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González-Romero E, Martínez-Valiente C, García-García G, Rosal-Vela A, Millán JM, Sanz MÁ, Sanz G, Liquori A, Cervera JV, Vázquez-Manrique RP. PCR-Based Strategy for Introducing CRISPR/Cas9 Machinery into Hematopoietic Cell Lines. Cancers (Basel) 2023; 15:4263. [PMID: 37686539 PMCID: PMC10487029 DOI: 10.3390/cancers15174263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Acute myeloid leukemia is a complex heterogeneous disease characterized by the clonal expansion of undifferentiated myeloid precursors. Due to the difficulty in the transfection of blood cells, several hematological models have recently been developed with CRISPR/Cas9, using viral vectors. In this study, we developed an alternative strategy in order to generate CRISPR constructs by fusion PCR, which any lab equipped with basic equipment can implement. Our PCR-generated constructs were easily introduced into hard-to-transfect leukemic cells, and their function was dually validated with the addition of MYBL2 and IDH2 genes into HEK293 cells. We then successfully modified the MYBL2 gene and introduced the R172 mutation into the IDH2 gene within NB4 and HL60 cells that constitutively expressed the Cas9 nuclease. The efficiency of mutation introduction with our methodology was similar to that of ribonucleoprotein strategies, and no off-target events were detected. Overall, our strategy represents a valid and intuitive alternative for introducing desired mutations into hard-to-transfect leukemic cells without viral transduction.
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Affiliation(s)
- Elisa González-Romero
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
| | - Cristina Martínez-Valiente
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
| | - Gema García-García
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Antonio Rosal-Vela
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- Biomedicine, Biotechnology and Public Health Department, Cádiz University, 11002 Cádiz, Spain
- Institute of Research and Innovation in Biomedical Sciences of Cadiz (INIBICA), 11009 Cádiz, Spain
| | - José María Millán
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Miguel Ángel Sanz
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
| | - Guillermo Sanz
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
- Hematology Department, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
| | - Alessandro Liquori
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
| | - José Vicente Cervera
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
- Hematology Department, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
| | - Rafael P. Vázquez-Manrique
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
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2
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Memar N, Sethi A, Luehr S, Lambie EJ, Conradt B. In vivo labeling of endogenous genomic loci in C. elegans using CRISPR/dCas9. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000701. [PMID: 36606081 PMCID: PMC9807462 DOI: 10.17912/micropub.biology.000701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/11/2022] [Accepted: 12/09/2022] [Indexed: 01/07/2023]
Abstract
Visualization of genomic loci with open chromatin state has been reported in mammalian tissue culture cells using a CRISPR/Cas9-based system that utilizes an EGFP-tagged endonuclease-deficient Cas9 protein (dCas9::EGFP) (Chen et al. 2013). Here, we adapted this approach for use in Caenorhabditis elegans . We generated a C. elegans strain that expresses the dCas9 protein fused to two nuclear-localized EGFP molecules (dCas9::NLS::2xEGFP::NLS) in an inducible manner. Using this strain, we report the visualization in live C. elegans embryos of two endogenous repetitive loci, rrn-4 and rrn-1 , from which 5S and 18S ribosomal RNAs are constitutively generated.
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Affiliation(s)
- Nadin Memar
- Institute for Basic Science (IBS), Ulsan 44919, South Korea
| | | | | | | | - Barbara Conradt
- University College London, United Kingdom
,
Correspondence to: Barbara Conradt (
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3
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Bokman E, Eliezer Y, Zaslaver A. A Fusion PCR Method for Expressing Genetic Tools in C. elegans. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2468:205-214. [PMID: 35320566 DOI: 10.1007/978-1-0716-2181-3_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
C. elegans offer a unique opportunity for understanding computation in neural networks. This is largely due to their relatively compact neural network for which a wiring diagram is available. Recent advances in genetic tools for interrogating neural activity (e.g., optogenetics) make C. elegans particularly compelling as they can be expressed in many different combinations in target individual neurons. Thus, the prospect to decipher principles underlying functionality in neural networks largely depends on the ease by which transgenic animals can be generated. Traditionally, to generate transgenic animals one would inject a plasmid containing the gene of interest under the regulation of the cell- or lineage-specific promoter. This often requires laborious cloning steps of both the gene and the promoter. The Hobert lab has developed a simpler protocol in which linear PCR fragments can be injected to generate transgenic animals. Relying on this PCR fusion-based method, here we provide a detailed protocol that we have optimized for expressing various genetically encoded calcium indicators and optogenetic tools in individual or sets of neurons. We use these simple procedures to generate multiple constructs within a very short time frame (typically 1-2 days).
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Affiliation(s)
- Eduard Bokman
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yifat Eliezer
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alon Zaslaver
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.
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4
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Medley JC, Hebbar S, Sydzyik JT, Zinovyeva AY. Single nucleotide substitutions effectively block Cas9 and allow for scarless genome editing in Caenorhabditis elegans. Genetics 2022; 220:iyab199. [PMID: 34791245 PMCID: PMC8733430 DOI: 10.1093/genetics/iyab199] [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: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
In Caenorhabditis elegans, germline injection of Cas9 complexes is reliably used to achieve genome editing through homology-directed repair of Cas9-generated DNA breaks. To prevent Cas9 from targeting repaired DNA, additional blocking mutations are often incorporated into homologous repair templates. Cas9 can be blocked either by mutating the PAM sequence that is essential for Cas9 activity or by mutating the guide sequence that targets Cas9 to a specific genomic location. However, it is unclear how many nucleotides within the guide sequence should be mutated, since Cas9 can recognize "off-target" sequences that are imperfectly paired to its guide. In this study, we examined whether single-nucleotide substitutions within the guide sequence are sufficient to block Cas9 and allow for efficient genome editing. We show that a single mismatch within the guide sequence effectively blocks Cas9 and allows for recovery of edited animals. Surprisingly, we found that a low rate of edited animals can be recovered without introducing any blocking mutations, suggesting a temporal block to Cas9 activity in C. elegans. Furthermore, we show that the maternal genome of hermaphrodite animals is preferentially edited over the paternal genome. We demonstrate that maternally provided haplotypes can be selected using balancer chromosomes and propose a method of mutant isolation that greatly reduces screening efforts postinjection. Collectively, our findings expand the repertoire of genome editing strategies in C. elegans and demonstrate that extraneous blocking mutations are not required to recover edited animals when the desired mutation is located within the guide sequence.
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Affiliation(s)
- Jeffrey C Medley
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Joel T Sydzyik
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
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5
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Hahnel SR, Dilks CM, Heisler I, Andersen EC, Kulke D. Caenorhabditis elegans in anthelmintic research - Old model, new perspectives. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:237-248. [PMID: 33249235 PMCID: PMC7704361 DOI: 10.1016/j.ijpddr.2020.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/13/2022]
Abstract
For more than four decades, the free-living nematode Caenorhabditis elegans has been extensively used in anthelmintic research. Classic genetic screens and heterologous expression in the C. elegans model enormously contributed to the identification and characterization of molecular targets of all major anthelmintic drug classes. Although these findings provided substantial insights into common anthelmintic mechanisms, a breakthrough in the treatment and control of parasitic nematodes is still not in sight. Instead, we are facing increasing evidence that the enormous diversity within the phylum Nematoda cannot be recapitulated by any single free-living or parasitic species and the development of novel broad-spectrum anthelmintics is not be a simple goal. In the present review, we summarize certain milestones and challenges of the C. elegans model with focus on drug target identification, anthelmintic drug discovery and identification of resistance mechanisms. Furthermore, we present new perspectives and strategies on how current progress in C. elegans research will support future anthelmintic research.
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Affiliation(s)
| | - Clayton M Dilks
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
| | | | - Erik C Andersen
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
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6
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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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7
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Mullen RD, Ontiveros AE, Moses MM, Behringer RR. AMH and AMHR2 mutations: A spectrum of reproductive phenotypes across vertebrate species. Dev Biol 2019; 455:1-9. [PMID: 31301298 PMCID: PMC6754765 DOI: 10.1016/j.ydbio.2019.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/04/2019] [Accepted: 07/09/2019] [Indexed: 01/02/2023]
Abstract
Anti-Müllerian hormone (AMH) is a member of the Transforming Growth Factor-β family of secreted signaling proteins. AMH is expressed in Sertoli cells of the fetal and adult testes and granulosa cells of the postnatal ovary. AMH is required for the regression of the Müllerian ducts in mammalian fetuses during male differentiation. AMH signals through its Type II receptor, AMHR2. AMHR2 is expressed in mesenchyme adjacent to the Müllerian ducts, and in Sertoli, Leydig, and granulosa cells. Although AMH and AMHR2 genes have been identified in numerous vertebrate species, spontaneous or engineered mutations or variants have been found or created in only a few mammals and teleost fishes. AMH or AMHR2 mutations in mammals lead to the development of Persistent Müllerian Duct Syndrome (PMDS), a recessive condition in which affected males are fully virilized but retain Müllerian duct-derived tissues, including a uterus and oviducts, and in human and dog, undescended testes. Amh mutant female mice had accelerated ovarian primordial follicle recruitment, suggesting a role for AMH in regulating germ cells. amh and amhr2 mutations have also been experimentally generated in various teleost fishes. Depending on the fish species, loss of AMH signaling results in infertility, germ cell tumors, or male-to-female sex reversal. Here we compare the spectrum of phenotypes caused by AMH and AMHR2 mutations in a variety of vertebrate species. There are both common and unique phenotypes between species, highlighting the range of biological processes regulated by AMH signaling.
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Affiliation(s)
- Rachel D Mullen
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alejandra E Ontiveros
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Malcolm M Moses
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, 77030, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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8
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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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9
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Patel DS, Xu N, Lu H. Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans. Lab Anim (NY) 2019; 48:207-216. [PMID: 31217565 DOI: 10.1038/s41684-019-0326-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/17/2019] [Indexed: 11/09/2022]
Abstract
Deep phenotyping is an emerging conceptual paradigm and experimental approach aimed at measuring and linking many aspects of a phenotype to understand its underlying biology. To date, deep phenotyping has been applied mostly in cultured cells and used less in multicellular organisms. However, in the past decade, it has increasingly been recognized that deep phenotyping could lead to a better understanding of how genetics, environment and stochasticity affect the development, physiology and behavior of an organism. The nematode Caenorhabditis elegans is an invaluable model system for studying how genes affect a phenotypic trait, and new technologies have taken advantage of the worm's physical attributes to increase the throughput and informational content of experiments. Coupling of these technical advancements with computational and analytical tools has enabled a boom in deep-phenotyping studies of C. elegans. In this Review, we highlight how these new technologies and tools are digging into the biological origins of complex, multidimensional phenotypes.
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Affiliation(s)
- Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nan Xu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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10
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Paschinger K, Yan S, Wilson IBH. N-glycomic Complexity in Anatomical Simplicity: Caenorhabditis elegans as a Non-model Nematode? Front Mol Biosci 2019; 6:9. [PMID: 30915340 PMCID: PMC6422873 DOI: 10.3389/fmolb.2019.00009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/12/2019] [Indexed: 12/28/2022] Open
Abstract
Caenorhabditis elegans is a genetically well-studied model nematode or "worm"; however, its N-glycomic complexity is actually baffling and still not completely unraveled. Some features of its N-glycans are, to date, unique and include bisecting galactose and up to five fucose residues associated with the asparagine-linked Man2-3GlcNAc2 core; the substitutions include galactosylation of fucose, fucosylation of galactose and methylation of mannose or fucose residues as well as phosphorylcholine on antennal (non-reducing) N-acetylglucosamine. Only some of these modifications are shared with various other nematodes, while others have yet to be detected in any other species. Thus, C. elegans can be used as a model for some aspects of N-glycan function, but its glycome is far from identical to those of other organisms and is actually far from simple. Possibly the challenges of its native environment, which differ from those of parasitic or necromenic species, led to an anatomically simple worm possessing a complex glycome.
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Affiliation(s)
| | - Shi Yan
- Institut für Parasitologie, Veterinärmedizinische Universität, Wien, Austria
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11
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Hodgens C, Nimchuk ZL, Kieber JJ. indCAPS: A tool for designing screening primers for CRISPR/Cas9 mutagenesis events. PLoS One 2017; 12:e0188406. [PMID: 29141013 PMCID: PMC5687723 DOI: 10.1371/journal.pone.0188406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/06/2017] [Indexed: 11/25/2022] Open
Abstract
Genetic manipulation of organisms using CRISPR/Cas9 technology generally produces small insertions/deletions (indels) that can be difficult to detect. Here, we describe a technique to easily and rapidly identify such indels. Sequence-identified mutations that alter a restriction enzyme recognition site can be readily distinguished from wild-type alleles using a cleaved amplified polymorphic sequence (CAPS) technique. If a restriction site is created or altered by the mutation such that only one allele contains the restriction site, a polymerase chain reaction (PCR) followed by a restriction digest can be used to distinguish the two alleles. However, in the case of most CRISPR-induced alleles, no such restriction sites are present in the target sequences. In this case, a derived CAPS (dCAPS) approach can be used in which mismatches are purposefully introduced in the oligonucleotide primers to create a restriction site in one, but not both, of the amplified templates. Web-based tools exist to aid dCAPS primer design, but when supplied sequences that include indels, the current tools often fail to suggest appropriate primers. Here, we report the development of a Python-based, species-agnostic web tool, called indCAPS, suitable for the design of PCR primers used in dCAPS assays that is compatible with indels. This tool should have wide utility for screening editing events following CRISPR/Cas9 mutagenesis as well as for identifying specific editing events in a pool of CRISPR-mediated mutagenesis events. This tool was field-tested in a CRISPR mutagenesis experiment targeting a cytokinin receptor (AHK3) in Arabidopsis thaliana. The tool suggested primers that successfully distinguished between wild-type and edited alleles of a target locus and facilitated the isolation of two novel ahk3 null alleles. Users can access indCAPS and design PCR primers to employ dCAPS to identify CRISPR/Cas9 alleles at http://indcaps.kieber.cloudapps.unc.edu/.
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Affiliation(s)
- Charles Hodgens
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Zachary L. Nimchuk
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Joseph J. Kieber
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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