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Ryniawec JM, Amoiroglou A, Rogers GC. Generating CRISPR-edited clonal lines of cultured Drosophila S2 cells. Biol Methods Protoc 2024; 9:bpae059. [PMID: 39206452 PMCID: PMC11357795 DOI: 10.1093/biomethods/bpae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/26/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
CRISPR/Cas9 genome editing is a pervasive research tool due to its relative ease of use. However, some systems are not amenable to generating edited clones due to genomic complexity and/or difficulty in establishing clonal lines. For example, Drosophila Schneider 2 (S2) cells possess a segmental aneuploid genome and are challenging to single-cell select. Here, we describe a streamlined CRISPR/Cas9 methodology for knock-in and knock-out experiments in S2 cells, whereby an antibiotic resistance gene is inserted in-frame with the coding region of a gene-of-interest. By using selectable markers, we have improved the ease and efficiency for the positive selection of null cells using antibiotic selection in feeder layers followed by cell expansion to generate clonal lines. Using this method, we generated the first acentrosomal S2 cell lines by knocking-out centriole genes Polo-like Kinase 4/Plk4 or Ana2 as proof of concept. These strategies for generating gene-edited clonal lines will add to the collection of CRISPR tools available for cultured Drosophila cells by making CRISPR more practical and therefore improving gene function studies.
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Affiliation(s)
- John M Ryniawec
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, United States
| | - Anastasia Amoiroglou
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, United States
| | - Gregory C Rogers
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, United States
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2
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Markley HC, Helms KJ, Maar M, Zentner GE, Wade MJ, Zelhof AC. Generating and testing the efficacy of reagents for CRISPR/Cas9 homology directed repair-based manipulations in Tribolium. JOURNAL OF INSECT SCIENCE (ONLINE) 2024; 24:15. [PMID: 39162172 PMCID: PMC11333919 DOI: 10.1093/jisesa/ieae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/01/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024]
Abstract
CRISPR/Cas9 manipulations are possible in many insects and ever expanding. Nonetheless, success in one species and techniques developed for it are not necessarily applicable to other species. As such, the development and expansion of CRISPR-based (clustered regularly interspaced short palindromic repeats) genome-editing tools and methodologies are dependent upon direct experimentation. One useful technique is Cas9-dependent homologous recombination, which is a critical tool for studying gene function but also for developing pest related applications like gene drive. Here, we report our attempts to induce Cas9 homology directed repair (HDR) and subsequent gene drive in Tribolium castaneum (Herbst; Insecta: Coleoptera: Tenebrionidae). Utilizing constructs containing 1 or 2 target gRNAs in combination with Cas9 under 2 different promoters and corresponding homology arms, we found a high incidence of CRISPR/Cas9 induced mutations but no evidence of homologous recombination. Even though the generated constructs provide new resources for CRISPR/Cas9 modification of the Tribolium genome, our results suggest that additional modifications and increased sample sizes will be necessary to increase the potential and detection for HDR of the Tribolium genome.
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Affiliation(s)
| | - Kennedy J Helms
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Megan Maar
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Michael J Wade
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Andrew C Zelhof
- Department of Biology, Indiana University, Bloomington, IN, USA
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3
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Sale JE, Stoddard BL. CRISPR in Nucleic Acids Research: the sequel. Nucleic Acids Res 2024; 52:3489-3492. [PMID: 38532709 DOI: 10.1093/nar/gkae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/28/2024] Open
Affiliation(s)
- Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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4
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Li P, Messina G, Lehner CF. Nuclear elongation during spermiogenesis depends on physical linkage of nuclear pore complexes to bundled microtubules by Drosophila Mst27D. PLoS Genet 2023; 19:e1010837. [PMID: 37428798 PMCID: PMC10359004 DOI: 10.1371/journal.pgen.1010837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
Spermatozoa in animal species are usually highly elongated cells with a long motile tail attached to a head that contains the haploid genome in a compact and often elongated nucleus. In Drosophila melanogaster, the nucleus is compacted two hundred-fold in volume during spermiogenesis and re-modeled into a needle that is thirty-fold longer than its diameter. Nuclear elongation is preceded by a striking relocalization of nuclear pore complexes (NPCs). While NPCs are initially located throughout the nuclear envelope (NE) around the spherical nucleus of early round spermatids, they are later confined to one hemisphere. In the cytoplasm adjacent to this NPC-containing NE, the so-called dense complex with a strong bundle of microtubules is assembled. While this conspicuous proximity argued for functional significance of NPC-NE and microtubule bundle, experimental confirmation of their contributions to nuclear elongation has not yet been reported. Our functional characterization of the spermatid specific Mst27D protein now resolves this deficit. We demonstrate that Mst27D establishes physical linkage between NPC-NE and dense complex. The C-terminal region of Mst27D binds to the nuclear pore protein Nup358. The N-terminal CH domain of Mst27D, which is similar to that of EB1 family proteins, binds to microtubules. At high expression levels, Mst27D promotes bundling of microtubules in cultured cells. Microscopic analyses indicated co-localization of Mst27D with Nup358 and with the microtubule bundles of the dense complex. Time-lapse imaging revealed that nuclear elongation is accompanied by a progressive bundling of microtubules into a single elongated bundle. In Mst27D null mutants, this bundling process does not occur and nuclear elongation is abnormal. Thus, we propose that Mst27D permits normal nuclear elongation by promoting the attachment of the NPC-NE to the microtubules of the dense complex, as well as the progressive bundling of these microtubules.
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Affiliation(s)
- Pengfei Li
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
| | - Giovanni Messina
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
| | - Christian F Lehner
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
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5
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Bui KC, Kamiyama D. CRISPR/Cas9-mediated knock-in in ebony gene using a PCR product donor template in Drosophila. GENE AND GENOME EDITING 2023; 5:100025. [PMID: 37426904 PMCID: PMC10327816 DOI: 10.1016/j.ggedit.2023.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
CRISPR/Cas9 technology has been a powerful tool for gene editing in Drosophila, particularly for knocking in base-pair mutations or a variety of gene cassettes into endogenous gene loci. Among the Drosophila community, there has been a concerted effort to establish CRISPR/Cas9-mediated knock-in protocols that decrease the amount of time spent on molecular cloning. Here, we report the CRISPR/Cas9-mediated insertion of a ~50 base-pair sequence into the ebony gene locus, using a linear double-stranded DNA (PCR product) donor template By circumventing the cloning step of the donor template, our approach suggests the PCR product as a useful alternative knock-in donor format.
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6
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Pargett M, Ram AR, Murthy V, Davies AE. Live-Cell Sender-Receiver Co-cultures for Quantitative Measurement of Paracrine Signaling Dynamics, Gene Expression, and Drug Response. Methods Mol Biol 2023; 2634:285-314. [PMID: 37074584 DOI: 10.1007/978-1-0716-3008-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Paracrine signaling is a fundamental process regulating tissue development, repair, and pathogenesis of diseases such as cancer. Herein we describe a method for quantitatively measuring paracrine signaling dynamics, and resultant gene expression changes, in living cells using genetically encoded signaling reporters and fluorescently tagged gene loci. We discuss considerations for selecting paracrine "sender-receiver" cell pairs, appropriate reporters, the use of this system to ask diverse experimental questions and screen drugs blocking intracellular communication, data collection, and the use of computational approaches to model and interpret these experiments.
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Affiliation(s)
- Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Abhineet R Ram
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Vaibhav Murthy
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
- Knight Cancer Institute, Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Alexander E Davies
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
- Knight Cancer Institute, Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA.
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7
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HEHR: Homing Endonuclease-Mediated Homologous Recombination for Efficient Adenovirus Genome Engineering. Genes (Basel) 2022; 13:genes13112129. [DOI: 10.3390/genes13112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
Adenoviruses are non-enveloped linear double-stranded DNA viruses with over 100 types in humans. Adenovirus vectors have gained tremendous attention as gene delivery vehicles, as vaccine vectors and as oncolytic viruses. Although various methods have been used to generate adenoviral vectors, the vector-producing process remains technically challenging regarding efficacious genome modification. Based on our previously reported adenoviral genome modification streamline via linear–circular homologous recombination, we further develop an HEHR (combining Homing Endonucleases and Homologous Recombination) method to engineer adenoviral genomes more efficiently. I-PpoI, a rare endonuclease encoded by a group I intron, was introduced into the previously described ccdB counter-selection marker. We found that the I-PpoI pre-treatment of counter-selection containing parental plasmid increased the homologous recombination efficiency up to 100%. The flanking of the counter-selection marker with either single or double I-PpoI sites showed enhanced efficacy. In addition, we constructed a third counter-selection marker flanked by an alternative restriction enzyme: AbsI, which could be applied in case the I-PpoI site already existed in the transgene cassette that was previously inserted in the adenovirus genome. Together, HEHR can be applied for seamless sequence replacements, deletions and insertions. The advantages of HEHR in seamless mutagenesis will facilitate rational design of adenoviral vectors for diverse purposes.
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8
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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9
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Harrod A, Lai CF, Goldsbrough I, Simmons GM, Oppermans N, Santos DB, Győrffy B, Allsopp RC, Toghill BJ, Balachandran K, Lawson M, Morrow CJ, Surakala M, Carnevalli LS, Zhang P, Guttery DS, Shaw JA, Coombes RC, Buluwela L, Ali S. Genome engineering for estrogen receptor mutations reveals differential responses to anti-estrogens and new prognostic gene signatures for breast cancer. Oncogene 2022; 41:4905-4915. [PMID: 36198774 PMCID: PMC7613769 DOI: 10.1038/s41388-022-02483-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022]
Abstract
Mutations in the estrogen receptor (ESR1) gene are common in ER-positive breast cancer patients who progress on endocrine therapies. Most mutations localise to just three residues at, or near, the C-terminal helix 12 of the hormone binding domain, at leucine-536, tyrosine-537 and aspartate-538. To investigate these mutations, we have used CRISPR-Cas9 mediated genome engineering to generate a comprehensive set of isogenic mutant breast cancer cell lines. Our results confirm that L536R, Y537C, Y537N, Y537S and D538G mutations confer estrogen-independent growth in breast cancer cells. Growth assays show mutation-specific reductions in sensitivities to drugs representing three classes of clinical anti-estrogens. These differential mutation- and drug-selectivity profiles have implications for treatment choices following clinical emergence of ER mutations. Our results further suggest that mutant expression levels may be determinants of the degree of resistance to some anti-estrogens. Differential gene expression analysis demonstrates up-regulation of estrogen-responsive genes, as expected, but also reveals that enrichment for interferon-regulated gene expression is a common feature of all mutations. Finally, a new gene signature developed from the gene expression profiles in ER mutant cells predicts clinical response in breast cancer patients with ER mutations.
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Affiliation(s)
- Alison Harrod
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
- Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Chun-Fui Lai
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | | | - Georgia M Simmons
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Natasha Oppermans
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Daniela B Santos
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Balazs Győrffy
- Semmelweis University Department of Bioinformatics, H-1094 Budapest, Hungary and TTK Cancer Biomarker Research Group, H-1117, Budapest, Hungary
| | - Rebecca C Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Bradley J Toghill
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Kirsty Balachandran
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Mandy Lawson
- Early Oncology R&D, AstraZeneca, Biomedical Campus, 1 Francis Crick Ave, Cambridge, CB2 0AA, UK
| | - Christopher J Morrow
- Early Oncology R&D, AstraZeneca, Biomedical Campus, 1 Francis Crick Ave, Cambridge, CB2 0AA, UK
| | - Manasa Surakala
- Early Oncology R&D, AstraZeneca, Biomedical Campus, 1 Francis Crick Ave, Cambridge, CB2 0AA, UK
| | - Larissa S Carnevalli
- Early Oncology R&D, AstraZeneca, Biomedical Campus, 1 Francis Crick Ave, Cambridge, CB2 0AA, UK
| | - Pei Zhang
- Early Oncology R&D, AstraZeneca, Biomedical Campus, 1 Francis Crick Ave, Cambridge, CB2 0AA, UK
| | - David S Guttery
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Jacqueline A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - R Charles Coombes
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Lakjaya Buluwela
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK.
| | - Simak Ali
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK.
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10
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Acharya D, Reis R, Volcic M, Liu G, Wang MK, Chia BS, Nchioua R, Groß R, Münch J, Kirchhoff F, Sparrer KMJ, Gack MU. Actin cytoskeleton remodeling primes RIG-I-like receptor activation. Cell 2022; 185:3588-3602.e21. [PMID: 36113429 PMCID: PMC9680832 DOI: 10.1016/j.cell.2022.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/17/2022] [Accepted: 08/10/2022] [Indexed: 01/26/2023]
Abstract
The current dogma of RNA-mediated innate immunity is that sensing of immunostimulatory RNA ligands is sufficient for the activation of intracellular sensors and induction of interferon (IFN) responses. Here, we report that actin cytoskeleton disturbance primes RIG-I-like receptor (RLR) activation. Actin cytoskeleton rearrangement induced by virus infection or commonly used reagents to intracellularly deliver RNA triggers the relocalization of PPP1R12C, a regulatory subunit of the protein phosphatase-1 (PP1), from filamentous actin to cytoplasmic RLRs. This allows dephosphorylation-mediated RLR priming and, together with the RNA agonist, induces effective RLR downstream signaling. Genetic ablation of PPP1R12C impairs antiviral responses and enhances susceptibility to infection with several RNA viruses including SARS-CoV-2, influenza virus, picornavirus, and vesicular stomatitis virus. Our work identifies actin cytoskeleton disturbance as a priming signal for RLR-mediated innate immunity, which may open avenues for antiviral or adjuvant design.
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Affiliation(s)
- Dhiraj Acharya
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Rebecca Reis
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Meta Volcic
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - May K Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Bing Shao Chia
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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11
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Rujano MA, Briand D, Ðelić B, Marc J, Spéder P. An interplay between cellular growth and atypical fusion defines morphogenesis of a modular glial niche in Drosophila. Nat Commun 2022; 13:4999. [PMID: 36008397 PMCID: PMC9411534 DOI: 10.1038/s41467-022-32685-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Neural stem cells (NSCs) live in an intricate cellular microenvironment supporting their activity, the niche. Whilst shape and function are inseparable, the morphogenetic aspects of niche development are poorly understood. Here, we use the formation of a glial niche to investigate acquisition of architectural complexity. Cortex glia (CG) in Drosophila regulate neurogenesis and build a reticular structure around NSCs. We first show that individual CG cells grow tremendously to ensheath several NSC lineages, employing elaborate proliferative mechanisms which convert these cells into syncytia rich in cytoplasmic bridges. CG syncytia further undergo homotypic cell-cell fusion, using defined cell surface receptors and actin regulators. Cellular exchange is however dynamic in space and time. This atypical cell fusion remodels cellular borders, restructuring the CG syncytia. Ultimately, combined growth and fusion builds the multi-level architecture of the niche, and creates a modular, spatial partition of the NSC population. Our findings provide insights into how a niche forms and organises while developing intimate contacts with a stem cell population.
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Affiliation(s)
| | | | - Bojana Ðelić
- Institut Pasteur, CNRS UMR3738, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Cell Division and Neurogenesis, Ecole Normale Supérieure, CNRS, Inserm, PSL Université Paris, Paris, France
| | - Julie Marc
- Institut Pasteur, CNRS UMR3738, Paris, France
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12
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Klinke N, Meyer H, Ratnavadivel S, Reinhardt M, Heinisch JJ, Malmendal A, Milting H, Paululat A. A Drosophila melanogaster model for TMEM43-related arrhythmogenic right ventricular cardiomyopathy type 5. Cell Mol Life Sci 2022; 79:444. [PMID: 35869176 PMCID: PMC9307560 DOI: 10.1007/s00018-022-04458-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022]
Abstract
AbstractArrhythmogenic right ventricular cardiomyopathy (ARVC) is a severe cardiac disease that leads to heart failure or sudden cardiac death (SCD). For the pathogenesis of ARVC, various mutations in at least eight different genes have been identified. A rare form of ARVC is associated with the mutation TMEM43 p.S358L, which is a fully penetrant variant in male carriers. TMEM43 p.S358 is homologous to CG8111 p.S333 in Drosophila melanogaster. We established CRISPR/Cas9-mediated CG8111 knock-out mutants in Drosophila, as well as transgenic fly lines carrying an overexpression construct of the CG8111 p.S333L substitution. Knock-out flies developed normally, whereas the overexpression of CG8111 p.S333L caused growth defects, loss of body weight, cardiac arrhythmias, and premature death. An evaluation of a series of model mutants that replaced S333 by selected amino acids proved that the conserved serine is critical for the physiological function of CG8111. Metabolomic and proteomic analyses revealed that the S333 in CG8111 is essential to proper energy homeostasis and lipid metabolism in the fly. Of note, metabolic impairments were also found in the murine Tmem43 disease model, and fibrofatty replacement is a hallmark of human ARVC5. These findings contribute to a more comprehensive understanding of the molecular functions of CG8111 in Drosophila, and can represent a valuable basis to assess the aetiology of the human TMEM43 p.S358L variant in more detail.
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13
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Böttcher R, Schmidts I, Nitschko V, Duric P, Förstemann K. RNA polymerase II is recruited to DNA double-strand breaks for dilncRNA transcription in Drosophila. RNA Biol 2021; 19:68-77. [PMID: 34965182 PMCID: PMC8786327 DOI: 10.1080/15476286.2021.2014694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
DNA double-strand breaks are among the most toxic lesions that can occur in a genome and their faithful repair is thus of great importance. Recent findings have uncovered local transcription that initiates at the break and forms a non-coding transcript, called damage-induced long non-coding RNA (dilncRNA), which helps to coordinate the DNA transactions necessary for repair. We provide nascent RNA sequencing-based evidence that RNA polymerase II transcribes the dilncRNA in Drosophila and that this is more efficient for DNA breaks in an intron-containing gene, consistent with the higher damage-induced siRNA levels downstream of an intron. The spliceosome thus stimulates recruitment of RNA polymerase II to the break, rather than merely promoting the annealing of sense and antisense RNA to form the siRNA precursor. In contrast, RNA polymerase III nascent RNA libraries did not contain reads corresponding to the cleaved loci and selective inhibition of RNA polymerase III did not reduce the yield of damage-induced siRNAs. Finally, the damage-induced siRNA density was unchanged downstream of a T8 sequence, which terminates RNA polymerase III transcription. We thus found no evidence for a participation of RNA polymerase III in dilncRNA transcription in cultured Drosophila cells.
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Affiliation(s)
- Romy Böttcher
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Ines Schmidts
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Volker Nitschko
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Petar Duric
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Klaus Förstemann
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
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14
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Li JJ, Shi Y, Wu JN, Li H, Smagghe G, Liu TX. CRISPR/Cas9 in lepidopteran insects: Progress, application and prospects. JOURNAL OF INSECT PHYSIOLOGY 2021; 135:104325. [PMID: 34743972 DOI: 10.1016/j.jinsphys.2021.104325] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/26/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Clustered regularly spaced short palindrome repeats (CRISPR) structure family forms the acquired immune system in bacteria and archaea. Recent advances in CRISPR/Cas genome editing as derived from prokaryotes, confirmed the characteristics of robustness, high target specificity and programmability, and also revolutionized the insect sciences field. The successful application of CRISPR in a wide variety of lepidopteran insects, with a high genetic diversity, provided opportunities to explore gene functions, insect modification and pest control. In this review, we present a detailed overview on the recent progress of CRISPR in lepidopteran insects, and described the basic principles of the system and its application. Major interest is on wing development, pigmentation, mating, reproduction, sex determination, metamorphosis, resistance and silkworm breeding innovation. Finally, we outlined the limitations of CRISPR/Cas system and discussed its application prospects in lepidopteran insects.
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Affiliation(s)
- Jiang-Jie Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China; Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Yan Shi
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China; Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Ji-Nan Wu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China
| | - Hao Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Tong-Xian Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China.
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15
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Jeronimo C, Angel A, Nguyen VQ, Kim JM, Poitras C, Lambert E, Collin P, Mellor J, Wu C, Robert F. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner. Mol Cell 2021; 81:3542-3559.e11. [PMID: 34380014 DOI: 10.1016/j.molcel.2021.07.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 05/25/2021] [Accepted: 07/12/2021] [Indexed: 12/29/2022]
Abstract
The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Vu Q Nguyen
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jee Min Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Christian Poitras
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Elie Lambert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Pierre Collin
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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16
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Sizova I, Kelterborn S, Verbenko V, Kateriya S, Hegemann P. Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting. G3 (BETHESDA, MD.) 2021; 11:jkab114. [PMID: 33836052 PMCID: PMC8495919 DOI: 10.1093/g3journal/jkab114] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent nonhomologous end-joining (cNHEJ) and DNA polymerase theta (POLQ)-mediated end joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair (HDR)/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect HDR of the inactivated paromomycin-resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate HDR/gene inactivation. Our data suggest that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced HDR and random integration of transgenes, whereas KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in C. reinhardtii and can be used for future development of algal biotechnology.
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Affiliation(s)
- Irina Sizova
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Simon Kelterborn
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
| | - Valeriy Verbenko
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Suneel Kateriya
- Laboratory of Optobiology School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Peter Hegemann
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
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17
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Bandyopadhyay S, Douglass J, Kapell S, Khan N, Feitosa-Suntheimer F, Klein JA, Temple J, Brown-Culbertson J, Tavares AH, Saeed M, Lau NC. DNA templates with blocked long 3' end single-stranded overhangs (BL3SSO) promote bona fide Cas9-stimulated homology-directed repair of long transgenes into endogenous gene loci. G3-GENES GENOMES GENETICS 2021; 11:6275753. [PMID: 33989385 PMCID: PMC8496256 DOI: 10.1093/g3journal/jkab169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022]
Abstract
Knock-in of large transgenes by Cas9-mediated homology-directed repair (HDR) is an extremely inefficient process. Although the use of single-stranded oligonucleotides (ssODN) as an HDR donor has improved the integration of smaller transgenes, they do not support efficient insertion of large DNA sequences. In an effort to gain insights into the mechanism(s) governing the HDR-mediated integration of larger transgenes and to improve the technology, we conducted knock-in experiments targeting the human EMX1 locus and applied rigorous genomic PCR analyses in the human HEK293 cell line. This exercise revealed an unexpected molecular complication arising from the transgene HDR being initiated at the single homology arm and the subsequent genomic integration of plasmid backbone sequences. To pivot around this problem, we devised a novel PCR-constructed template containing blocked long 3' single-stranded overhangs (BL3SSO) that greatly improved the efficiency of bona fide Cas9-stimulated HDR at the EMX1 locus. We further refined BL3SSO technology and successfully used it to insert GFP transgenes into two important interferon-stimulated genes (ISGs) loci, Viperin/RSAD2, and ISG15. This study demonstrates the utility of the BL3SSO platform for inserting long DNA sequences into both constitutive and inducible endogenous loci to generate novel human cell lines for the study of important biological processes.
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Affiliation(s)
- Saptaparni Bandyopadhyay
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Joseph Douglass
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Sebastian Kapell
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | | | - Jenny A Klein
- Department of Biology, Brandeis University, Waltham, MA 02453, USA.,Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Jasmine Temple
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Jayce Brown-Culbertson
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Nelson C Lau
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA.,Genome Science Institute, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
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18
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Trivedi D. Using CRISPR-Cas9-based genome engineering tools in Drosophila melanogaster. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:85-121. [PMID: 33934839 DOI: 10.1016/bs.pmbts.2021.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drosophila melanogaster has been used as a model organism for over a century. Mutant-based analyses have been used extensively to understand the genetic basis of different cellular processes, including development, neuronal function and diseases. Most of the earlier genetic mutants and specific tools were generated by random insertions and deletion strategies and then mapped to specific genomic loci. Since all genomic regions are not equally accessible to random mutations and insertions, many genes still remain uncharacterized. Low efficiency of targeted genomic manipulation approaches that rely on homologous recombination, and difficulty in generating resources for sequence-specific endonucleases, such as ZFNs (Zinc Finger Nucleases) and TALENs (Transcription Activator-Like Effector Nucleases), could not make these gene targeting techniques very popular. However, recently RNA directed DNA endonucleases, such as CRISPR-Cas, have transformed genome engineering owing to their comparative ease, versatility, and low expense. With the added advantage of preexisting genetic tools, CRISPR-Cas-based manipulations are being extensively used in Drosophila melanogaster and simultaneously being fine-tuned for specific experimental requirements. In this chapter, I will discuss various uses of CRISPR-Cas-based genetic engineering and specific design methods in Drosophila melanogaster. I will summarize various already available tools that are being utilized in conjunction with CRISPR-Cas technology to generate specific genetic manipulation and are being optimized to address specific questions. Finally, I will discuss the future directions of Drosophila genetics research and how CRISPR-Cas can be utilized to target specific questions, addressing which has not been possible thus far.
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Affiliation(s)
- Deepti Trivedi
- National Centre for Biological Sciences-TIFR, Bengaluru, India.
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19
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On K, Crevel G, Cotterill S, Itoh M, Kato Y. Drosophila telomere capping protein HOAP interacts with DSB sensor proteins Mre11 and Nbs. Genes Cells 2021; 26:219-229. [PMID: 33556205 DOI: 10.1111/gtc.12836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022]
Abstract
In eukaryotes, specific DNA-protein structures called telomeres exist at linear chromosome ends. Telomere stability is maintained by a specific capping protein complex. This capping complex is essential for the inhibition of the DNA damage response (DDR) at telomeres and contributes to genome integrity. In Drosophila, the central factors of telomere capping complex are HOAP and HipHop. Furthermore, a DDR protein complex Mre11-Rad50-Nbs (MRN) is known to be important for the telomere association of HOAP and HipHop. However, whether MRN interacts with HOAP and HipHop, and the telomere recognition mechanisms of HOAP and HipHop are poorly understood. Here, we show that Nbs interacts with Mre11 and transports the Mre11-Rad50 complex from the cytoplasm to the nucleus. In addition, we report that HOAP interacts with both Mre11 and Nbs. The N-terminal region of HOAP is essential for its co-localization with HipHop. Finally, we reveal that Nbs interacts with the N-terminal region of HOAP.
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Affiliation(s)
- Kinyo On
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Gilles Crevel
- Department of Basic Medical Sciences, St Georges, University of London, London, UK
| | - Sue Cotterill
- Department of Basic Medical Sciences, St Georges, University of London, London, UK
| | - Masanobu Itoh
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.,Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Kyoto, Japan
| | - Yasuko Kato
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.,Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Kyoto, Japan
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20
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Lau CH, Tin C, Suh Y. CRISPR-based strategies for targeted transgene knock-in and gene correction. Fac Rev 2020; 9:20. [PMID: 33659952 PMCID: PMC7886068 DOI: 10.12703/r/9-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The last few years have seen tremendous advances in CRISPR-mediated genome editing. Great efforts have been made to improve the efficiency, specificity, editing window, and targeting scope of CRISPR/Cas9-mediated transgene knock-in and gene correction. In this article, we comprehensively review recent progress in CRISPR-based strategies for targeted transgene knock-in and gene correction in both homology-dependent and homology-independent approaches. We cover homology-directed repair (HDR), synthesis-dependent strand annealing (SDSA), microhomology-mediated end joining (MMEJ), and homology-mediated end joining (HMEJ) pathways for a homology-dependent strategy and alternative DNA repair pathways such as non-homologous end joining (NHEJ), base excision repair (BER), and mismatch repair (MMR) for a homology-independent strategy. We also discuss base editing and prime editing that enable direct conversion of nucleotides in genomic DNA without damaging the DNA or requiring donor DNA. Notably, we illustrate the key mechanisms and design principles for each strategy, providing design guidelines for multiplex, flexible, scarless gene insertion and replacement at high efficiency and specificity. In addition, we highlight next-generation base editors that provide higher editing efficiency, fewer undesired by-products, and broader targeting scope.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
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21
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Stevenson ZC, Moerdyk-Schauwecker MJ, Jamison B, Phillips PC. Rapid Self-Selecting and Clone-Free Integration of Transgenes into Engineered CRISPR Safe Harbor Locations in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2020; 10:3775-3782. [PMID: 32816924 PMCID: PMC7534419 DOI: 10.1534/g3.120.401400] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/10/2020] [Indexed: 12/26/2022]
Abstract
Precision genome editing for model organisms has revolutionized functional analysis and validation of a wide variety of molecular systems. To date, the capacity to insert single-copy transgenes into the model nematode Caenorhabditis elegans has focused on utilizing either transposable elements or CRISPR-based safe harbor strategies. These methods require plate-level screening processes to avoid selecting heritable extrachromosomal arrays or rely on co-CRISPR markers to identify knock-in events. As a result, verification of transgene insertion requires anti-array selection screening methods and PCR genotyping. These approaches also rely on cloning plasmids for the addition of transgenes. Here, we present a novel safe harbor CRISPR-based integration strategy that utilizes engineered insertion locations containing a synthetic guide RNA target and a split-selection system to eliminate false positives from array formation, thereby providing integration-specific selection. This approach allows the experimenter to confirm an integration event has taken place without molecular validation or anti-array screening methods and is capable of producing integrated transgenic lines in as little as five days post-injection. To further increase the speed of generating transgenic lines, we also utilized the C. elegans native microhomology-based recombination, to assemble transgenes in-situ, removing the cloning step. We show that complete transgenes can be made and inserted into our split-selection safe harbor locations starting from PCR products, providing a clone-free and molecular-validation-free strategy for single-copy transgene integration. Overall, this combination of approaches provides an economical and rapid system for generating highly reproducible complex transgenics in C. elegans.
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22
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Application of CRISPR/Cas9-Based Reverse Genetics in Leishmania braziliensis: Conserved Roles for HSP100 and HSP23. Genes (Basel) 2020; 11:genes11101159. [PMID: 33007987 PMCID: PMC7601497 DOI: 10.3390/genes11101159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/18/2023] Open
Abstract
The protozoan parasite Leishmania (Viannia) braziliensis (L. braziliensis) is the main cause of human tegumentary leishmaniasis in the New World, a disease affecting the skin and/or mucosal tissues. Despite its importance, the study of the unique biology of L. braziliensis through reverse genetics analyses has so far lagged behind in comparison with Old World Leishmania spp. In this study, we successfully applied a cloning-free, PCR-based CRISPR–Cas9 technology in L. braziliensis that was previously developed for Old World Leishmania major and New World L. mexicana species. As proof of principle, we demonstrate the targeted replacement of a transgene (eGFP) and two L. braziliensis single-copy genes (HSP23 and HSP100). We obtained homozygous Cas9-free HSP23- and HSP100-null mutants in L. braziliensis that matched the phenotypes reported previously for the respective L. donovani null mutants. The function of HSP23 is indeed conserved throughout the Trypanosomatida as L. majorHSP23 null mutants could be complemented phenotypically with transgenes from a range of trypanosomatids. In summary, the feasibility of genetic manipulation of L. braziliensis by CRISPR–Cas9-mediated gene editing sets the stage for testing the role of specific genes in that parasite’s biology, including functional studies of virulence factors in relevant animal models to reveal novel therapeutic targets to combat American tegumentary leishmaniasis.
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23
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Young TZ, Liu P, Urbonaite G, Acar M. Quantitative Insights into Age-Associated DNA-Repair Inefficiency in Single Cells. Cell Rep 2020; 28:2220-2230.e7. [PMID: 31433994 PMCID: PMC6744837 DOI: 10.1016/j.celrep.2019.07.082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/02/2019] [Accepted: 07/23/2019] [Indexed: 01/03/2023] Open
Abstract
Although double-strand break (DSB) repair is essential for a cell's survival, little is known about how DSB repair mechanisms are affected by age. Here we characterize the impact of cellular aging on the efficiency of single-strand annealing (SSA), a DSB repair mechanism. We measure SSA repair efficiency in young and old yeast cells and report a 23.4% decline in repair efficiency. This decline is not due to increased use of non-homologous end joining. Instead, we identify increased G1 phase duration in old cells as a factor responsible for the decreased SSA repair efficiency. Expression of 3xCLN2 leads to higher SSA repair efficiency in old cells compared with expression of 1xCLN2, confirming the involvement of cell-cycle regulation in age-associated repair inefficiency. Examining how SSA repair efficiency is affected by sequence heterology, we find that heteroduplex rejection remains high in old cells. Our work provides insights into the links between single-cell aging and DSB repair efficiency.
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Affiliation(s)
- Thomas Z Young
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Ping Liu
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Guste Urbonaite
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA.
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24
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Dehnen L, Janz M, Verma JK, Psathaki OE, Langemeyer L, Fröhlich F, Heinisch JJ, Meyer H, Ungermann C, Paululat A. A trimeric metazoan Rab7 GEF complex is crucial for endocytosis and scavenger function. J Cell Sci 2020; 133:jcs247080. [PMID: 32499409 DOI: 10.1242/jcs.247080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
Endosome biogenesis in eukaryotic cells is critical for nutrient uptake and plasma membrane integrity. Early endosomes initially contain Rab5, which is replaced by Rab7 on late endosomes prior to their fusion with lysosomes. Recruitment of Rab7 to endosomes requires the Mon1-Ccz1 guanine-nucleotide-exchange factor (GEF). Here, we show that full function of the Drosophila Mon1-Ccz1 complex requires a third stoichiometric subunit, termed Bulli (encoded by CG8270). Bulli localises to Rab7-positive endosomes, in agreement with its function in the GEF complex. Using Drosophila nephrocytes as a model system, we observe that absence of Bulli results in (i) reduced endocytosis, (ii) Rab5 accumulation within non-acidified enlarged endosomes, (iii) defective Rab7 localisation and (iv) impaired endosomal maturation. Moreover, longevity of animals lacking bulli is affected. Both the Mon1-Ccz1 dimer and a Bulli-containing trimer display Rab7 GEF activity. In summary, this suggests a key role for Bulli in the Rab5 to Rab7 transition during endosomal maturation rather than a direct influence on the GEF activity of Mon1-Ccz1.
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Affiliation(s)
- Lena Dehnen
- Department of Biology and Chemistry, Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Maren Janz
- Department of Biology and Chemistry, Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Jitender Kumar Verma
- Department of Biology and Chemistry, Biochemistry, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Olympia Ekaterini Psathaki
- Center of Cellular Nanoanalytics, Integrated Bioimaging Facility Osnabrück (iBiOs), University of Osnabrück, 49076 Osnabrück, Germany
| | - Lars Langemeyer
- Department of Biology and Chemistry, Biochemistry, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Florian Fröhlich
- Department of Biology and Chemistry, Molecular Membrane Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Jürgen J Heinisch
- Department of Biology and Chemistry, Genetics, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
- Center of Cellular Nanoanalytics, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Heiko Meyer
- Department of Biology and Chemistry, Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
- Center of Cellular Nanoanalytics, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Christian Ungermann
- Department of Biology and Chemistry, Biochemistry, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
- Center of Cellular Nanoanalytics, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Achim Paululat
- Department of Biology and Chemistry, Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
- Center of Cellular Nanoanalytics, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
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25
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Nitschko V, Kunzelmann S, Fröhlich T, Arnold GJ, Förstemann K. Trafficking of siRNA precursors by the dsRBD protein Blanks in Drosophila. Nucleic Acids Res 2020; 48:3906-3921. [PMID: 32025726 PMCID: PMC7144943 DOI: 10.1093/nar/gkaa072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 01/03/2023] Open
Abstract
RNA interference targets aberrant transcripts with cognate small interfering RNAs, which derive from double-stranded RNA precursors. Several functional screens have identified Drosophila blanks/lump (CG10630) as a facilitator of RNAi, yet its molecular function has remained unknown. The protein carries two dsRNA binding domains (dsRBD) and blanks mutant males have a spermatogenesis defect. We demonstrate that blanks selectively boosts RNAi triggered by dsRNA of nuclear origin. Blanks binds dsRNA via its second dsRBD in vitro, shuttles between nucleus and cytoplasm and the abundance of siRNAs arising at many sites of convergent transcription is reduced in blanks mutants. Since features of nascent RNAs - such as introns and transcription beyond the polyA site – contribute to the small RNA pool, we propose that Blanks binds dsRNA formed by cognate nascent RNAs in the nucleus and fosters its export to the cytoplasm for dicing. We refer to the resulting small RNAs as blanks exported siRNAs (bepsiRNAs). While bepsiRNAs were fully dependent on RNA binding to the second dsRBD of blanks in transgenic flies, male fertility was not. This is consistent with a previous report that linked fertility to the first dsRBD of Blanks. The role of blanks in spermatogenesis appears thus unrelated to its role in dsRNA export.
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Affiliation(s)
- Volker Nitschko
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Stefan Kunzelmann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Thomas Fröhlich
- Laboratory of Functional Genome Analysis, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Georg J Arnold
- Laboratory of Functional Genome Analysis, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Klaus Förstemann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
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Kochanova NY, Schauer T, Mathias GP, Lukacs A, Schmidt A, Flatley A, Schepers A, Thomae AW, Imhof A. A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation. Nucleic Acids Res 2020; 48:4161-4178. [PMID: 32182352 PMCID: PMC7192626 DOI: 10.1093/nar/gkaa145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 12/26/2022] Open
Abstract
During interphase centromeres often coalesce into a small number of chromocenters, which can be visualized as distinct, DAPI dense nuclear domains. Intact chromocenters play a major role in maintaining genome stability as they stabilize the transcriptionally silent state of repetitive DNA while ensuring centromere function. Despite its biological importance, relatively little is known about the molecular composition of the chromocenter or the processes that mediate chromocenter formation and maintenance. To provide a deeper molecular insight into the composition of the chromocenter and to demonstrate the usefulness of proximity-based biotinylation as a tool to investigate those questions, we performed super resolution microscopy and proximity-based biotinylation experiments of three distinct proteins associated with the chromocenter in Drosophila. Our work revealed an intricate internal architecture of the chromocenter suggesting a complex multilayered structure of this intranuclear domain.
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Affiliation(s)
- Natalia Y Kochanova
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Tamas Schauer
- Biomedical Center, Bioinformatics Core Facility, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Grusha Primal Mathias
- Biomedical Center, Core Facility Bioimaging, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Andrea Lukacs
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Andreas Schmidt
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Andrew Flatley
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Aloys Schepers
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Andreas W Thomae
- Biomedical Center, Core Facility Bioimaging, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
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Boukhatmi H, Martins T, Pillidge Z, Kamenova T, Bray S. Notch Mediates Inter-tissue Communication to Promote Tumorigenesis. Curr Biol 2020; 30:1809-1820.e4. [DOI: 10.1016/j.cub.2020.02.088] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/03/2020] [Accepted: 02/27/2020] [Indexed: 12/19/2022]
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Bosch JA, Knight S, Kanca O, Zirin J, Yang-Zhou D, Hu Y, Rodiger J, Amador G, Bellen HJ, Perrimon N, Mohr SE. Use of the CRISPR-Cas9 System in Drosophila Cultured Cells to Introduce Fluorescent Tags into Endogenous Genes. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2020; 130:e112. [PMID: 31869524 PMCID: PMC7213786 DOI: 10.1002/cpmb.112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The CRISPR-Cas9 system makes it possible to cause double-strand breaks in specific regions, inducing repair. In the presence of a donor construct, repair can involve insertion or 'knock-in' of an exogenous cassette. One common application of knock-in technology is to generate cell lines expressing fluorescently tagged endogenous proteins. The standard approach relies on production of a donor plasmid with ∼500 to 1000 bp of homology on either side of an insertion cassette that contains the fluorescent protein open reading frame (ORF). We present two alternative methods for knock-in of fluorescent protein ORFs into Cas9-expressing Drosophila S2R+ cultured cells, the single-stranded DNA (ssDNA) Drop-In method and the CRISPaint universal donor method. Both methods eliminate the need to clone a large plasmid donor for each target. We discuss the advantages and limitations of the standard, ssDNA Drop-In, and CRISPaint methods for fluorescent protein tagging in Drosophila cultured cells. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Knock-in into Cas9-positive S2R+ cells using the ssDNA Drop-In approach Basic Protocol 2: Knock-in into Cas9-positive S2R+ cells by homology-independent insertion of universal donor plasmids that provide mNeonGreen (CRISPaint method) Support Protocol 1: sgRNA design and cloning Support Protocol 2: ssDNA donor synthesis Support Protocol 3: Transfection using Effectene Support Protocol 4: Electroporation of S2R+-MT::Cas9 Drosophila cells Support Protocol 5: Single-cell isolation of fluorescent cells using FACS.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Shannon Knight
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Jonathan Zirin
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Donghui Yang-Zhou
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Rodiger
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Gabriel Amador
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
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In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila. Nat Commun 2020; 11:894. [PMID: 32060283 PMCID: PMC7021724 DOI: 10.1038/s41467-020-14651-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/23/2020] [Indexed: 02/06/2023] Open
Abstract
Chromosomes are organized into high-frequency chromatin interaction domains called topologically associating domains (TADs), which are separated from each other by domain boundaries. The molecular mechanisms responsible for TAD formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by architectural proteins (APs) remains controversial. Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as defects in transcription. Together, our results provide compelling evidence of the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila. In Drosophila, transcription is thought to be required for TAD formation, while the role of architectural proteins remains controversial. Here, the authors find that deletion of domain boundaries at the fly Notch locus results in TAD fusion and long-range topological defects, loss of architectural protein and RNA Pol II chromatin binding, and transcription defects.
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30
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Zucchini consensus motifs determine the mechanism of pre-piRNA production. Nature 2020; 578:311-316. [PMID: 31996847 DOI: 10.1038/s41586-020-1966-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022]
Abstract
PIWI-interacting RNAs (piRNAs) of between approximately 24 and 31 nucleotides in length guide PIWI proteins to silence transposons in animal gonads, thereby ensuring fertility1. In the biogenesis of piRNAs, PIWI proteins are first loaded with 5'-monophosphorylated RNA fragments called pre-pre-piRNAs, which then undergo endonucleolytic cleavage to produce pre-piRNAs1,2. Subsequently, the 3'-ends of pre-piRNAs are trimmed by the exonuclease Trimmer (PNLDC1 in mouse)3-6 and 2'-O-methylated by the methyltransferase Hen1 (HENMT1 in mouse)7-9, generating mature piRNAs. It is assumed that the endonuclease Zucchini (MitoPLD in mouse) is a major enzyme catalysing the cleavage of pre-pre-piRNAs into pre-piRNAs10-13. However, direct evidence for this model is lacking, and how pre-piRNAs are generated remains unclear. Here, to analyse pre-piRNA production, we established a Trimmer-knockout silkworm cell line and derived a cell-free system that faithfully recapitulates Zucchini-mediated cleavage of PIWI-loaded pre-pre-piRNAs. We found that pre-piRNAs are generated by parallel Zucchini-dependent and -independent mechanisms. Cleavage by Zucchini occurs at previously unrecognized consensus motifs on pre-pre-piRNAs, requires the RNA helicase Armitage, and is accompanied by 2'-O-methylation of pre-piRNAs. By contrast, slicing of pre-pre-piRNAs with weak Zucchini motifs is achieved by downstream complementary piRNAs, producing pre-piRNAs without 2'-O-methylation. Regardless of the endonucleolytic mechanism, pre-piRNAs are matured by Trimmer and Hen1. Our findings highlight multiplexed processing of piRNA precursors that supports robust and flexible piRNA biogenesis.
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Zhang WW, Lypaczewski P, Matlashewski G. Application of CRISPR/Cas9-Mediated Genome Editing in Leishmania. Methods Mol Biol 2020; 2116:199-224. [PMID: 32221923 DOI: 10.1007/978-1-0716-0294-2_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas9 is an RNA guided endonuclease derived from the bacterium Streptococcus pyogenes. Due to its simplicity, versatility, and high efficiency, it has been widely used for genome editing in a variety of organisms including the protozoan parasite Leishmania, the causative agent of human leishmaniasis. Compared to the traditional homologous recombination gene targeting method, CRISPR-Cas9 has been shown to be a more efficient method to delete or disrupt Leishmania genes, generate point mutations, and add tags to endogenous genes. Notably, the stable CRISPR expression systems were shown to delete multicopy family Leishmania genes and genes present in multiploid chromosomes, identify essential Leishmania genes, and create specific chromosome translocations. In this chapter, we describe detailed procedures on using the stable CRISPR expression system for genome editing in Leishmania. These procedures include CRISPR targeting site selection, gRNA design, cloning single and double gRNA coding sequences into the Leishmania CRISPR vector pLdCN, oligonucleotide donor and drug resistance selection donor design, Leishmania cell transfection, screening, and isolation of CRISPR-edited mutants. As the principles of gene editing are generally similar, many of these procedures could also apply to the transient Leishmania CRISPR systems described by other labs.
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Affiliation(s)
- Wen-Wei Zhang
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Patrick Lypaczewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Greg Matlashewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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Bosch JA, Colbeth R, Zirin J, Perrimon N. Gene Knock-Ins in Drosophila Using Homology-Independent Insertion of Universal Donor Plasmids. Genetics 2020; 214:75-89. [PMID: 31685521 PMCID: PMC6944404 DOI: 10.1534/genetics.119.302819] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/25/2019] [Indexed: 11/18/2022] Open
Abstract
Targeted genomic knock-ins are a valuable tool to probe gene function. However, knock-in methods involving homology-directed repair (HDR) can be laborious. Here, we adapt the mammalian CRISPaint [clustered regularly interspaced short palindromic repeat (CRISPR)-assisted insertion tagging] homology-independent knock-in method for Drosophila melanogaster, which uses CRISPR/Cas9 and nonhomologous end joining to insert "universal" donor plasmids into the genome. Using this method in cultured S2R+ cells, we efficiently tagged four endogenous proteins with the bright fluorescent protein mNeonGreen, thereby demonstrating that an existing collection of CRISPaint universal donor plasmids is compatible with insect cells. In addition, we inserted the transgenesis marker 3xP3-red fluorescent protein into seven genes in the fly germ line, producing heritable loss-of-function alleles that were isolated by simple fluorescence screening. Unlike in cultured cells, insertions/deletions always occurred at the genomic insertion site, which prevents predictably matching the insert coding frame to the target gene. Despite this effect, we were able to isolate T2A-Gal4 insertions in four genes that serve as in vivo expression reporters. Therefore, homology-independent insertion in Drosophila is a fast and simple alternative to HDR that will enable researchers to dissect gene function.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Ryan Colbeth
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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Yan N, Sun Y, Fang Y, Deng J, Mu L, Xu K, Mymryk JS, Zhang Z. A Universal Surrogate Reporter for Efficient Enrichment of CRISPR/Cas9-Mediated Homology-Directed Repair in Mammalian Cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:775-789. [PMID: 31955009 PMCID: PMC6970138 DOI: 10.1016/j.omtn.2019.12.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022]
Abstract
CRISPR/Cas9-mediated homology-directed repair (HDR) can be leveraged to precisely engineer mammalian genomes. However, the inherently low efficiency of HDR often hampers to identify the desired modified cells. Here, we developed a novel universal surrogate reporter system that efficiently enriches for genetically modified cells arising from CRISPR/Cas9-induced HDR events (namely, the "HDR-USR" system). This episomally based reporter can be self-cleaved and self-repaired via HDR to create a functional puromycin selection cassette without compromising genome integrity. Co-transfection of the HDR-USR system into host cells and transient puromycin selection efficiently achieves enrichment of HDR-modified cells. We tested the system for precision point mutation at 16 loci in different human cell lines and one locus in two rodent cell lines. This system exhibited dramatic improvements in HDR efficiency at a single locus (up to 20.7-fold) and two loci at once (42% editing efficiency compared to zero in the control), as well as greatly improved knockin efficiency (8.9-fold) and biallelic deletion (35.9-fold) at test loci. Further increases were achieved by co-expression of yeast Rad52 and linear single-/double-stranded DNA donors. Taken together, our HDR-USR system provides a simple, robust and efficient surrogate reporter for the enrichment of CRISPR/Cas9-induced HDR-based precision genome editing across various targeting loci in different cell lines.
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Affiliation(s)
- Nana Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongsen Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanyuan Fang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jingrong Deng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Mu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kun Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Joe S Mymryk
- Department of Microbiology & Immunology, Oncology and Otolaryngology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Zhiying Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Mačinković I, Theofel I, Hundertmark T, Kovač K, Awe S, Lenz J, Forné I, Lamp B, Nist A, Imhof A, Stiewe T, Renkawitz-Pohl R, Rathke C, Brehm A. Distinct CoREST complexes act in a cell-type-specific manner. Nucleic Acids Res 2019; 47:11649-11666. [PMID: 31701127 PMCID: PMC7145674 DOI: 10.1093/nar/gkz1050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 01/10/2023] Open
Abstract
CoREST has been identified as a subunit of several protein complexes that generate transcriptionally repressive chromatin structures during development. However, a comprehensive analysis of the CoREST interactome has not been carried out. We use proteomic approaches to define the interactomes of two dCoREST isoforms, dCoREST-L and dCoREST-M, in Drosophila. We identify three distinct histone deacetylase complexes built around a common dCoREST/dRPD3 core: A dLSD1/dCoREST complex, the LINT complex and a dG9a/dCoREST complex. The latter two complexes can incorporate both dCoREST isoforms. By contrast, the dLSD1/dCoREST complex exclusively assembles with the dCoREST-L isoform. Genome-wide studies show that the three dCoREST complexes associate with chromatin predominantly at promoters. Transcriptome analyses in S2 cells and testes reveal that different cell lineages utilize distinct dCoREST complexes to maintain cell-type-specific gene expression programmes: In macrophage-like S2 cells, LINT represses germ line-related genes whereas other dCoREST complexes are largely dispensable. By contrast, in testes, the dLSD1/dCoREST complex prevents transcription of germ line-inappropriate genes and is essential for spermatogenesis and fertility, whereas depletion of other dCoREST complexes has no effect. Our study uncovers three distinct dCoREST complexes that function in a lineage-restricted fashion to repress specific sets of genes thereby maintaining cell-type-specific gene expression programmes.
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Affiliation(s)
- Igor Mačinković
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Ina Theofel
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Tim Hundertmark
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Kristina Kovač
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Stephan Awe
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Jonathan Lenz
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstrasse 9, 82152 Martinsried, Germany
| | - Boris Lamp
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstrasse 9, 82152 Martinsried, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Renate Renkawitz-Pohl
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Christina Rathke
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Alexander Brehm
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
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35
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Kanca O, Zirin J, Garcia-Marques J, Knight SM, Yang-Zhou D, Amador G, Chung H, Zuo Z, Ma L, He Y, Lin WW, Fang Y, Ge M, Yamamoto S, Schulze KL, Hu Y, Spradling AC, Mohr SE, Perrimon N, Bellen HJ. An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms. eLife 2019; 8:e51539. [PMID: 31674908 PMCID: PMC6855806 DOI: 10.7554/elife.51539] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
We previously reported a CRISPR-mediated knock-in strategy into introns of Drosophila genes, generating an attP-FRT-SA-T2A-GAL4-polyA-3XP3-EGFP-FRT-attP transgenic library for multiple uses (Lee et al., 2018a). The method relied on double stranded DNA (dsDNA) homology donors with ~1 kb homology arms. Here, we describe three new simpler ways to edit genes in flies. We create single stranded DNA (ssDNA) donors using PCR and add 100 nt of homology on each side of an integration cassette, followed by enzymatic removal of one strand. Using this method, we generated GFP-tagged proteins that mark organelles in S2 cells. We then describe two dsDNA methods using cheap synthesized donors flanked by 100 nt homology arms and gRNA target sites cloned into a plasmid. Upon injection, donor DNA (1 to 5 kb) is released from the plasmid by Cas9. The cassette integrates efficiently and precisely in vivo. The approach is fast, cheap, and scalable.
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Affiliation(s)
- Oguz Kanca
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Jonathan Zirin
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | | | - Shannon Marie Knight
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Donghui Yang-Zhou
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Gabriel Amador
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Hyunglok Chung
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Zhongyuan Zuo
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Liwen Ma
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Yuchun He
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Howard Hughes Medical Institute, Baylor College of MedicineHoustonUnited States
| | - Wen-Wen Lin
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Ying Fang
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Ming Ge
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Shinya Yamamoto
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| | - Karen L Schulze
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Howard Hughes Medical Institute, Baylor College of MedicineHoustonUnited States
| | - Yanhui Hu
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Allan C Spradling
- Department of EmbryologyHoward Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Stephanie E Mohr
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Norbert Perrimon
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Hugo J Bellen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Howard Hughes Medical Institute, Baylor College of MedicineHoustonUnited States
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
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36
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Bisht DS, Bhatia V, Bhattacharya R. Improving plant-resistance to insect-pests and pathogens: The new opportunities through targeted genome editing. Semin Cell Dev Biol 2019; 96:65-76. [PMID: 31039395 DOI: 10.1016/j.semcdb.2019.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 12/26/2022]
Abstract
The advantages of high input agriculture are fading away due to degenerating soil health and adverse effects of climate change. Safeguarding crop yields in the changing environment and dynamics of pest and pathogens, has posed new challenges to global agriculture. Thus, integration of new technologies in crop improvement has been imperative for achieving the breeding objectives in faster ways. Recently, enormous potential of genome editing through engineered nucleases has been demonstrated in plants. Continuous refinements of the genome editing tools have increased depth and breadth of their applications. So far, genome editing has been demonstrated in more than fifty plant species. These include model species like Arabidopsis, as well as important crops like rice, wheat, maize etc. Particularly, CRISPR/Cas9 based two component genome editing system has been facile with wider applicability. Potential of genome editing has unfurled enormous possibilities for engineering diverse agronomic traits including durable resistance against insect-pests and pathogens. Novel propositions of developing insect and pathogen resistant crops by genome editing include altering the effector-target interaction, knocking out of host-susceptibility genes, engineering synthetic immune receptor eliciting broad spectrum resistance, uncoupling of antagonistic action of defense hormones etc. Alternatively, modification of insect genomes has been used either to create gene drive or to counteract resistance to various insecticides. The distinct advantage of genome editing system is that it can knock out specific target region in the genome without leaving the unwanted vector backbone. In this article, we have reviewed the novel opportunities offered by the genome editing technologies for developing insect and pathogen resistant crop-types, their future prospects and anticipated challenges.
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Affiliation(s)
- Deepak Singh Bisht
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, India
| | - Varnika Bhatia
- Deen Dayal Upadhyaya College, University of Delhi, Delhi, India
| | - Ramcharan Bhattacharya
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, India.
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Lemke SB, Weidemann T, Cost AL, Grashoff C, Schnorrer F. A small proportion of Talin molecules transmit forces at developing muscle attachments in vivo. PLoS Biol 2019; 17:e3000057. [PMID: 30917109 PMCID: PMC6453563 DOI: 10.1371/journal.pbio.3000057] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 04/08/2019] [Accepted: 03/08/2019] [Indexed: 11/19/2022] Open
Abstract
Cells in developing organisms are subjected to particular mechanical forces that shape tissues and instruct cell fate decisions. How these forces are sensed and transmitted at the molecular level is therefore an important question, one that has mainly been investigated in cultured cells in vitro. Here, we elucidate how mechanical forces are transmitted in an intact organism. We studied Drosophila muscle attachment sites, which experience high mechanical forces during development and require integrin-mediated adhesion for stable attachment to tendons. Therefore, we quantified molecular forces across the essential integrin-binding protein Talin, which links integrin to the actin cytoskeleton. Generating flies expressing 3 Förster resonance energy transfer (FRET)-based Talin tension sensors reporting different force levels between 1 and 11 piconewton (pN) enabled us to quantify physiologically relevant molecular forces. By measuring primary Drosophila muscle cells, we demonstrate that Drosophila Talin experiences mechanical forces in cell culture that are similar to those previously reported for Talin in mammalian cell lines. However, in vivo force measurements at developing flight muscle attachment sites revealed that average forces across Talin are comparatively low and decrease even further while attachments mature and tissue-level tension remains high. Concomitantly, the Talin concentration at attachment sites increases 5-fold as quantified by fluorescence correlation spectroscopy (FCS), suggesting that only a small proportion of Talin molecules are mechanically engaged at any given time. Reducing Talin levels at late stages of muscle development results in muscle–tendon rupture in the adult fly, likely as a result of active muscle contractions. We therefore propose that a large pool of adhesion molecules is required to share high tissue forces. As a result, less than 15% of the molecules experience detectable forces at developing muscle attachment sites at the same time. Our findings define an important new concept of how cells can adapt to changes in tissue mechanics to prevent mechanical failure in vivo. The protein Talin links the transmembrane cell adhesion molecule integrin to the actin cytoskeleton. Quantitative FRET-based force measurements across Talin in vivo reveal that only few Talin molecules are under force during the development of muscle attachment sites. Cells in our body are constantly exposed to mechanical forces, which they need to sense and react to. In previous studies, fluorescent force sensors were developed to demonstrate that individual proteins in adhesion structures of a cell experience forces in the piconewton (pN) range. However, these cells were analyzed in isolation in an artificial plastic or glass environment. Here, we explored forces on adhesion proteins in their natural environment within a developing animal and used the muscle–tendon tissue in the fruit fly Drosophila as a model system. We made genetically modified fly lines with force sensors or controls inserted into the gene that produces the essential adhesion protein Talin. Using these force sensor flies, we found that only a small proportion of all the Talin proteins (<15%) present at developing muscle–tendon attachments experience detectable forces at the same time. Nevertheless, a large amount of Talin is accumulated at these attachments during fly development. We found that this large Talin pool is important to prevent rupture of the muscle–tendon connection in adult flies that produce high muscle forces during flight. In conclusion, we demonstrated that a large pool of Talin proteins is required for stable muscle–tendon attachment, likely with the individual Talin molecules dynamically sharing the mechanical load.
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Affiliation(s)
- Sandra B. Lemke
- Max Planck Institute of Biochemistry, Martinsried, Germany
- * E-mail: (FS); (CG); (SBL)
| | | | - Anna-Lena Cost
- Max Planck Institute of Biochemistry, Martinsried, Germany
- University of Münster, Institute for Molecular Cell Biology, Münster, Germany
| | - Carsten Grashoff
- Max Planck Institute of Biochemistry, Martinsried, Germany
- University of Münster, Institute for Molecular Cell Biology, Münster, Germany
- * E-mail: (FS); (CG); (SBL)
| | - Frank Schnorrer
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Aix Marseille University, CNRS, IBDM, Marseille, France
- * E-mail: (FS); (CG); (SBL)
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CRISPR/Cas9 Methodology for the Generation of Knockout Deletions in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2019; 9:135-144. [PMID: 30420468 PMCID: PMC6325907 DOI: 10.1534/g3.118.200778] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Caenorhabditis elegans Gene Knockout Consortium is tasked with obtaining null mutations in each of the more than 20,000 open reading frames (ORFs) of this organism. To date, approximately 15,000 ORFs have associated putative null alleles. As there has been substantial success in using CRISPR/Cas9 in C. elegans, this appears to be the most promising technique to complete the task. To enhance the efficiency of using CRISPR/Cas9 to generate gene deletions in C. elegans we provide a web-based interface to access our database of guide RNAs (http://genome.sfu.ca/crispr). When coupled with previously developed selection vectors, optimization for homology arm length, and the use of purified Cas9 protein, we demonstrate a robust and effective protocol for generating deletions for this large-scale project. Debate and speculation in the larger scientific community concerning off-target effects due to non-specific Cas9 cutting has prompted us to investigate through whole genome sequencing the occurrence of single nucleotide variants and indels accompanying targeted deletions. We did not detect any off-site variants above the natural spontaneous mutation rate and therefore conclude that this modified protocol does not generate off-target events to any significant degree in C. elegans. We did, however, observe a number of non-specific alterations at the target site itself following the Cas9-induced double-strand break and offer a protocol for best practice quality control for such events.
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Luhur A, Klueg KM, Zelhof AC. Generating and working with Drosophila cell cultures: Current challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 8:e339. [PMID: 30561900 DOI: 10.1002/wdev.339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/30/2018] [Accepted: 11/21/2018] [Indexed: 12/26/2022]
Abstract
The use of Drosophila cell cultures has positively impacted both fundamental and biomedical research. The most widely used cell lines: Schneider, Kc, the CNS and imaginal disc lines continue to be the choice for many applications. Drosophila cell lines provide a homogenous source of cells suitable for biochemical experimentations, transcriptomics, functional genomics, and biomedical applications. They are amenable to RNA interference and serve as a platform for high-throughput screens to identify relevant candidate genes or drugs for any biological process. Currently, CRISPR-based functional genomics are also being developed for Drosophila cell lines. Even though many uniquely derived cell lines exist, cell genetic techniques such the transgenic UAS-GAL4-based RasV12 oncogene expression, CRISPR-Cas9 editing and recombination mediated cassette exchange are likely to drive the establishment of many more lines from specific tissues, cells, or genotypes. However, the pace of creating new lines is hindered by several factors inherent to working with Drosophila cell cultures: single cell cloning, optimal media formulations and culture conditions capable of supporting lines from novel tissue sources or genotypes. Moreover, even though many Drosophila cell lines are morphologically and transcriptionally distinct it may be necessary to implement a standard for Drosophila cell line authentication, ensuring the identity and purity of each cell line. Altogether, recent advances and a standardized authentication effort should improve the utility of Drosophila cell cultures as a relevant model for fundamental and biomedical research. This article is categorized under: Technologies > Analysis of Cell, Tissue, and Animal Phenotypes.
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Affiliation(s)
- Arthur Luhur
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Kristin M Klueg
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Andrew C Zelhof
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
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Boese CJ, Nye J, Buster DW, McLamarrah TA, Byrnes AE, Slep KC, Rusan NM, Rogers GC. Asterless is a Polo-like kinase 4 substrate that both activates and inhibits kinase activity depending on its phosphorylation state. Mol Biol Cell 2018; 29:2874-2886. [PMID: 30256714 PMCID: PMC6249866 DOI: 10.1091/mbc.e18-07-0445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/13/2018] [Accepted: 09/19/2018] [Indexed: 11/26/2022] Open
Abstract
Centriole assembly initiates when Polo-like kinase 4 (Plk4) interacts with a centriole "targeting-factor." In Drosophila, Asterless/Asl (Cep152 in humans) fulfills the targeting role. Interestingly, Asl also regulates Plk4 levels. The N-terminus of Asl (Asl-A; amino acids 1-374) binds Plk4 and promotes Plk4 self-destruction, although it is unclear how this is achieved. Moreover, Plk4 phosphorylates the Cep152 N-terminus, but the functional consequence is unknown. Here, we show that Plk4 phosphorylates Asl and mapped 13 phospho-residues in Asl-A. Nonphosphorylatable alanine (13A) and phosphomimetic (13PM) mutants did not alter Asl function, presumably because of the dominant role of the Asl C-terminus in Plk4 stabilization and centriolar targeting. To address how Asl-A phosphorylation specifically affects Plk4 regulation, we generated Asl-A fragment phospho-mutants and expressed them in cultured Drosophila cells. Asl-A-13A stimulated kinase activity by relieving Plk4 autoinhibition. In contrast, Asl-A-13PM inhibited Plk4 activity by a novel mechanism involving autophosphorylation of Plk4's kinase domain. Thus, Asl-A's phosphorylation state determines which of Asl-A's two opposing effects are exerted on Plk4. Initially, nonphosphorylated Asl binds Plk4 and stimulates its kinase activity, but after Asl is phosphorylated, a negative-feedback mechanism suppresses Plk4 activity. This dual regulatory effect by Asl-A may limit Plk4 to bursts of activity that modulate centriole duplication.
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Affiliation(s)
- Cody J. Boese
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724
| | - Jonathan Nye
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724
| | - Daniel W. Buster
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724
| | - Tiffany A. McLamarrah
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724
| | - Amy E. Byrnes
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kevin C. Slep
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nasser M. Rusan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Gregory C. Rogers
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724
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Yee CM, Zak AJ, Hill BD, Wen F. The Coming Age of Insect Cells for Manufacturing and Development of Protein Therapeutics. Ind Eng Chem Res 2018; 57:10061-10070. [PMID: 30886455 PMCID: PMC6420222 DOI: 10.1021/acs.iecr.8b00985] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein therapeutics is a rapidly growing segment of the pharmaceutical market. Currently, the majority of protein therapeutics are manufactured in mammalian cells for their ability to generate safe and efficacious human-like glycoproteins. The high cost of using mammalian cells for manufacturing has motivated a constant search for alternative host platforms. Insect cells have begun to emerge as a promising candidate, largely due to the development of the baculovirus expression vector system. While there are continuing efforts to improve insect-baculovirus expression for producing protein therapeutics, key limitations including cell lysis and the lack of homogeneous humanized glycosylation still remain. The field has started to see a movement toward virus-less gene expression approaches, notably the use of clustered regularly interspaced short palindromic repeats to address these shortcomings. This review highlights recent technological advances that are realizing the transformative potential of insect cells for the manufacturing and development of protein therapeutics.
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Affiliation(s)
- Christine M. Yee
- Department of Chemical Engineering, University of Michigan, Ann Arbor,
Michigan 48109, United States
| | - Andrew J. Zak
- Department of Chemical Engineering, University of Michigan, Ann Arbor,
Michigan 48109, United States
| | - Brett D. Hill
- Department of Chemical Engineering, University of Michigan, Ann Arbor,
Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor,
Michigan 48109, United States
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42
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Sun Y, Long J, Yin Y, Li H, Jiang E, Zeng C, Zhu W. Characterization of CSF2A fusion gene and its effect on Epstein-Barr virus-positive tumor cells. J Med Virol 2018; 90:1750-1756. [PMID: 29900557 DOI: 10.1002/jmv.25240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/30/2018] [Indexed: 11/06/2022]
Abstract
We build the latent membrane protein gene latent membrane protein 2A (LMP2A) and the granulocyte-macrophase colony-stimulating factor (GM-CSF) gene fusion gene (CSF2A) and discuss how the CSF2A fusion protein influenced the proliferation and apoptosis of Epstein-Barr virus-positive (EBV+ ) tumor cells. Reverse-transcription polymerase chain reaction (RT-PCR) method was used to amplify the LMP2A gene and GM-CSF gene fragments, respectively, according to the principle of overlap extension in the coding (Gly4Ser)3 polypeptide gene fragments of DNA restructured under the connection. The CSF2A gene could be connected with the pIRES2-enhanced green fluorescent protein vector by recombinant DNA technology and identified by enzyme electrophoresis analysis and DNA sequencing. Then, the recombinant vector was transfected into dendritic cells (DCs); RT-PCR and Western blot analysis were used for testing the CSF2A gene messenger RNA and protein expression. The impacts of CSF2A on the proliferation and apoptosis of EBV+ tumor cells were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and Hochest 33342 staining. We successfully obtained the recombinant vector named pIRES2-CSF2A. The expression of CSF2A could be detected by transfecting pIRES2-CSF2A into DCs. The DCs were cocultured with T lymphocytes and then acted on the EBV+ CNE2 nasopharyngeal carcinoma cells. MTT assay showed that the inhibiting effect of CSF2A obviously increased and the time dependency (**P < 0.01, *P < 0.05) also existed. Hochest 33342 staining showed apoptosis morphological changes of cells in nucleus staining and generated the apoptotic body. Apoptosis cells of the pIRES2-CSF2A group increased significantly at 48 hours. The results showed that the pIRES2-CSF2A recombinant vector was effectively transfected into DCs and the fusion gene CSF2A could promote EBV+ CNE2 cell apoptosis, laying the foundation for the specificity of EBV+ tumor targeting immune gene therapy in the future.
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Affiliation(s)
- Yanqin Sun
- Department of Pathology, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Jiali Long
- Department of Pathology, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Yuting Yin
- Department of Pathology, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Hongmei Li
- Department of Pathology, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Enping Jiang
- Department of Pathology, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Chao Zeng
- Department of Pathology, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Wei Zhu
- Department of Pathology, School of Basic Medicine, Guangdong Medical University, Dongguan, China
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43
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Koch B, Nijmeijer B, Kueblbeck M, Cai Y, Walther N, Ellenberg J. Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing. Nat Protoc 2018; 13:1465-1487. [PMID: 29844520 PMCID: PMC6556379 DOI: 10.1038/nprot.2018.042] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gene tagging with fluorescent proteins is essential for investigations of the dynamic properties of cellular proteins. CRISPR-Cas9 technology is a powerful tool for inserting fluorescent markers into all alleles of the gene of interest (GOI) and allows functionality and physiological expression of the fusion protein. It is essential to evaluate such genome-edited cell lines carefully in order to preclude off-target effects caused by (i) incorrect insertion of the fluorescent protein, (ii) perturbation of the fusion protein by the fluorescent proteins or (iii) nonspecific genomic DNA damage by CRISPR-Cas9. In this protocol, we provide a step-by-step description of our systematic pipeline to generate and validate homozygous fluorescent knock-in cell lines.We have used the paired Cas9D10A nickase approach to efficiently insert tags into specific genomic loci via homology-directed repair (HDR) with minimal off-target effects. It is time-consuming and costly to perform whole-genome sequencing of each cell clone to check for spontaneous genetic variations occurring in mammalian cell lines. Therefore, we have developed an efficient validation pipeline of the generated cell lines consisting of junction PCR, Southern blotting analysis, Sanger sequencing, microscopy, western blotting analysis and live-cell imaging for cell-cycle dynamics. This protocol takes between 6 and 9 weeks. With this protocol, up to 70% of the targeted genes can be tagged homozygously with fluorescent proteins, thus resulting in physiological levels and phenotypically functional expression of the fusion proteins.
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Affiliation(s)
- Birgit Koch
- EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
- current address: Max Planck Insitute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | | | | | - Yin Cai
- EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
- current address: Roche SIS, Maybachstr. 30, 71332 Waiblingen, Germany
| | - Nike Walther
- EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Jan Ellenberg
- EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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44
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Scacchetti A, Brueckner L, Jain D, Schauer T, Zhang X, Schnorrer F, van Steensel B, Straub T, Becker PB. CHRAC/ACF contribute to the repressive ground state of chromatin. Life Sci Alliance 2018; 1:e201800024. [PMID: 30456345 PMCID: PMC6238394 DOI: 10.26508/lsa.201800024] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 01/24/2018] [Accepted: 01/26/2018] [Indexed: 12/22/2022] Open
Abstract
Chromatin accessibility complex/ATP-utilizing chromatin assembly and remodeling factor help to establish basal transcriptional repression, conceivably through improving the regular spacing of nucleosomes in euchromatin. The chromatin remodeling complexes chromatin accessibility complex and ATP-utilizing chromatin assembly and remodeling factor (ACF) combine the ATPase ISWI with the signature subunit ACF1. These enzymes catalyze well-studied nucleosome sliding reactions in vitro, but how their actions affect physiological gene expression remains unclear. Here, we explored the influence of Drosophila melanogaster chromatin accessibility complex/ACF on transcription by using complementary gain- and loss-of-function approaches. Targeting ACF1 to multiple reporter genes inserted at many different genomic locations revealed a context-dependent inactivation of poorly transcribed reporters in repressive chromatin. Accordingly, single-embryo transcriptome analysis of an Acf knock-out allele showed that only lowly expressed genes are derepressed in the absence of ACF1. Finally, the nucleosome arrays in Acf-deficient chromatin show loss of physiological regularity, particularly in transcriptionally inactive domains. Taken together, our results highlight that ACF1-containing remodeling factors contribute to the establishment of an inactive ground state of the genome through chromatin organization.
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Affiliation(s)
- Alessandro Scacchetti
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University Munich, Planegg-Martinsried, Germany.,Center for Integrated Protein Science Munich, München, Germany
| | - Laura Brueckner
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dhawal Jain
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University Munich, Planegg-Martinsried, Germany.,Center for Integrated Protein Science Munich, München, Germany
| | - Tamas Schauer
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University Munich, Planegg-Martinsried, Germany.,Center for Integrated Protein Science Munich, München, Germany
| | - Xu Zhang
- Developmental Biology Institute of Marseille, Aix Marseille University, Centre Nationnal de la Recherche Scientifique, Marseille, France.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Frank Schnorrer
- Developmental Biology Institute of Marseille, Aix Marseille University, Centre Nationnal de la Recherche Scientifique, Marseille, France
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tobias Straub
- Bioinformatic Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University Munich, Planegg-Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University Munich, Planegg-Martinsried, Germany.,Center for Integrated Protein Science Munich, München, Germany
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45
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Bier E, Harrison MM, O'Connor-Giles KM, Wildonger J. Advances in Engineering the Fly Genome with the CRISPR-Cas System. Genetics 2018; 208:1-18. [PMID: 29301946 PMCID: PMC5753851 DOI: 10.1534/genetics.117.1113] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/08/2017] [Indexed: 12/26/2022] Open
Abstract
Drosophila has long been a premier model for the development and application of cutting-edge genetic approaches. The CRISPR-Cas system now adds the ability to manipulate the genome with ease and precision, providing a rich toolbox to interrogate relationships between genotype and phenotype, to delineate and visualize how the genome is organized, to illuminate and manipulate RNA, and to pioneer new gene drive technologies. Myriad transformative approaches have already originated from the CRISPR-Cas system, which will likely continue to spark the creation of tools with diverse applications. Here, we provide an overview of how CRISPR-Cas gene editing has revolutionized genetic analysis in Drosophila and highlight key areas for future advances.
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Affiliation(s)
- Ethan Bier
- Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093-0349
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Kate M O'Connor-Giles
- Laboratory of Genetics and Laboratory of Cell and Molecular Biology, Wisconsin 53706
| | - Jill Wildonger
- Biochemistry Department, University of Wisconsin-Madison, Wisconsin 53706
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46
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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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47
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Tants JN, Fesser S, Kern T, Stehle R, Geerlof A, Wunderlich C, Juen M, Hartlmüller C, Böttcher R, Kunzelmann S, Lange O, Kreutz C, Förstemann K, Sattler M. Molecular basis for asymmetry sensing of siRNAs by the Drosophila Loqs-PD/Dcr-2 complex in RNA interference. Nucleic Acids Res 2017; 45:12536-12550. [PMID: 29040648 PMCID: PMC5716069 DOI: 10.1093/nar/gkx886] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/22/2017] [Accepted: 09/22/2017] [Indexed: 12/26/2022] Open
Abstract
RNA interference defends against RNA viruses and retro-elements within an organism's genome. It is triggered by duplex siRNAs, of which one strand is selected to confer sequence-specificity to the RNA induced silencing complex (RISC). In Drosophila, Dicer-2 (Dcr-2) and the double-stranded RNA binding domain (dsRBD) protein R2D2 form the RISC loading complex (RLC) and select one strand of exogenous siRNAs according to the relative thermodynamic stability of base-pairing at either end. Through genome editing we demonstrate that Loqs-PD, the Drosophila homolog of human TAR RNA binding protein (TRBP) and a paralog of R2D2, forms an alternative RLC with Dcr-2 that is required for strand choice of endogenous siRNAs in S2 cells. Two canonical dsRBDs in Loqs-PD bind to siRNAs with enhanced affinity compared to miRNA/miRNA* duplexes. Structural analysis, NMR and biophysical experiments indicate that the Loqs-PD dsRBDs can slide along the RNA duplex to the ends of the siRNA. A moderate but notable binding preference for the thermodynamically more stable siRNA end by Loqs-PD alone is greatly amplified in complex with Dcr-2 to initiate strand discrimination by asymmetry sensing in the RLC.
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Affiliation(s)
- Jan-Niklas Tants
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Stephanie Fesser
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Thomas Kern
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Christoph Wunderlich
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Michael Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Hartlmüller
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Romy Böttcher
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Stefan Kunzelmann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Oliver Lange
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Klaus Förstemann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
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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: 90] [Impact Index Per Article: 12.9] [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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49
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Abstract
The ease of generating genetically modified animals and cell lines has been markedly increased by the recent development of the versatile CRISPR/Cas9 tool. However, while the isolation of isogenic cell populations is usually straightforward for mammalian cell lines, the generation of clonal Drosophila cell lines has remained a longstanding challenge, hampered by the difficulty of getting Drosophila cells to grow at low densities. Here, we describe a highly efficient workflow to generate clonal Cas9-engineered Drosophila cell lines using a combination of cell pools, limiting dilution in conditioned medium and PCR with allele-specific primers, enabling the efficient selection of a clonal cell line with a suitable mutation profile. We validate the protocol by documenting the isolation, selection and verification of eight independently Cas9-edited armadillo mutant Drosophila cell lines. Our method provides a powerful and simple workflow that improves the utility of Drosophila cells for genetic studies with CRISPR/Cas9.
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Affiliation(s)
- Alexandra Franz
- a Institute of Molecular Life Sciences, University of Zurich , Zurich , Switzerland
| | - Erich Brunner
- a Institute of Molecular Life Sciences, University of Zurich , Zurich , Switzerland
| | - Konrad Basler
- a Institute of Molecular Life Sciences, University of Zurich , Zurich , Switzerland
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50
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Kunzelmann S, Förstemann K. Reversible perturbations of gene regulation after genome editing in Drosophila cells. PLoS One 2017; 12:e0180135. [PMID: 28658280 PMCID: PMC5489201 DOI: 10.1371/journal.pone.0180135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/09/2017] [Indexed: 12/04/2022] Open
Abstract
The prokaryotic phage defense CRISPR/cas-system has developed into a versatile toolbox for genome engineering and genetic studies in many organisms. While many efforts were spent on analyzing the consequences of off-target effects, only few studies addressed side-effects that occur due to the targeted manipulation of the genome. Here, we show that the CRISPR/cas9-mediated integration of an epitope tag in combination with a selection cassette can trigger an siRNA-mediated, epigenetic genome surveillance pathway in Drosophila melanogaster cells. After homology-directed insertion of the sequence coding for the epitope tag and the selection marker, a moderate level of siRNAs covering the inserted sequence and extending into the targeted locus was detected. This response affected protein levels less than two-fold and it persisted even after single cell cloning. However, removal of the selection cassette abolished the siRNA generation, demonstrating that this response is reversible. Consistently, marker-free genome engineering did not trigger the same surveillance mechanism. These two observations indicate that the selection cassette we employed induces an aberrant transcriptional arrangement and ultimately sets off the siRNA production. There have been prior concerns about undesirable effects induced by selection markers, but fortunately we were able to show that at least one of the epigenetic changes reverts as the marker gene is excised. Although the effects observed were rather weak (less than twofold de-repression upon ago2 or dcr-2 knock-down), we recommend that when selection markers are used during genome editing, a strategy for their subsequent removal should always be included.
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Affiliation(s)
- Stefan Kunzelmann
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Klaus Förstemann
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität München, München, Germany
- * E-mail:
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