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Sharma N, Marques F, Kratsios P. Efficacy of auxin-inducible protein degradation in C. elegans tissues using different auxins and TIR1-expressing strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575916. [PMID: 38293206 PMCID: PMC10827146 DOI: 10.1101/2024.01.16.575916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The auxin-inducible degradation system has emerged as a powerful tool to deplete proteins of interest in cells and tissues of various model organisms, including C. elegans 2-5 . Here, we present a detailed protocol to perform AID-driven spatiotemporal depletion of specific proteins in C. elegans tissues. First, we introduced the AID degron and a fluorescent reporter at two conserved proteins: (a) the transcription factor CFI-1 (human ARID3), which is expressed in the nucleus of multiple C. elegans neurons and head muscle cells 6,7 , and (b) the broadly expressed translation initiation factor Y47D3A.21 (human DENR) that localizes in the cytoplasm. Second, we provide a step-by-step guide on how to generate C. elegans strains suitable for AID-mediated protein (CFI-1 and DENR) depletion. Third, we find that the degree of CFI-1 and DENR depletion in C. elegans tissues is comparable upon treatment with either natural auxin (indole-3-acetic acid (IAA) or a water-soluble synthetic auxin analog (K-NAA). Last, we compare the degree of AID-mediated CFI-1 depletion in C. elegans neurons when the transport inhibitor response 1 (TIR1), component of the SCF ubiquitin ligase complex, is provided in neurons or all somatic cells. Altogether, this protocol provides side-by-side comparisons of different auxins and TIR1-expressing lines. Such comparisons may benefit future studies of AID-mediated protein depletion in C. elegans . Graphical abstract Image provided as pdf (together with Figures). Highlights Efficient protein depletion in C. elegans tissues upon treatment with either natural or synthetic auxins. Pansomatic TIR1 expression leads to efficient depletion of CFI-1 and DENR.Panneuronal TIR1 expression leads to neuron-specific, yet variable CFI-1 depletion.The AID system is compatible with fluorescence microscopy, Western blotting and behavioral assays.
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2
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Huang TT, Mori I. Analyses of Genetic Regulation of the Nervous System in the Nematode Caenorhabditis elegans. Methods Mol Biol 2024; 2794:313-319. [PMID: 38630240 DOI: 10.1007/978-1-0716-3810-1_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
This chapter aims to provide a comprehensive overview of the methodologies available to dissect genetic regulation of the nervous systems in the nematode Caenorhabditis elegans. These techniques encompass genetic screens and genetic tools to unravel the spatial-temporal contribution of genes on neural structure and function. Unbiased genetic screens on random mutations induced by ethyl methanesulfonate (EMS) or target gene silencing by genome-wide RNA interference (RNAi) help progress our understanding of the genetic control of neural development and functions. Complement to unbiased genetic approaches, gene- and protein-targeted manipulation by Cre/LoxP recombination system and auxin-inducible degron (AID) protein degradation system, respectively, helps identify tissues/cells and the time window critical for gene and protein function during the proper execution of a particular behavior. Considering the remarkable conservation of genetic pathways between C. elegans and mammalian systems, elucidating the genetic underpinnings of neural functions and learning behaviors in C. elegans may furnish invaluable insights into analogous processes in more complex organisms. As shown in the following chapter, leveraging these diverse methodologies enable researchers to elucidate the intricate network governing neural function and structure, laying the foundation for innovating strategies to ameliorate cognitive alterations.
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Affiliation(s)
- Tzu-Ting Huang
- Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ikue Mori
- Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan.
- Chinese Institute for Brain Research, Beijing (CIBR), Changping District, Beijing, China.
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3
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Zeng WX, Liu H, Hao Y, Qian KY, Tian FM, Li L, Yu B, Zeng XT, Gao S, Hu Z, Tong XJ. CaMKII mediates sexually dimorphic synaptic transmission at neuromuscular junctions in C. elegans. J Cell Biol 2023; 222:e202301117. [PMID: 37624117 PMCID: PMC10457463 DOI: 10.1083/jcb.202301117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Sexually dimorphic behaviors are ubiquitous throughout the animal kingdom. Although both sex-specific and sex-shared neurons have been functionally implicated in these diverse behaviors, less is known about the roles of sex-shared neurons. Here, we discovered sexually dimorphic cholinergic synaptic transmission in C. elegans occurring at neuromuscular junctions (NMJs), with males exhibiting increased release frequencies, which result in sexually dimorphic locomotion behaviors. Scanning electron microscopy revealed that males have significantly more synaptic vesicles (SVs) at their cholinergic synapses than hermaphrodites. Analysis of previously published transcriptome identified the male-enriched transcripts and focused our attention on UNC-43/CaMKII. We ultimately show that differential accumulation of UNC-43 at cholinergic neurons controls axonal SV abundance and synaptic transmission. Finally, we demonstrate that sex reversal of all neurons in hermaphrodites generates male-like cholinergic transmission and locomotion behaviors. Thus, beyond demonstrating UNC-43/CaMKII as an essential mediator of sex-specific synaptic transmission, our study provides molecular and cellular insights into how sex-shared neurons can generate sexually dimorphic locomotion behaviors.
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Affiliation(s)
- Wan-Xin Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haowen Liu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, Australia
| | - Yue Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kang-Ying Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Tian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lei Li
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, Australia
| | - Bin Yu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xian-Ting Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shangbang Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhitao Hu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, Australia
- Department of Neuroscience, City University of Hong Kong, Kowloon, China
| | - Xia-Jing Tong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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4
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Reich H, Savage-Dunn C. Signaling circuits and the apical extracellular matrix in aging: connections identified in the nematode Caenorhabditis elegans. Am J Physiol Cell Physiol 2023; 325:C1201-C1211. [PMID: 37721005 PMCID: PMC10861026 DOI: 10.1152/ajpcell.00195.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/24/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Numerous conserved signaling pathways play critical roles in aging, including insulin/IGF-1, TGF-β, and Wnt pathways. Some of these pathways also play prominent roles in the formation and maintenance of the extracellular matrix. The nematode Caenorhabditis elegans has been an enduringly productive system for the identification of conserved mechanisms of biological aging. Recent studies in C. elegans highlight the regulatory circuits between conserved signaling pathways and the extracellular matrix, revealing a bidirectional relationship between these factors and providing a platform to address how regulation of and by the extracellular matrix can impact lifespan and organismal health during aging. These discoveries provide new opportunities for clinical advances and novel therapeutic strategies.
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Affiliation(s)
- Hannah Reich
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
- PhD Program in Biology, The Graduate Center, City University of New York, New York, New York, United States
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5
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Fang J, Wang J, Wang Y, Liu X, Chen B, Zou W. Ribo-On and Ribo-Off tools using a self-cleaving ribozyme allow manipulation of endogenous gene expression in C. elegans. Commun Biol 2023; 6:816. [PMID: 37542105 PMCID: PMC10403566 DOI: 10.1038/s42003-023-05184-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
Investigating gene function relies on the efficient manipulation of endogenous gene expression. Currently, a limited number of tools are available to robustly manipulate endogenous gene expression between "on" and "off" states. In this study, we insert a 63 bp coding sequence of T3H38 ribozyme into the 3' untranslated region (UTR) of C. elegans endogenous genes using the CRISPR/Cas9 technology, which reduces the endogenous gene expression to a nearly undetectable level and generated loss-of-function phenotypes similar to that of the genetic null animals. To achieve conditional knockout, a cassette of loxP-flanked transcriptional termination signal and ribozyme is inserted into the 3' UTR of endogenous genes, which eliminates gene expression spatially or temporally via the controllable expression of the Cre recombinase. Conditional endogenous gene turn-on can be achieved by either injecting morpholino, which blocks the ribozyme self-cleavage activity or using the Cre recombinase to remove the loxP-flanked ribozyme. Together, our results demonstrate that these ribozyme-based tools can efficiently manipulate endogenous gene expression both in space and time and expand the toolkit for studying the functions of endogenous genes.
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Affiliation(s)
- Jie Fang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, 322000, Yiwu, China
- Institute of Translational Medicine, Zhejiang University, 310058, Hangzhou, China
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Jie Wang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, 322000, Yiwu, China
- Institute of Translational Medicine, Zhejiang University, 310058, Hangzhou, China
| | - Yuzhi Wang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, 322000, Yiwu, China
- Institute of Translational Medicine, Zhejiang University, 310058, Hangzhou, China
| | - Xiaofan Liu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, 322000, Yiwu, China
- Institute of Translational Medicine, Zhejiang University, 310058, Hangzhou, China
| | - Baohui Chen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China.
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, 322000, Yiwu, China.
- Institute of Translational Medicine, Zhejiang University, 310058, Hangzhou, China.
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6
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Kurashina M, Mizumoto K. Targeting endogenous proteins for spatial and temporal knockdown using auxin-inducible degron in Caenorhabditis elegans. STAR Protoc 2023; 4:102028. [PMID: 36640369 PMCID: PMC9860162 DOI: 10.1016/j.xpro.2022.102028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/21/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
The auxin-inducible degron (AID) provides reversible, spatiotemporal control for the knockdown of target proteins. Here, we present a protocol for AID-mediated protein knockdown in Caenorhabditis elegans. We describe steps for generating the knock-in mutants using two CRISPR-Cas9 genome editing techniques and preparing the auxin-containing nematode growth media (NGM) plates. We also detail AID-mediated spatiotemporal protein knockdown. For complete details on the use and execution of this protocol, please refer to Kurashina et al. (2021).1.
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Affiliation(s)
- Mizuki Kurashina
- Department of Zoology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Cell & Developmental Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; The Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Kota Mizumoto
- Department of Zoology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Cell & Developmental Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; The Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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7
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Hao Y, Liu H, Zeng XT, Wang Y, Zeng WX, Qian KY, Li L, Chi MX, Gao S, Hu Z, Tong XJ. UNC-43/CaMKII-triggered anterograde signals recruit GABA ARs to mediate inhibitory synaptic transmission and plasticity at C. elegans NMJs. Nat Commun 2023; 14:1436. [PMID: 36918518 PMCID: PMC10015018 DOI: 10.1038/s41467-023-37137-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
Disturbed inhibitory synaptic transmission has functional impacts on neurodevelopmental and psychiatric disorders. An essential mechanism for modulating inhibitory synaptic transmission is alteration of the postsynaptic abundance of GABAARs, which are stabilized by postsynaptic scaffold proteins and recruited by presynaptic signals. However, how GABAergic neurons trigger signals to transsynaptically recruit GABAARs remains elusive. Here, we show that UNC-43/CaMKII functions at GABAergic neurons to recruit GABAARs and modulate inhibitory synaptic transmission at C. elegans neuromuscular junctions. We demonstrate that UNC-43 promotes presynaptic MADD-4B/Punctin secretion and NRX-1α/Neurexin surface delivery. Together, MADD-4B and NRX-1α recruit postsynaptic NLG-1/Neuroligin and stabilize GABAARs. Further, the excitation of GABAergic neurons potentiates the recruitment of NLG-1-stabilized-GABAARs, which depends on UNC-43, MADD-4B, and NRX-1. These data all support that UNC-43 triggers MADD-4B and NRX-1α, which act as anterograde signals to recruit postsynaptic GABAARs. Thus, our findings elucidate a mechanism for pre- and postsynaptic communication and inhibitory synaptic transmission and plasticity.
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Affiliation(s)
- Yue Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Haowen Liu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xian-Ting Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ya Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wan-Xin Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Kang-Ying Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Lei Li
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ming-Xuan Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shangbang Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhitao Hu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xia-Jing Tong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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8
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Crittenden SL, Seidel HS, Kimble J. Analysis of the C. elegans Germline Stem Cell Pool. Methods Mol Biol 2023; 2677:1-36. [PMID: 37464233 DOI: 10.1007/978-1-0716-3259-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The Caenorhabditis elegans germline is an excellent model for studying the genetic and molecular regulation of stem cell self-renewal and progression of cells from a stem cell state to a differentiated state. The germline tissue is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated gametes at the other. A simple mesenchymal niche caps the GSC pool and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Notch signaling activates transcription of the key GSC regulators lst-1 and sygl-1 proteins in a gradient through the GSC pool. LST-1 and SYGL-1 proteins work with PUF RNA regulators in a self-renewal hub to maintain the GSC pool. In this chapter, we present methods for characterizing the C. elegans GSC pool and early stages of germ cell differentiation. The methods include examination of germlines in living and fixed worms, cell cycle analysis, and analysis of markers. We also discuss assays to separate mutant phenotypes that affect the stem cell vs. differentiation decision from those that affect germ cell processes more generally.
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Affiliation(s)
- Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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9
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Fragoso-Luna A, Romero-Bueno R, Eibl M, Ayuso C, Muñoz-Jiménez C, Benes V, Cases I, Askjaer P. Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in Caenorhabditis elegans. Genetics 2022; 223:6793861. [PMID: 36321973 PMCID: PMC9836023 DOI: 10.1093/genetics/iyac166] [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] [Received: 10/03/2022] [Accepted: 10/24/2022] [Indexed: 11/05/2022] Open
Abstract
Control of gene expression in specific tissues and/or at certain stages of development allows the study and manipulation of gene function with high precision. Site-specific genome recombination by the flippase (FLP) and cyclization recombination (Cre) enzymes has proved particularly relevant. Joint efforts of many research groups have led to the creation of efficient FLP and Cre drivers to regulate gene expression in a variety of tissues in Caenorhabditis elegans. Here, we extend this toolkit by the addition of FLP lines that drive recombination specifically in distal tip cells, the somatic gonad, coelomocytes, and the epithelial P lineage. In some cases, recombination-mediated gene knockouts do not completely deplete protein levels due to persistence of long-lived proteins. To overcome this, we developed a spatiotemporally regulated degradation system for green fluorescent fusion proteins based on FLP-mediated recombination. Using 2 stable nuclear pore proteins, MEL-28/ELYS and NPP-2/NUP85 as examples, we report the benefit of combining tissue-specific gene knockout and protein degradation to achieve complete protein depletion. We also demonstrate that FLP-mediated recombination can be utilized to identify transcriptomes in a C. elegans tissue of interest. We have adapted RNA polymerase DamID for the FLP toolbox and by focusing on a well-characterized tissue, the hypodermis, we show that the vast majority of genes identified by RNA polymerase DamID are known to be expressed in this tissue. These tools allow combining FLP activity for simultaneous gene inactivation and transcriptomic profiling, thus enabling the inquiry of gene function in various complex biological processes.
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Affiliation(s)
| | | | | | - Cristina Ayuso
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide, Junta de Andalucía, 41013 Sevilla, Spain
| | - Celia Muñoz-Jiménez
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide, Junta de Andalucía, 41013 Sevilla, Spain
| | | | - Ildefonso Cases
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide, Junta de Andalucía, 41013 Sevilla, Spain
| | - Peter Askjaer
- Corresponding author: Andalusian Centre for Developmental Biology, Gene Regulation and Morphogenesis, CSIC—Universidad Pablo de Olavide, Carretera de Utrera, km 1, 41013 Seville, Spain.
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10
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Gibson SB, Ness-Cohn E, Andersen EC. Benzimidazoles cause lethality by inhibiting the function of Caenorhabditis elegans neuronal beta-tubulin. Int J Parasitol Drugs Drug Resist 2022; 20:89-96. [PMID: 36332489 PMCID: PMC9771835 DOI: 10.1016/j.ijpddr.2022.10.004] [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] [Received: 07/19/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/08/2022]
Abstract
Parasitic nematode infections cause an enormous global burden to both humans and livestock. Resistance to the limited arsenal of anthelmintic drugs used to combat these infections is widespread, including benzimidazole (BZ) compounds. Previous studies using the free-living nematode Caenorhabditis elegans to model parasitic nematode resistance have shown that loss-of-function mutations in the beta-tubulin gene ben-1 confer resistance to BZ drugs. However, the mechanism of resistance and the tissue-specific susceptibility are not well known in any nematode species. To identify in which tissue(s) ben-1 function underlies BZ susceptibility, transgenic strains that express ben-1 in different tissues, including hypodermis, muscles, neurons, intestine, and ubiquitous expression were generated. High-throughput fitness assays were performed to measure and compare the quantitative responses to BZ compounds among different transgenic lines. Significant BZ susceptibility was observed in animals expressing ben-1 in neurons, comparable to expression using the ben-1 promoter. This result suggests that ben-1 function in neurons underlies susceptibility to BZ. Subsetting neuronal expression of ben-1 based on the neurotransmitter system further restricted ben-1 function in cholinergic neurons to cause BZ susceptibility. These results better inform our current understanding of the cellular mode of action of BZs and also suggest additional treatments that might potentiate the effects of BZs in neurons.
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Affiliation(s)
- Sophia B. Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Elan Ness-Cohn
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA,Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, IL, 60611, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA,Corresponding author. Department of Molecular Biosciences Northwestern University 4619 Silverman Hall 2205 Tech Drive Evanston, IL, 60208, USA.
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11
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Yamauchi Y, Matsukura H, Motone K, Ueda M, Aoki W. Evaluation of a library of loxP variants with a wide range of recombination efficiencies by Cre. PLoS One 2022; 17:e0276657. [PMID: 36269789 PMCID: PMC9586403 DOI: 10.1371/journal.pone.0276657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/11/2022] [Indexed: 11/18/2022] Open
Abstract
Sparse labeling of individual cells is an important approach in neuroscience and many other fields of research. Various methods have been developed to sparsely label only a small population of cells; however, there is no simple and reproducible strategy for managing the probability of sparse labeling at desired levels. Here, we aimed to develop a novel methodology based on the Cre-lox system to regulate sparseness at desired levels, and we purely analyzed cleavage efficiencies of loxP mutants by Cre. We hypothesized that mutations in the loxP sequence reduce the recognition efficiency by Cre, which enables the regulation of the sparseness level of gene expression. In this research, we mutagenized the loxP sequence and analyzed a library of loxP variants. We evaluated more than 1000 mutant loxP sequences, including mutants with reduced excision efficiencies by Cre ranging from 0.51% to 59%. This result suggests that these mutant loxP sequences can be useful in regulating the sparseness of genetic labeling at desired levels.
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Affiliation(s)
- Yuji Yamauchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
- Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
| | - Hidenori Matsukura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Keisuke Motone
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
- * E-mail:
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12
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Yoshina S, Mitani S. Integration of multicopy extrachromosomal transgenes into defined loci without phenotypes. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000571. [PMID: 35693894 PMCID: PMC9187222 DOI: 10.17912/micropub.biology.000571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 01/01/1970] [Accepted: 05/16/2022] [Indexed: 11/10/2022]
Abstract
We show how presumably non-phenotypic loci can be used for integration sites of multi-copy extrachromosomal transgenes, using the CRISPR/Cas9 system. We used four loci, which show no apparent phenotype in our hands, as a model for any other loci with no phenotype.
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Affiliation(s)
- Sawako Yoshina
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, Tokyo 162-8666, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, Tokyo 162-8666, Japan.
,
Correspondence to: Shohei Mitani (
)
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13
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Moseley-Alldredge M, Sheoran S, Yoo H, O’Keefe C, Richmond JE, Chen L. A role for the Erk MAPK pathway in modulating SAX-7/L1CAM-dependent locomotion in Caenorhabditis elegans. Genetics 2022; 220:iyab215. [PMID: 34849872 PMCID: PMC9097276 DOI: 10.1093/genetics/iyab215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/11/2021] [Indexed: 01/13/2023] Open
Abstract
L1CAMs are immunoglobulin cell adhesion molecules that function in nervous system development and function. Besides being associated with autism and schizophrenia spectrum disorders, impaired L1CAM function also underlies the X-linked L1 syndrome, which encompasses a group of neurological conditions, including spastic paraplegia and congenital hydrocephalus. Studies on vertebrate and invertebrate L1CAMs established conserved roles that include axon guidance, dendrite morphogenesis, synapse development, and maintenance of neural architecture. We previously identified a genetic interaction between the Caenorhabditis elegans L1CAM encoded by the sax-7 gene and RAB-3, a GTPase that functions in synaptic neurotransmission; rab-3; sax-7 mutant animals exhibit synthetic locomotion abnormalities and neuronal dysfunction. Here, we show that this synergism also occurs when loss of SAX-7 is combined with mutants of other genes encoding key players of the synaptic vesicle (SV) cycle. In contrast, sax-7 does not interact with genes that function in synaptogenesis. These findings suggest a postdevelopmental role for sax-7 in the regulation of synaptic activity. To assess this possibility, we conducted electrophysiological recordings and ultrastructural analyses at neuromuscular junctions; these analyses did not reveal obvious synaptic abnormalities. Lastly, based on a forward genetic screen for suppressors of the rab-3; sax-7 synthetic phenotypes, we determined that mutants in the ERK Mitogen-activated Protein Kinase (MAPK) pathway can suppress the rab-3; sax-7 locomotion defects. Moreover, we established that Erk signaling acts in a subset of cholinergic neurons in the head to promote coordinated locomotion. In combination, these results suggest a modulatory role for Erk MAPK in L1CAM-dependent locomotion in C. elegans.
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Affiliation(s)
- Melinda Moseley-Alldredge
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Seema Sheoran
- Department of Biological Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Hayoung Yoo
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Calvin O’Keefe
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Janet E Richmond
- Department of Biological Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Lihsia Chen
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
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14
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Das R, Lin LC, Català-Castro F, Malaiwong N, Sanfeliu-Cerdán N, Porta-de-la-Riva M, Pidde A, Krieg M. An asymmetric mechanical code ciphers curvature-dependent proprioceptor activity. SCIENCE ADVANCES 2021; 7:eabg4617. [PMID: 34533987 PMCID: PMC8448456 DOI: 10.1126/sciadv.abg4617] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/27/2021] [Indexed: 05/07/2023]
Abstract
A repetitive gait cycle is an archetypical component within the behavioral repertoire of many animals including humans. It originates from mechanical feedback within proprioceptors to adjust the motor program during locomotion and thus leads to a periodic orbit in a low-dimensional space. Here, we investigate the mechanics, molecules, and neurons responsible for proprioception in Caenorhabditis elegans to gain insight into how mechanosensation shapes the orbital trajectory to a well-defined limit cycle. We used genome editing, force spectroscopy, and multiscale modeling and found that alternating tension and compression with the spectrin network of a single proprioceptor encodes body posture and informs TRP-4/NOMPC and TWK-16/TREK2 homologs of mechanosensitive ion channels during locomotion. In contrast to a widely accepted model of proprioceptive “stretch” reception, we found that proprioceptors activated locally under compressive stresses in-vivo and in-vitro and propose that this property leads to compartmentalized activity within long axons delimited by curvature-dependent mechanical stresses.
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15
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Gómez-Saldivar G, Glauser DA, Meister P. Tissue-specific DamID protocol using nanopore sequencing. J Biol Methods 2021; 8:e152. [PMID: 34514013 PMCID: PMC8411031 DOI: 10.14440/jbm.2021.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
DNA adenine methylation identification (DamID) is a powerful method to determine DNA binding profiles of proteins at a genomic scale. The method leverages the fusion between a protein of interest and the Dam methyltransferase of E. coli, which methylates proximal DNA in vivo. Here, we present an optimized procedure, which was developed for tissue-specific analyses in Caenorhabditis elegans and successfully used to footprint genes actively transcribed by RNA polymerases and to map transcription factor binding in gene regulatory regions. The present protocol details C. elegans-specific steps involved in the preparation of transgenic lines and genomic DNA samples, as well as broadly applicable steps for the DamID procedure, including the isolation of methylated DNA fragments, the preparation of multiplexed libraries, Nanopore sequencing, and data analysis. Two distinctive features of the approach are (i) the use of an efficient recombination-based strategy to selectively analyze rare cell types and (ii) the use of Nanopore sequencing, which streamlines the process. The method allows researchers to go from genomic DNA samples to sequencing results in less than a week, while being sensitive enough to report reliable DNA footprints in cell types as rare as 2 cells per animal.
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Affiliation(s)
| | | | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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16
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Xia SL, Li M, Chen B, Wang C, Yan YH, Dong MQ, Qi YB. The LRR-TM protein PAN-1 interacts with MYRF to promote its nuclear translocation in synaptic remodeling. eLife 2021; 10:e67628. [PMID: 33950834 PMCID: PMC8099431 DOI: 10.7554/elife.67628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
Neural circuits develop through a plastic phase orchestrated by genetic programs and environmental signals. We have identified a leucine-rich-repeat domain transmembrane protein PAN-1 as a factor required for synaptic rewiring in C. elegans. PAN-1 localizes on cell membrane and binds with MYRF, a membrane-bound transcription factor indispensable for promoting synaptic rewiring. Full-length MYRF was known to undergo self-cleavage on ER membrane and release its transcriptional N-terminal fragment in cultured cells. We surprisingly find that MYRF trafficking to cell membrane before cleavage is pivotal for C. elegans development and the timing of N-MYRF release coincides with the onset of synaptic rewiring. On cell membrane PAN-1 and MYRF interact with each other via their extracellular regions. Loss of PAN-1 abolishes MYRF cell membrane localization, consequently blocking myrf-dependent neuronal rewiring process. Thus, through interactions with a cooperating factor on the cell membrane, MYRF may link cell surface activities to transcriptional cascades required for development.
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Affiliation(s)
- Shi-Li Xia
- School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhouChina
| | - Meng Li
- School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhouChina
| | - Bing Chen
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhouChina
| | - Chao Wang
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhouChina
| | - Yong-Hong Yan
- National Institute of Biological SciencesBeijingChina
| | - Meng-Qiu Dong
- National Institute of Biological SciencesBeijingChina
| | - Yingchuan B Qi
- School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhouChina
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17
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Driesschaert B, Mergan L, Temmerman L. Conditional gene expression in invertebrate animal models. J Genet Genomics 2021; 48:14-31. [PMID: 33814307 DOI: 10.1016/j.jgg.2021.01.005] [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: 11/06/2020] [Revised: 12/11/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
A mechanistic understanding of biology requires appreciating spatiotemporal aspects of gene expression and its functional implications. Conditional expression allows for (ir)reversible switching of genes on or off, with the potential of spatial and/or temporal control. This provides a valuable complement to the more often used constitutive gene (in)activation through mutagenesis, providing tools to answer a wider array of research questions across biological disciplines. Spatial and/or temporal control are granted primarily by (combinations of) specific promoters, temperature regimens, compound addition, or illumination. The use of such genetic tool kits is particularly widespread in invertebrate animal models because they can be applied to study biological processes in short time frames and on large scales, using organisms amenable to easy genetic manipulation. Recent years witnessed an exciting expansion and optimization of such tools, of which we provide a comprehensive overview and discussion regarding their use in invertebrates. The mechanism, applicability, benefits, and drawbacks of each of the systems, as well as further developments to be expected in the foreseeable future, are highlighted.
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Affiliation(s)
- Brecht Driesschaert
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59 - Box 2465, B-3000 Leuven, Belgium
| | - Lucas Mergan
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59 - Box 2465, B-3000 Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59 - Box 2465, B-3000 Leuven, Belgium.
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18
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Du X, McManus DP, French JD, Jones MK, You H. CRISPR/Cas9: A new tool for the study and control of helminth parasites. Bioessays 2020; 43:e2000185. [PMID: 33145822 DOI: 10.1002/bies.202000185] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022]
Abstract
Recent reports of CRISPR/Cas9 genome editing in parasitic helminths open up new avenues for research on these dangerous pathogens. However, the complex morphology and life cycles inherent to these parasites present obstacles for the efficient application of CRISPR/Cas9-targeted mutagenesis. This is especially true with the trematode flukes where only modest levels of gene mutation efficiency have been achieved. Current major challenges in the application of CRISPR/Cas9 for study of parasitic worms thus lie in enhancing gene mutation efficiency and overcoming issues involved in host passage so that mutated parasites survive. Strategies developed for CRISPR/Cas9 studies on Caenorhabditis elegans, protozoa and mammalian cells, including novel delivery methods, the choice of selectable markers, and refining mutation precision represent novel tactics whereby these impediments can be overcome. Furthermore, employing CRISPR/Cas9-mediated gene drive to interfere with vector transmission represents a novel approach for the control of parasitic worms that is worthy of further exploration.
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Affiliation(s)
- Xiaofeng Du
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Herston, Brisbane, Queensland, Australia
| | - Donald P McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Herston, Brisbane, Queensland, Australia
| | - Juliet D French
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Malcolm K Jones
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
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19
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Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 2020; 216:931-945. [PMID: 33037050 PMCID: PMC7768263 DOI: 10.1534/genetics.120.303774] [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: 08/17/2020] [Accepted: 10/09/2020] [Indexed: 11/23/2022] Open
Abstract
Differential gene expression across cell types underlies development and cell physiology in multicellular organisms. Caenorhabditis elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the RNA Polymerase DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, in sorted embryonic blastomeres and in different tissues from intact young adults by driving tissue-specific Dam fusion expression. We obtained meaningful transcriptional footprints in line with RNA-sequencing (RNA-seq) studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 3901 candidate genes with putatively active transcription in XXX cells, including the few previously known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX cells and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of RNA polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.
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20
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Castelletto ML, Gang SS, Hallem EA. Recent advances in functional genomics for parasitic nematodes of mammals. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb206482. [PMID: 32034038 DOI: 10.1242/jeb.206482] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human-parasitic nematodes infect over a quarter of the world's population and are a major cause of morbidity in low-resource settings. Currently available treatments have not been sufficient to eliminate infections in endemic areas, and drug resistance is an increasing concern, making new treatment options a priority. The development of new treatments requires an improved understanding of the basic biology of these nematodes. Specifically, a better understanding of parasitic nematode development, reproduction and behavior may yield novel drug targets or new opportunities for intervention such as repellents or traps. Until recently, our ability to study parasitic nematode biology was limited because few tools were available for their genetic manipulation. This is now changing as a result of recent advances in the large-scale sequencing of nematode genomes and the development of new techniques for their genetic manipulation. Notably, skin-penetrating gastrointestinal nematodes in the genus Strongyloides are now amenable to transgenesis, RNAi and CRISPR/Cas9-mediated targeted mutagenesis, positioning the Strongyloides species as model parasitic nematode systems. A number of other mammalian-parasitic nematodes, including the giant roundworm Ascaris suum and the tissue-dwelling filarial nematode Brugia malayi, are also now amenable to transgenesis and/or RNAi in some contexts. Using these tools, recent studies of Strongyloides species have already provided insight into the molecular pathways that control the developmental decision to form infective larvae and that drive the host-seeking behaviors of infective larvae. Ultimately, a mechanistic understanding of these processes could lead to the development of new avenues for nematode control.
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Affiliation(s)
- Michelle L Castelletto
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Spencer S Gang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92161, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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21
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Lee J, Taylor CA, Barnes KM, Shen A, Stewart EV, Chen A, Xiang YK, Bao Z, Shen K. A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes. eLife 2019; 8:e46703. [PMID: 31386623 PMCID: PMC6684318 DOI: 10.7554/elife.46703] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022] Open
Abstract
Cellular differentiation requires both activation of target cell transcriptional programs and repression of non-target cell programs. The Myt1 family of zinc finger transcription factors contributes to fibroblast to neuron reprogramming in vitro. Here, we show that ztf-11 (Zinc-finger Transcription Factor-11), the sole Caenorhabditis elegans Myt1 homolog, is required for neurogenesis in multiple neuronal lineages from previously differentiated epithelial cells, including a neuron generated by a developmental epithelial-to-neuronal transdifferentiation event. ztf-11 is exclusively expressed in all neuronal precursors with remarkable specificity at single-cell resolution. Loss of ztf-11 leads to upregulation of non-neuronal genes and reduced neurogenesis. Ectopic expression of ztf-11 in epidermal lineages is sufficient to produce additional neurons. ZTF-11 functions together with the MuvB corepressor complex to suppress the activation of non-neuronal genes in neurons. These results dovetail with the ability of Myt1l (Myt1-like) to drive neuronal transdifferentiation in vitro in vertebrate systems. Together, we identified an evolutionarily conserved mechanism to specify neuronal cell fate by repressing non-neuronal genes.
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Affiliation(s)
- Joo Lee
- Department of BiochemistryStanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Caitlin A Taylor
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
| | | | - Ao Shen
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | | | - Allison Chen
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Yang K Xiang
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | - Zhirong Bao
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Kang Shen
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
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22
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Nance J, Frøkjær-Jensen C. The Caenorhabditis elegans Transgenic Toolbox. Genetics 2019; 212:959-990. [PMID: 31405997 PMCID: PMC6707460 DOI: 10.1534/genetics.119.301506] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/01/2019] [Indexed: 12/30/2022] Open
Abstract
The power of any genetic model organism is derived, in part, from the ease with which gene expression can be manipulated. The short generation time and invariant developmental lineage have made Caenorhabditis elegans very useful for understanding, e.g., developmental programs, basic cell biology, neurobiology, and aging. Over the last decade, the C. elegans transgenic toolbox has expanded considerably, with the addition of a variety of methods to control expression and modify genes with unprecedented resolution. Here, we provide a comprehensive overview of transgenic methods in C. elegans, with an emphasis on recent advances in transposon-mediated transgenesis, CRISPR/Cas9 gene editing, conditional gene and protein inactivation, and bipartite systems for temporal and spatial control of expression.
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Affiliation(s)
- Jeremy Nance
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York 10016
| | - Christian Frøkjær-Jensen
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal 23955-6900, Saudi Arabia
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23
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Cell Non-autonomous Function of daf-18/PTEN in the Somatic Gonad Coordinates Somatic Gonad and Germline Development in C. elegans Dauer Larvae. Curr Biol 2019; 29:1064-1072.e8. [PMID: 30827916 DOI: 10.1016/j.cub.2019.01.076] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 12/21/2022]
Abstract
C. elegans larvae integrate environmental information and developmental decisions [1-3]. In favorable conditions, worms develop rapidly and continuously through four larval stages into reproductive adulthood. However, if conditions are unfavorable through the second larval stage, worms enter dauer diapause, a state of global and reversible developmental arrest in which precursor cells remain quiescent and preserve developmental potential, anticipating developmental progression if conditions improve. Signaling from neurons, hypodermis, and intestine regulate the appearance and behavior of dauer larvae and many aspects of developmental arrest of the non-gonadal soma [1, 4, 5]. Here, we show that the decision of somatic gonad blast cells (SGBs) and germline stem cells (GSCs) to be quiescent or progress developmentally is regulated differently from the non-gonadal soma: daf-18/PTEN acts non-autonomously within the somatic gonad to maintain developmental quiescence of both SGBs and GSCs. Our analysis suggests that daf-18 acts in somatic gonad cells to produce a "pro-quiescence" signal (or signals) that acts inter se and between the somatic gonad and the germline. The inferred signal does not require DAF-2/insulin receptor or maintain quiescence of the nearby sex myoblasts, and developmental progression in daf-18(0) does not require dafachronic acids. Abrogating quiescence in dauer results in post-dauer sterility. Our results implicate the somatic gonad as an endocrine organ to synchronize somatic gonad and germline development during dauer diapause and recovery, and our finding that PTEN acts non-autonomously to control blast cell quiescence may be relevant to its function as a tumor suppressor in mammals and to combating parasitic nematodes.
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24
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Zou L, Wu D, Zang X, Wang Z, Wu Z, Chen D. Construction of a germline-specific RNAi tool in C. elegans. Sci Rep 2019; 9:2354. [PMID: 30787374 PMCID: PMC6382888 DOI: 10.1038/s41598-019-38950-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/15/2019] [Indexed: 01/08/2023] Open
Abstract
Analysis of complex biological functions usually requires tissue-specific genetic manipulations in multicellular organisms. The C. elegans germline plays regulatory roles not only in reproduction, but also in metabolism, stress response and ageing. Previous studies have used mutants of rrf-1, which encodes an RNA-directed RNA polymerase, as a germline-specific RNAi tool. However, the rrf-1 mutants showed RNAi activities in somatic tissues. Here we constructed a germline-specific RNAi strain by combining an indel mutation of rde-1, which encodes an Argonaute protein that functions cell autonomously to ensure RNAi efficiency, and a single copy rde-1 transgene driven by the sun-1 germline-specific promoter. The germline RNAi efficiency and specificity are confirmed by RNAi phenocopy of known mutations, knockdown of GFP reporter expression, as well as quantitative RT-PCR measurement of tissue-specific mRNAs upon RNAi knockdown. The germline-specific RNAi strain shows no obvious deficiencies in reproduction, lipid accumulation, thermo-tolerance and life span compared to wild-type animals. By screening an RNAi sub-library of phosphatase genes, we identified novel regulators of thermo-tolerance. Together, we have created a useful tool that can facilitate the genetic analysis of germline-specific functions in C. elegans.
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Affiliation(s)
- Lina Zou
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Rd, Pukou, Nanjing, Jiangsu, 210061, China
| | - Di Wu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Rd, Pukou, Nanjing, Jiangsu, 210061, China
| | - Xiao Zang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Rd, Pukou, Nanjing, Jiangsu, 210061, China
| | - Zi Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Rd, Pukou, Nanjing, Jiangsu, 210061, China
| | - Zixing Wu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Rd, Pukou, Nanjing, Jiangsu, 210061, China
| | - Di Chen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Rd, Pukou, Nanjing, Jiangsu, 210061, China.
- Institute for Brain Sciences, Nanjing University, Nanjing, China.
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25
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Redox Signaling of NADPH Oxidases Regulates Oxidative Stress Responses, Immunity and Aging. Antioxidants (Basel) 2018; 7:antiox7100130. [PMID: 30274229 PMCID: PMC6210377 DOI: 10.3390/antiox7100130] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/14/2022] Open
Abstract
An accumulating body of evidence suggests that transient or physiological reactive oxygen species (ROS) generated by nicotinamide adenine dinucleotide phosphate (NADPH) oxidases act as a redox signal to re-establish homeostasis. The capacity to re-establish homeostasis progressively declines during aging but is maintained in long-lived animals to promote healthy aging. In the model organism Caenorhabditis elegans, ROS generated by dual oxidases (Duox) are important for extracellular matrix integrity, pathogen defense, oxidative stress resistance, and longevity. The Duox enzymatic activity is tightly regulated and under cellular control. Developmental molting cycles, pathogen infections, toxins, mitochondrial-derived ROS, drugs, and small GTPases (e.g., RHO-1) can activate Duox (BLI-3) to generate ROS, whereas NADPH oxidase inhibitors and negative regulators, such as MEMO-1, can inhibit Duox from generating ROS. Three mechanisms-of-action have been discovered for the Duox/BLI-3-generated ROS: (1) enzymatic activity to catalyze crosslinking of free tyrosine ethyl ester in collagen bundles to stabilize extracellular matrices, (2) high ROS bursts/levels to kill pathogens, and (3) redox signaling activating downstream kinase cascades to transcription factors orchestrating oxidative stress and immunity responses to re-establish homeostasis. Although Duox function at the cell surface is well established, recent genetic and biochemical data also suggests a novel role for Duoxs at the endoplasmic reticulum membrane to control redox signaling. Evidence underlying these mechanisms initiated by ROS from NADPH oxidases, and their relevance for human aging, are discussed in this review. Appropriately controlling NADPH oxidase activity for local and physiological redox signaling to maintain cellular homeostasis might be a therapeutic strategy to promote healthy aging.
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26
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Split cGAL, an intersectional strategy using a split intein for refined spatiotemporal transgene control in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2018; 115:3900-3905. [PMID: 29581308 DOI: 10.1073/pnas.1720063115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bipartite expression systems, such as the GAL4-UAS system, allow fine manipulation of gene expression and are powerful tools for interrogating gene function. Recently, we established cGAL, a GAL4-based bipartite expression system for transgene control in Caenorhabditis elegans, where a single promoter dictates the expression pattern of a cGAL driver, which then binds target upstream activation sequences to drive expression of a downstream effector gene. Here, we report a split strategy for cGAL using the split intein gp41-1 for intersectional control of transgene expression. Split inteins are protein domains that associate, self-excise, and covalently ligate their flanking peptides together. We split the DNA binding domain and transcriptional activation domain of cGAL and fused them to the N terminal of gp41-1-N-intein and the C terminal of gp41-1-C-intein, respectively. In cells where both halves of cGAL are expressed, a functional cGAL driver is reconstituted via intein-mediated protein splicing. This reconstitution allows expression of the driver to be dictated by two promoters for refined spatial control or spatiotemporal control of transgene expression. We apply the split cGAL system to genetically access the single pair of MC neurons (previously inaccessible with a single promoter), and reveal an important role of protein kinase A in rhythmic pharyngeal pumping in C. elegans Thus, the split cGAL system gives researchers a greater degree of spatiotemporal control over transgene expression, and will be a valuable genetic tool in C. elegans for dissecting gene function with finer cell-specific resolution.
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MITANI S. Comprehensive functional genomics using Caenorhabditis elegans as a model organism. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:561-577. [PMID: 29021508 PMCID: PMC5743858 DOI: 10.2183/pjab.93.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
We have been working on functional genomics using C. elegans as a model organism. We first used cell-type specific markers and preexisting mutants to investigate how genotype-phenotype causal relationships are regulated. With the aid of transgenic methods, we analyzed various biological processes in C. elegans. We have developed efficient methods to isolate gene knockout strains. Thousands of strains isolated this way are used by many researchers and have revealed many biological mechanisms. We have also developed methods to examine the functions of genes in a comprehensive manner by integrating transgenes into chromosomes, designing conditional knockouts, and creating balancers for lethal mutations. A combination of these biological resources and techniques will be useful to understand the functions of genes in C. elegans, which has many genes that are orthologous to those of higher organisms including humans.
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Affiliation(s)
- Shohei MITANI
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, Tokyo, Japan
- Tokyo Women’s Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
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Abstract
The Caenorhabditis elegans germline is an excellent model for studying the regulation of a pool of stem cells and progression of cells from a stem cell state to a differentiated state. At the tissue level, the germline is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated cells at the other. A simple mesenchymal niche caps the GSC region of the germline and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Downstream of Notch signaling, key regulators include novel LST-1 and SYGL-1 proteins and a network of RNA regulatory proteins. In this chapter we present methods for characterizing the C. elegans GSC pool and early germ cell differentiation. The methods include examination of the germline in living and fixed worms, cell cycle analysis, and analysis of markers. We also discuss assays to separate mutants that affect the stem cell vs. differentiation decision from those that affect germ cell processes more generally.
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Affiliation(s)
- Sarah L Crittenden
- HHMI/Department of Biochemistry, Howard Hughes Medical Institute and University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706-1544, USA.
| | - Hannah S Seidel
- HHMI/Department of Biochemistry, Howard Hughes Medical Institute and University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706-1544, USA
| | - Judith Kimble
- HHMI/Department of Biochemistry, Howard Hughes Medical Institute and University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706-1544, USA
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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Li W, Ou G. The application of somatic CRISPR-Cas9 to conditional genome editing in Caenorhabditis elegans. Genesis 2016; 54:170-81. [PMID: 26934570 DOI: 10.1002/dvg.22932] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/20/2022]
Abstract
Forward and reverse genetic approaches have been well developed in the nematode Caenorhabditis elegans; however, efficient genetic tools to generate conditional gene mutations are still in high demand. Recently, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR-Cas9) system for genome modification has provided an additional tool for C. elegans researchers to achieve simple and efficient conditional targeted mutagenesis. Here, we review recent advances in the somatic expression of Cas9 endonuclease for conditional gene editing. We present some practical considerations for improving the efficiency and reducing the off-target effects of somatic CRISPR-Cas9 and highlight a strategy to analyze somatic mutation at single-cell resolution. Finally, we outline future applications and consider challenges for this emerging genome editing platform that will need to be addressed in the future.
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Affiliation(s)
- Wei Li
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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