sgRNA off-target sites can easily be avoided. Here, we provide a step-by-step protocol for designing sgRNA target sites using the Drosophila RNAi Screening Center (DRSC) Find CRISPRs tool (version 2). We also describe the generation of sgRNA expression plasmids for the use in cultured Drosophila cells or in vivo. Finally, we discuss specific design requirements for various genome engineering applications.
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Affiliation(s)
- Benjamin E Housden
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115; Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115
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38
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Tanaka R, Murakami H, Ote M, Yamamoto D. Clustered regulatory interspaced short palindromic repeats (CRISPR)-mediated mutagenesis and phenotype rescue by piggyBac transgenesis in a nonmodel Drosophila species. INSECT MOLECULAR BIOLOGY 2016; 25:355-361. [PMID: 27015359 DOI: 10.1111/imb.12232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
How behavioural diversity emerged in evolution is an unexplored subject in biology. To tackle this problem, genes and circuits for a behaviour need to be determined in different species for phylogenetic comparisons. The recently developed clustered regulatory interspaced short palindromic repeats/CRISPR associated protein9 (CRISPR/Cas9) system made such a challenge possible by providing the means to induce mutations in a gene of interest in any organism. Aiming at elucidating diversification in genetic and neural networks for courtship behaviour, we attempted to generate a genetic tool kit in Drosophila subobscura, a nonmodel species distantly related to the genetic model Drosophila melanogaster. Here we report the generation of yellow (y) and white mutations with the aid of the CRISPR/Cas9 system, and the rescue of the y mutant phenotype by germline transformation of the newly established y mutant fly line with a y(+) -marked piggyBac vector. This successful mutagenesis and transformation in D. subobscura open up an avenue for comprehensive genetic analyses of higher functions in this and other nonmodel Drosophila species, representing a key step toward systematic comparisons of genes and circuitries underlying behaviour amongst species.
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Affiliation(s)
- R Tanaka
- Division of Neurogenetics, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Division for International Advanced Research and Education, Tohoku University, Sendai, Japan
| | - H Murakami
- Division of Neurogenetics, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - M Ote
- Division of Neurogenetics, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - D Yamamoto
- Division of Neurogenetics, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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39
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Rocha-Martins M, Cavalheiro GR, Matos-Rodrigues GE, Martins RAP. From Gene Targeting to Genome Editing: Transgenic animals applications and beyond. AN ACAD BRAS CIENC 2016; 87:1323-48. [PMID: 26397828 DOI: 10.1590/0001-3765201520140710] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Genome modification technologies are powerful tools for molecular biology and related areas. Advances in animal transgenesis and genome editing technologies during the past three decades allowed systematic interrogation of gene function that can help model how the genome influences cellular physiology. Genetic engineering via homologous recombination (HR) has been the standard method to modify genomic sequences. Nevertheless, nuclease-guided genome editing methods that were developed recently, such as ZFN, TALEN and CRISPR/Cas, opened new perspectives for biomedical research. Here, we present a brief historical perspective of genome modification methods, focusing on transgenic mice models. Moreover, we describe how new techniques were discovered and improved, present the paradigm shifts and discuss their limitations and applications for biomedical research as well as possible future directions.
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Affiliation(s)
- Maurício Rocha-Martins
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, BR
| | - Gabriel R Cavalheiro
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, BR
| | | | - Rodrigo A P Martins
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, BR
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40
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Ghosh S, Tibbit C, Liu JL. Effective knockdown of Drosophila long non-coding RNAs by CRISPR interference. Nucleic Acids Res 2016; 44:e84. [PMID: 26850642 PMCID: PMC4872081 DOI: 10.1093/nar/gkw063] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as regulators of gene expression across metazoa. Interestingly, some lncRNAs function independently of their transcripts - the transcription of the lncRNA locus itself affects target genes. However, current methods of loss-of-function analysis are insufficient to address the role of lncRNA transcription from the transcript which has impeded analysis of their function. Using the minimal CRISPR interference (CRISPRi) system, we show that coexpression of the catalytically inactive Cas9 (dCas9) and guide RNAs targeting the endogenous roX locus in the Drosophila cells results in a robust and specific knockdown of roX1 and roX2 RNAs, thus eliminating the need for recruiting chromatin modifying proteins for effective gene silencing. Additionally, we find that the human and Drosophila codon optimized dCas9 genes are functional and show similar transcription repressive activity. Finally, we demonstrate that the minimal CRISPRi system suppresses roX transcription efficiently in vivo resulting in loss-of-function phenotype, thus validating the method for the first time in a multicelluar organism. Our analysis expands the genetic toolkit available for interrogating lncRNA function in situ and is adaptable for targeting multiple genes across model organisms.
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Affiliation(s)
- Sanjay Ghosh
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Charlotte Tibbit
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
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41
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Abstract
The zebrafish has been a powerful model in forward genetic screens to identify genes essential for organogenesis and embryonic development. Conversely, using reverse genetics to investigate specific gene function requires phenotypic analysis of complete gene inactivation. Despite the availability and efficacy of morpholinos, the lack of tractable and efficient knockout technologies has impeded reverse genetic studies in the zebrafish, particularly in adult animals. The recent development of genome-editing technologies such as CRISPR/Cas9 greatly widened the scope of loss-of-function studies in the zebrafish, allowing for the rapid phenotypic assessment of gene silencing in embryos, the generation of knockout lines, and large-scale reverse genetic screens. Tissue-specific gene inactivation would be ideal for these studies given the caveats of whole-embryo gene silencing, yet spatial control of gene targeting remains a challenge. In this chapter, we focus on tissue-specific gene inactivation using the CRISPR/Cas9 technology. We first explain the rationale for this technique, including some of its potential applications to tackle important biological issues and the inability of current technologies to address these issues. We then present a method to target genes in a tissue-specific manner in the zebrafish. Finally, we discuss technical difficulties and limitations of this method as well as possible future developments.
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Affiliation(s)
- J Ablain
- Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
| | - L I Zon
- Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
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42
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Li W, Ou G. The application of somatic CRISPR-Cas9 to conditional genome editing in Caenorhabditis elegans. Genesis 2016; 54:170-81. [PMID: 26934570 DOI: 10.1002/dvg.22932] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/20/2022]
Abstract
Forward and reverse genetic approaches have been well developed in the nematode Caenorhabditis elegans; however, efficient genetic tools to generate conditional gene mutations are still in high demand. Recently, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR-Cas9) system for genome modification has provided an additional tool for C. elegans researchers to achieve simple and efficient conditional targeted mutagenesis. Here, we review recent advances in the somatic expression of Cas9 endonuclease for conditional gene editing. We present some practical considerations for improving the efficiency and reducing the off-target effects of somatic CRISPR-Cas9 and highlight a strategy to analyze somatic mutation at single-cell resolution. Finally, we outline future applications and consider challenges for this emerging genome editing platform that will need to be addressed in the future.
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Affiliation(s)
- Wei Li
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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43
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Xu H, O'Brochta DA. Advanced technologies for genetically manipulating the silkworm Bombyx mori, a model Lepidopteran insect. Proc Biol Sci 2016; 282:rspb.2015.0487. [PMID: 26108630 DOI: 10.1098/rspb.2015.0487] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic technologies based on transposon-mediated transgenesis along with several recently developed genome-editing technologies have become the preferred methods of choice for genetically manipulating many organisms. The silkworm, Bombyx mori, is a Lepidopteran insect of great economic importance because of its use in silk production and because it is a valuable model insect that has greatly enhanced our understanding of the biology of insects, including many agricultural pests. In the past 10 years, great advances have been achieved in the development of genetic technologies in B. mori, including transposon-based technologies that rely on piggyBac-mediated transgenesis and genome-editing technologies that rely on protein- or RNA-guided modification of chromosomes. The successful development and application of these technologies has not only facilitated a better understanding of B. mori and its use as a silk production system, but also provided valuable experiences that have contributed to the development of similar technologies in non-model insects. This review summarizes the technologies currently available for use in B. mori, their application to the study of gene function and their use in genetically modifying B. mori for biotechnology applications. The challenges, solutions and future prospects associated with the development and application of genetic technologies in B. mori are also discussed.
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Affiliation(s)
- Hanfu Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, People's Republic of China
| | - David A O'Brochta
- Department of Entomology, The Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, MD 20850, USA
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44
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Abstract
Since its introduction in 1993, the GAL4 system has become an essential part of the Drosophila geneticist's toolkit. Widely used to drive gene expression in a multitude of cell- and tissue-specific patterns, the system has been adapted and extended to form the basis of many modern tools for the manipulation of gene expression in Drosophila and other model organisms.
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45
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Abstract
Reverse genetics-the creation of mutations in preselected target genes-has until recently been a bottleneck in many Drosophila projects. The advent of clustered, regularly interspaced, short palindromic repeat (CRISPR) genome engineering systems has transformed this situation. A short time after the in vitro demonstration of target site cleavage by the RNA-guided endonuclease CRISPR-associated nuclease 9 (Cas9) (Jinek et al., Science 337:816-821, 2012), hundreds of fly researchers are using CRISPR technology to generate loss-of-function mutant alleles in specific genes, as well as to create specific point mutations or tagged protein products. It appears that most target genes can be edited with remarkably high efficiency, with engineered strains often available a few weeks after conception of a project. Here, we provide a step-by-step protocol for creating loss-of-function mutations in Drosophila using transgenic Cas9 sources, which is based on optimized reagents and procedures that have been evaluated in our laboratory. We also provide guidance on extending this protocol to produce precise genomic alterations by homology-directed repair in the presence of a donor sequence. Additional information and updates are available from our website, www.crisprflydesign.org .
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Affiliation(s)
- Fillip Port
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Division of Signaling andFunctional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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46
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Venken KJT, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. Genome engineering: Drosophila melanogaster and beyond. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:233-67. [PMID: 26447401 DOI: 10.1002/wdev.214] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 08/03/2015] [Accepted: 08/20/2015] [Indexed: 12/26/2022]
Abstract
A central challenge in investigating biological phenomena is the development of techniques to modify genomic DNA with nucleotide precision that can be transmitted through the germ line. Recent years have brought a boon in these technologies, now collectively known as genome engineering. Defined genomic manipulations at the nucleotide level enable a variety of reverse engineering paradigms, providing new opportunities to interrogate diverse biological functions. These genetic modifications include controlled removal, insertion, and substitution of genetic fragments, both small and large. Small fragments up to a few kilobases (e.g., single nucleotide mutations, small deletions, or gene tagging at single or multiple gene loci) to large fragments up to megabase resolution can be manipulated at single loci to create deletions, duplications, inversions, or translocations of substantial sections of whole chromosome arms. A specialized substitution of chromosomal portions that presumably are functionally orthologous between different organisms through syntenic replacement, can provide proof of evolutionary conservation between regulatory sequences. Large transgenes containing endogenous or synthetic DNA can be integrated at defined genomic locations, permitting an alternative proof of evolutionary conservation, and sophisticated transgenes can be used to interrogate biological phenomena. Precision engineering can additionally be used to manipulate the genomes of organelles (e.g., mitochondria). Novel genome engineering paradigms are often accelerated in existing, easily genetically tractable model organisms, primarily because these paradigms can be integrated in a rigorous, existing technology foundation. The Drosophila melanogaster fly model is ideal for these types of studies. Due to its small genome size, having just four chromosomes, the vast amount of cutting-edge genetic technologies, and its short life-cycle and inexpensive maintenance requirements, the fly is exceptionally amenable to complex genetic analysis using advanced genome engineering. Thus, highly sophisticated methods developed in the fly model can be used in nearly any sequenced organism. Here, we summarize different ways to perform precise inheritable genome engineering using integrases, recombinases, and DNA nucleases in the D. melanogaster. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Koen J T Venken
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Paul J Vandeventer
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Audrey E Christiansen
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Kristi L Hoffman
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
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47
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Praxenthaler H, Smylla TK, Nagel AC, Preiss A, Maier D. Generation of New Hairless Alleles by Genomic Engineering at the Hairless Locus in Drosophila melanogaster. PLoS One 2015; 10:e0140007. [PMID: 26448463 PMCID: PMC4598140 DOI: 10.1371/journal.pone.0140007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/27/2015] [Indexed: 11/18/2022] Open
Abstract
Hairless (H) is the major antagonist within the Notch signalling pathway of Drosophila melanogaster. By binding to Suppressor of Hairless [Su(H)] and two co-repressors, H induces silencing of Notch target genes in the absence of Notch signals. We have applied genomic engineering to create several new H alleles. To this end the endogenous H locus was replaced with an attP site by homologous recombination, serving as a landing platform for subsequent site directed integration of different H constructs. This way we generated a complete H knock out allele HattP, reintroduced a wild type H genomic and a cDNA-construct (Hgwt, Hcwt) as well as two constructs encoding H proteins defective of Su(H) binding (HLD, HiD). Phenotypes regarding viability, bristle and wing development were recorded, and the expression of Notch target genes wingless and cut was analysed in mutant wing discs or in mutant cell clones. Moreover, genetic interactions with Notch (N5419) and Delta (DlB2) mutants were addressed. Overall, phenotypes were largely as expected: both HLD and HiD were similar to the HattP null allele, indicating that most of H activity requires the binding of Su(H). Both rescue constructs Hgwt and Hcwt were homozygous viable without phenotype. Unexpectedly, the hemizygous condition uncovered that they were not identical to the wild type allele: notably Hcwt showed a markedly reduced activity, suggesting the presence of as yet unidentified regulatory or stabilizing elements in untranslated regions of the H gene. Interestingly, Hgwt homozygous cells expressed higher levels of H protein, perhaps unravelling gene-by-environment interactions.
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Affiliation(s)
- Heiko Praxenthaler
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599, Stuttgart, Germany
| | - Thomas K. Smylla
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599, Stuttgart, Germany
| | - Anja C. Nagel
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599, Stuttgart, Germany
| | - Anette Preiss
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599, Stuttgart, Germany
| | - Dieter Maier
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599, Stuttgart, Germany
- * E-mail:
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48
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Yin L, Maddison LA, Li M, Kara N, LaFave MC, Varshney GK, Burgess SM, Patton JG, Chen W. Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs. Genetics 2015; 200:431-41. [PMID: 25855067 PMCID: PMC4492370 DOI: 10.1534/genetics.115.176917] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/06/2015] [Indexed: 12/13/2022] Open
Abstract
Determining the mechanism of gene function is greatly enhanced using conditional mutagenesis. However, generating engineered conditional alleles is inefficient and has only been widely used in mice. Importantly, multiplex conditional mutagenesis requires extensive breeding. Here we demonstrate a system for one-generation multiplex conditional mutagenesis in zebrafish (Danio rerio) using transgenic expression of both cas9 and multiple single guide RNAs (sgRNAs). We describe five distinct zebrafish U6 promoters for sgRNA expression and demonstrate efficient multiplex biallelic inactivation of tyrosinase and insulin receptor a and b, resulting in defects in pigmentation and glucose homeostasis. Furthermore, we demonstrate temporal and tissue-specific mutagenesis using transgenic expression of Cas9. Heat-shock-inducible expression of cas9 allows temporal control of tyr mutagenesis. Liver-specific expression of cas9 disrupts insulin receptor a and b, causing fasting hypoglycemia and postprandial hyperglycemia. We also show that delivery of sgRNAs targeting ascl1a into the eye leads to impaired damage-induced photoreceptor regeneration. Our findings suggest that CRISPR/Cas9-based conditional mutagenesis in zebrafish is not only feasible but rapid and straightforward.
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Affiliation(s)
- Linlin Yin
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Lisette A Maddison
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Mingyu Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Nergis Kara
- Department of Biological Science, Vanderbilt University, Nashville, Tennessee 37240
| | - Matthew C LaFave
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - James G Patton
- Department of Biological Science, Vanderbilt University, Nashville, Tennessee 37240
| | - Wenbiao Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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49
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Port F, Muschalik N, Bullock SL. Systematic Evaluation of Drosophila CRISPR Tools Reveals Safe and Robust Alternatives to Autonomous Gene Drives in Basic Research. G3 (BETHESDA, MD.) 2015; 5:1493-502. [PMID: 25999583 PMCID: PMC4502383 DOI: 10.1534/g3.115.019083] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/16/2015] [Indexed: 12/19/2022]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR associated (CRISPR/Cas) technology allows rapid, site-specific genome modification in a wide variety of organisms . Proof-of-principle studies in Drosophila melanogaster have used various CRISPR/Cas tools and experimental designs, leading to significant uncertainty in the community about how to put this technology into practice. Moreover, it is unclear what proportion of genomic target sites can be modified with high efficiency. Here, we address these issues by systematically evaluating available CRISPR/Cas reagents and methods in Drosophila. Our findings allow evidence-based choices of Cas9 sources and strategies for generating knock-in alleles. We perform gene editing at a large number of target sites using a highly active Cas9 line and a collection of transgenic gRNA strains. The vast majority of target sites can be mutated with remarkable efficiency using these tools. We contrast our method to recently developed autonomous gene drive technology for somatic and germline genome engineering and conclude that optimized CRISPR with independent transgenes is as efficient, more versatile, and does not represent a biosafety risk.
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Affiliation(s)
- Fillip Port
- Cell Biology Division, MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Nadine Muschalik
- Cell Biology Division, MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Simon L Bullock
- Cell Biology Division, MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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50
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Dong S, Lin J, Held NL, Clem RJ, Passarelli AL, Franz AWE. Heritable CRISPR/Cas9-mediated genome editing in the yellow fever mosquito, Aedes aegypti. PLoS One 2015; 10:e0122353. [PMID: 25815482 PMCID: PMC4376861 DOI: 10.1371/journal.pone.0122353] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/12/2015] [Indexed: 12/26/2022] Open
Abstract
In vivo targeted gene disruption is a powerful tool to study gene function. Thus far, two tools for genome editing in Aedes aegypti have been applied, zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN). As a promising alternative to ZFN and TALEN, which are difficult to produce and validate using standard molecular biological techniques, the clustered regularly interspaced short palindromic repeats/CRISPR-associated sequence 9 (CRISPR/Cas9) system has recently been discovered as a "do-it-yourself" genome editing tool. Here, we describe the use of CRISPR/Cas9 in the mosquito vector, Aedes aegypti. In a transgenic mosquito line expressing both Dsred and enhanced cyan fluorescent protein (ECFP) from the eye tissue-specific 3xP3 promoter in separated but tightly linked expression cassettes, we targeted the ECFP nucleotide sequence for disruption. When supplying the Cas9 enzyme and two sgRNAs targeting different regions of the ECFP gene as in vitro transcribed mRNAs for germline transformation, we recovered four different G1 pools (5.5% knockout efficiency) where individuals still expressed DsRed but no longer ECFP. PCR amplification, cloning, and sequencing of PCR amplicons revealed indels in the ECFP target gene ranging from 2-27 nucleotides. These results show for the first time that CRISPR/Cas9 mediated gene editing is achievable in Ae. aegypti, paving the way for further functional genomics related studies in this mosquito species.
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Affiliation(s)
- Shengzhang Dong
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Jingyi Lin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Nicole L Held
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Rollie J Clem
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - A Lorena Passarelli
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Alexander W E Franz
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
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