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Herrera Sandoval C, Borchers C, Aoki ST. An effective Caenorhabditis elegans CRISPR training module for high school and undergraduate summer research experiences in molecular biology. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024. [PMID: 39072870 DOI: 10.1002/bmb.21856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 06/21/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
Engaging in research experiences as a high school or undergraduate student interested in science, technology, engineering, and mathematics (STEM) is pivotal for their academic and professional development. A structured teaching framework can help cultivate a student's curiosity and passion for learning and research. In this study, an eight-week training program was created to encompass fundamental molecular biology principles and hands-on laboratory activities. This curriculum focuses on using clustered regularly interspaced short palindromic repeats (CRISPR) gene editing in the Caenorhabditis elegans model organism. Through pre- and post-program assessments, enhancements in students' molecular biology proficiency and enthusiasm for scientific exploration were observed. Overall, this training module demonstrated its accessibility and ability to engage inexperienced students in molecular biology and gene editing methodologies.
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Affiliation(s)
- Carmen Herrera Sandoval
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
- Indiana BioMedical Gateway (IBMG) Program, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
| | - Christopher Borchers
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
- Indiana BioMedical Gateway (IBMG) Program, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
| | - Scott T Aoki
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
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Szabała BM, Święcicka M, Łyżnik LA. Microinjection of the CRISPR/Cas9 editing system through the germ pore of a wheat microspore induces mutations in the target Ms2 gene. Mol Biol Rep 2024; 51:706. [PMID: 38824203 DOI: 10.1007/s11033-024-09644-w] [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: 04/03/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Microinjection is a direct procedure for delivering various compounds via micropipette into individual cells. Combined with the CRISPR/Cas9 editing technology, it has been used to produce genetically engineered animal cells. However, genetic micromanipulation of intact plant cells has been a relatively unexplored area of research, partly due to the cytological characteristics of these cells. This study aimed to gain insight into the genetic micromanipulation of wheat microspores using microinjection procedures combined with the CRISPR/Cas9 editing system targeting the Ms2 gene. METHODS AND RESULTS Microspores were first reprogrammed by starvation and heat shock treatment to make them structurally suitable for microinjection. The large central vacuole was fragmented and the nucleus with cytoplasm was positioned in the center of the cell. This step and an additional maltose gradient provided an adequate source of intact single cells in the three wheat genotypes. The microcapillary was inserted into the cell through the germ pore to deliver a working solution with a fluorescent marker. This procedure was much more efficient and less harmful to the microspore than inserting the microcapillary through the cell wall. The CRISPR/Cas9 binary vectors injected into reprogrammed microspores induced mutations in the target Ms2 gene with deletions ranging from 1 to 16 bp. CONCLUSIONS This is the first report of successful genome editing in an intact microspore/wheat cell using the microinjection technique and the CRISPR/Cas9 editing system. The study presented offers a range of molecular and cellular biology tools that can aid in genetic micromanipulation and single-cell analysis.
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Affiliation(s)
- Bartosz M Szabała
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland.
| | - Magdalena Święcicka
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland
| | - Leszek A Łyżnik
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland
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Mauro MS, Martin SL, Dumont J, Shirasu-Hiza M, Canman JC. Patterning, regulation, and role of FoxO/DAF-16 in the early embryo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.594029. [PMID: 38798632 PMCID: PMC11118310 DOI: 10.1101/2024.05.13.594029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Insulin resistance and diabetes are associated with many health issues including higher rates of birth defects and miscarriage during pregnancy. Because insulin resistance and diabetes are both associated with obesity, which also affects fertility, the role of insulin signaling itself in embryo development is not well understood. A key downstream target of the insulin/insulin-like growth factor signaling (IIS) pathway is the forkhead family transcription factor FoxO (DAF-16 in C. elegans ). Here, we used quantitative live imaging to measure the patterning of endogenously tagged FoxO/DAF-16 in the early worm embryo. In 2-4-cell stage embryos, FoxO/DAF-16 initially localized uniformly to all cell nuclei, then became dramatically enriched in germ precursor cell nuclei beginning at the 8-cell stage. This nuclear enrichment in early germ precursor cells required germ fate specification, PI3K (AGE-1)- and PTEN (DAF-18)-mediated phospholipid regulation, and the deubiquitylase USP7 (MATH-33), yet was unexpectedly insulin receptor (DAF-2)- and AKT-independent. Functional analysis revealed that FoxO/DAF-16 acts as a cell cycle pacer for early cleavage divisions-without FoxO/DAF-16 cell cycles were shorter than in controls, especially in germ lineage cells. These results reveal the germ lineage specific patterning, upstream regulation, and cell cycle role for FoxO/DAF-16 during early C. elegans embryogenesis.
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Lima L, Berni M, Mota J, Bressan D, Julio A, Cavalcante R, Macias V, Li Z, Rasgon JL, Bier E, Araujo H. Gene Editing in the Chagas Disease Vector Rhodnius prolixus by Cas9-Mediated ReMOT Control. CRISPR J 2024; 7:88-99. [PMID: 38564197 DOI: 10.1089/crispr.2023.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Rhodnius prolixus is currently the model vector of choice for studying Chagas disease transmission, a debilitating disease caused by Trypanosoma cruzi parasites. However, transgenesis and gene editing protocols to advance the field are still lacking. Here, we tested protocols for the maternal delivery of CRISPR-Cas9 (clustered regularly spaced palindromic repeats/Cas-9 associated) elements to developing R. prolixus oocytes and strategies for the identification of insertions and deletions (indels) in target loci of resulting gene-edited generation zero (G0) nymphs. We demonstrate successful gene editing of the eye color markers Rp-scarlet and Rp-white, and the cuticle color marker Rp-yellow, with highest effectiveness obtained using Receptor-Mediated Ovary Transduction of Cargo (ReMOT Control) with the ovary-targeting BtKV ligand. These results provide proof of concepts for generating somatic mutations in R. prolixus and potentially for generating germ line-edited lines in triatomines, laying the foundation for gene editing protocols that could lead to the development of novel control strategies for vectors of Chagas disease.
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Affiliation(s)
- Leonardo Lima
- Program in Cell and Developmental Biology, Institute for Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil, Rio de Janeiro, Brazil
| | - Mateus Berni
- Program in Cell and Developmental Biology, Institute for Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil, Rio de Janeiro, Brazil
| | - Jamile Mota
- Program in Cell and Developmental Biology, Institute for Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil, Rio de Janeiro, Brazil
| | - Daniel Bressan
- Program in Cell and Developmental Biology, Institute for Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil, Rio de Janeiro, Brazil
| | - Alison Julio
- Program in Cell and Developmental Biology, Institute for Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil, Rio de Janeiro, Brazil
| | - Robson Cavalcante
- Program in Cell and Developmental Biology, Institute for Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil, Rio de Janeiro, Brazil
| | - Vanessa Macias
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
| | - Zhiqian Li
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
| | - Jason L Rasgon
- Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
| | - Helena Araujo
- Program in Cell and Developmental Biology, Institute for Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil
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Binti S, Edeen PT, Fay DS. Loss of the Na + /K + cation pump CATP-1 suppresses nekl -associated molting defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585189. [PMID: 38559007 PMCID: PMC10979969 DOI: 10.1101/2024.03.15.585189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The conserved C. elegans protein kinases NEKL-2 and NEKL-3 regulate multiple steps of membrane trafficking and are required for larval molting. Through a forward genetic screen we identified a loss-of-function mutation in catp-1 as a suppressor of molting defects in synthetically lethal nekl-2; nekl-3 double mutants. catp-1 is predicted to encode a membrane- associated P4-type ATPase involved in Na + -K + exchange. Moreover, a mutation predicted to abolish CATP-1 ion-pump activity also suppressed nekl-2; nekl-3 mutants. Endogenously tagged CATP-1 was primarily expressed in epidermal (hypodermal) cells within punctate structures located at or near the apical plasma membrane. Through whole genome sequencing, we identified two additional nekl-2; nekl-3 suppressor strains containing coding-altering mutations in catp-1 but found that neither mutation, when introduced into nekl-2; nekl-3 mutants using CRISPR methods, was sufficient to elicit robust suppression of molting defects. Our data also suggested that the two catp-1 isoforms, catp-1a and catp-1b , may in some contexts be functionally redundant. On the basis of previously published studies, we tested the hypothesis that loss of catp-1 may suppress nekl -associated defects by inducing partial entry into the dauer pathway. Contrary to expectations, however, we failed to obtain evidence that loss of catp-1 suppresses nekl-2; nekl-3 defects through a dauer-associated mechanism or that loss of catp-1 leads to entry into the pre-dauer L2d stage. As such, loss of catp-1 may suppress nekl- associated molting and membrane trafficking defects by altering electrochemical gradients within membrane-bound compartments.
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De Saeger J, Coulembier Vandelannoote E, Lee H, Park J, Blomme J. Genome editing in macroalgae: advances and challenges. Front Genome Ed 2024; 6:1380682. [PMID: 38516199 PMCID: PMC10955705 DOI: 10.3389/fgeed.2024.1380682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
This minireview examines the current state and challenges of genome editing in macroalgae. Despite the ecological and economic significance of this group of organisms, genome editing has seen limited applications. While CRISPR functionality has been established in two brown (Ectocarpus species 7 and Saccharina japonica) and one green seaweed (Ulva prolifera), these studies are limited to proof-of-concept demonstrations. All studies also (co)-targeted ADENINE PHOSPHORIBOSYL TRANSFERASE to enrich for mutants, due to the relatively low editing efficiencies. To advance the field, there should be a focus on advancing auxiliary technologies, particularly stable transformation, so that novel editing reagents can be screened for their efficiency. More work is also needed on understanding DNA repair in these organisms, as this is tightly linked with the editing outcomes. Developing efficient genome editing tools for macroalgae will unlock the ability to characterize their genes, which is largely uncharted terrain. Moreover, given their economic importance, genome editing will also impact breeding campaigns to develop strains that have better yields, produce more commercially valuable compounds, and show improved resilience to the impacts of global change.
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Affiliation(s)
- Jonas De Saeger
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Emma Coulembier Vandelannoote
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hojun Lee
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jihae Park
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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Schwartz HT, Tan CH, Peraza J, Raymundo KLT, Sternberg PW. Molecular identification of a peroxidase gene controlling body size in the entomopathogenic nematode Steinernema hermaphroditum. Genetics 2024; 226:iyad209. [PMID: 38078889 DOI: 10.1093/genetics/iyad209] [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: 11/10/2023] [Accepted: 12/01/2023] [Indexed: 02/08/2024] Open
Abstract
The entomopathogenic nematode Steinernema hermaphroditum was recently rediscovered and is being developed as a genetically tractable experimental system for the study of previously unexplored biology, including parasitism of its insect hosts and mutualism with its bacterial endosymbiont Xenorhabdus griffiniae. Through whole-genome re-sequencing and genetic mapping we have for the first time molecularly identified the gene responsible for a mutationally defined phenotypic locus in an entomopathogenic nematode. In the process we observed an unexpected mutational spectrum following ethyl methansulfonate mutagenesis in this species. We find that the ortholog of the essential Caenorhabditis elegans peroxidase gene skpo-2 controls body size and shape in S. hermaphroditum. We confirmed this identification by generating additional loss-of-function mutations in the gene using CRISPR-Cas9. We propose that the identification of skpo-2 will accelerate gene targeting in other Steinernema entomopathogenic nematodes used commercially in pest control, as skpo-2 is X-linked and males hemizygous for loss of its function can mate, making skpo-2 an easily recognized and maintained marker for use in co-CRISPR.
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Affiliation(s)
- Hillel T Schwartz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chieh-Hsiang Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jackeline Peraza
- Department of Biology, Barnard College of Columbia University, NewYork, NY 10027, USA
| | | | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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De Rouck S, Mocchetti A, Dermauw W, Van Leeuwen T. SYNCAS: Efficient CRISPR/Cas9 gene-editing in difficult to transform arthropods. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 165:104068. [PMID: 38171463 DOI: 10.1016/j.ibmb.2023.104068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
The genome editing technique CRISPR/Cas9 has led to major advancements in many research fields and this state-of-the-art tool has proven its use in genetic studies for various arthropods. However, most transformation protocols rely on microinjection of CRISPR/Cas9 components into embryos, a method which is challenging for many species. Alternatively, injections can be performed on adult females, but transformation efficiencies can be very low as was shown for the two-spotted spider mite, Tetranychus urticae, a minute but important chelicerate pest on many crops. In this study, we explored different CRISPR/Cas9 formulations to optimize a maternal injection protocol for T. urticae. We observed a strong synergy between branched amphipathic peptide capsules and saponins, resulting in a significant increase of CRISPR/Cas9 knock-out efficiency, exceeding 20%. This CRISPR/Cas9 formulation, termed SYNCAS, was used to knock-out different T. urticae genes - phytoene desaturase, CYP384A1 and Antennapedia - but also allowed to develop a co-CRISPR strategy and facilitated the generation of T. urticae knock-in mutants. In addition, SYNCAS was successfully applied to knock-out white and white-like genes in the western flower thrips, Frankliniella occidentalis. The SYNCAS method allows routine genome editing in these species and can be a game changer for genetic research in other hard to transform arthropods.
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Affiliation(s)
- Sander De Rouck
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Antonio Mocchetti
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Belgium.
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Belgium.
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Chen L, Zhang S, Liu S, Gao S. Amyotrophic Lateral Sclerosis Mechanism: Insights from the Caenorhabditis elegans Models. Cells 2024; 13:99. [PMID: 38201303 PMCID: PMC10778397 DOI: 10.3390/cells13010099] [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: 11/06/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a debilitating neurodegenerative condition characterized by the progressive degeneration of motor neurons. Despite extensive research in various model animals, the cellular signal mechanisms of ALS remain elusive, impeding the development of efficacious treatments. Among these models, a well-characterized and diminutive organism, Caenorhabditis elegans (C. elegans), has emerged as a potent tool for investigating the molecular and cellular dimensions of ALS pathogenesis. This review summarizes the contributions of C. elegans models to our comprehension of ALS, emphasizing pivotal findings pertaining to genetics, protein aggregation, cellular pathways, and potential therapeutic strategies. We analyze both the merits and constraints of the C. elegans system in the realm of ALS research and point towards future investigations that could bridge the chasm between C. elegans foundational discoveries and clinical applications.
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Affiliation(s)
| | | | | | - Shangbang Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (L.C.); (S.Z.); (S.L.)
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Wong CH, Rahat A, Chang HC. Fused in sarcoma regulates glutamate signaling and oxidative stress response. Free Radic Biol Med 2024; 210:172-182. [PMID: 38007141 PMCID: PMC10872661 DOI: 10.1016/j.freeradbiomed.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/21/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023]
Abstract
Mutations in fused in sarcoma (fust-1) are linked to ALS. However, how these ALS causative mutations alter physiological processes and lead to the onset of ALS remains largely unknown. By obtaining humanized fust-1 ALS mutations via CRISPR-CAS9, we generated a C. elegans ALS model. Homozygous fust-1 ALS mutant and fust-1 deletion animals are viable in C. elegans. This allows us to better characterize the molecular mechanisms of fust-1-dependent responses. We found FUST-1 plays a role in regulating superoxide dismutase, glutamate signaling, and oxidative stress. FUST-1 suppresses SOD-1 and VGLUT/EAT-4 in the nervous system. FUST-1 also regulates synaptic AMPA-type glutamate receptor GLR-1. We found that fust-1 ALS mutations act as loss-of-function in SOD-1 and VGLUT/EAT-4 phenotypes, whereas the fust-1 ALS mutations act as gain-of-function in redox homeostasis and the microbe-induced oxidative stress response. We hypothesized that FUST-1 is a link between glutamate signaling and SOD-1. Our results may provide new insights into the human ALS alleles and their roles in pathological mechanisms that lead to ALS.
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Affiliation(s)
- Chiong-Hee Wong
- Department of Emergency Medicine, MacKay Memorial Hospital, Taipei, 104217, Taiwan
| | - Abu Rahat
- Integrative Neuroscience Program, SUNY Binghamton, Vestal, NY, 13850, USA
| | - Howard C Chang
- Department of Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, NJ, 08084, USA.
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Cevik S, Zhao P, Zorluer A, Pir MS, Bian W, Kaplan OI. Matching variants for functional characterization of genetic variants. G3 (BETHESDA, MD.) 2023; 13:jkad227. [PMID: 37933433 PMCID: PMC10700107 DOI: 10.1093/g3journal/jkad227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/06/2023] [Indexed: 11/08/2023]
Abstract
Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we used Caenorhabditis elegans mutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carrying C. elegans mutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors into cilia. Functional analysis of all 10 variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of nonciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic in C. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9.
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Affiliation(s)
- Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | - Pei Zhao
- School of Applied Science and Engineering, Fuzhou Institute of Technology, Fuzhou 350014, China
- SunyBiotech Co., Ltd., Fuzhou 35000, China
| | - Atiyye Zorluer
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | - Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | | | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
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Cao M. CRISPR-Cas9 genome editing in Steinernema entomopathogenic nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.24.568619. [PMID: 38045388 PMCID: PMC10690278 DOI: 10.1101/2023.11.24.568619] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Molecular tool development in traditionally non-tractable animals opens new avenues to study gene functions in the relevant ecological context. Entomopathogenic nematodes (EPN) Steinernema and their symbiotic bacteria of Xenorhabdus spp are a valuable experimental system in the laboratory and are applicable in the field to promote agricultural productivity. The infective juvenile (IJ) stage of the nematode packages mutualistic symbiotic bacteria in the intestinal pocket and invades insects that are agricultural pests. The lack of consistent and heritable genetics tools in EPN targeted mutagenesis severely restricted the study of molecular mechanisms underlying both parasitic and mutualistic interactions. Here, I report a protocol for CRISPR-Cas9 based genome-editing that is successful in two EPN species, S. carpocapsae and S. hermaphroditum . I adapted a gonadal microinjection technique in S. carpocapsae , which created on-target modifications of a homologue Sc-dpy-10 (cuticular collagen) by homology-directed repair. A similar delivery approach was used to introduce various alleles in S. hermaphroditum including Sh-dpy-10 and Sh-unc-22 (a muscle gene), resulting in visible and heritable phenotypes of dumpy and twitching, respectively. Using conditionally dominant alleles of Sh-unc-22 as a co-CRISPR marker, I successfully modified a second locus encoding Sh-Daf-22 (a homologue of human sterol carrier protein SCPx), predicted to function as a core enzyme in the biosynthesis of nematode pheromone that is required for IJ development. As a proof of concept, Sh-daf-22 null mutant showed IJ developmental defects in vivo ( in insecta) . This research demonstrates that Steinernema spp are highly tractable for targeted mutagenesis and has great potential in the study of gene functions under controlled laboratory conditions within the relevant context of its ecological niche.
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Clark B, Kuwalekar M, Fischer B, Woltering J, Biran J, Juntti S, Kratochwil CF, Santos ME, Almeida MV. Genome editing in East African cichlids and tilapias: state-of-the-art and future directions. Open Biol 2023; 13:230257. [PMID: 38018094 PMCID: PMC10685126 DOI: 10.1098/rsob.230257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.
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Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Muktai Kuwalekar
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Joost Woltering
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg 78457, Germany
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Scott Juntti
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Claudius F. Kratochwil
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | | | - Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
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14
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Fung W, Tan TM, Kolotuev I, Heiman MG. A sex-specific switch in a single glial cell patterns the apical extracellular matrix. Curr Biol 2023; 33:4174-4186.e7. [PMID: 37708887 PMCID: PMC10578079 DOI: 10.1016/j.cub.2023.08.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/17/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
Apical extracellular matrix (aECM) constitutes the interface between every tissue and the outside world. It is patterned into diverse tissue-specific structures through unknown mechanisms. Here, we show that a male-specific genetic switch in a single C. elegans glial cell patterns the overlying aECM from a solid sheet to an ∼200 nm pore, thus allowing a male sensory neuron to access the environment. Using cell-specific genetic sex reversal, we find that this switch reflects an inherent sex difference in the glial cell that is independent of the sex identity of the surrounding neurons. Through candidate and unbiased genetic screens, we find that this glial sex difference is controlled by factors shared with neurons (mab-3, lep-2, and lep-5) as well as previously unidentified regulators whose effects may be glia specific (nfya-1, bed-3, and jmjd-3.1). The switch results in male-specific glial expression of a secreted Hedgehog-related protein, GRL-18, that we discover localizes to transient nanoscale rings at sites where aECM pores will form. Using electron microscopy, we find that blocking male-specific gene expression in glia prevents pore formation, whereas forcing male-specific glial gene expression induces an ectopic pore. Thus, a switch in gene expression in a single cell is necessary and sufficient to pattern aECM into a specific structure. Our results highlight that aECM is not a simple homogeneous meshwork, but instead is composed of discrete local features that reflect the identity of the underlying cells.
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Affiliation(s)
- Wendy Fung
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Taralyn M Tan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, 1015 Lausanne, Switzerland
| | - Maxwell G Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA.
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15
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Gibney TV, Favichia M, Latifi L, Medwig-Kinney TN, Matus DQ, McIntyre DC, Arrigo AB, Branham KR, Bubrig LT, Ghaddar A, Jiranek JA, Liu KE, Marcucci CG, Porter RJ, Pani AM. A simple method to dramatically increase C. elegans germline microinjection efficiency. Dev Biol 2023; 502:63-67. [PMID: 37433390 PMCID: PMC10559938 DOI: 10.1016/j.ydbio.2023.07.003] [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: 04/19/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Genome manipulation methods in C. elegans require microinjecting DNA or ribonucleoprotein complexes into the microscopic core of the gonadal syncytium. These microinjections are technically demanding and represent a key bottleneck for all genome engineering and transgenic approaches in C. elegans. While there have been steady improvements in the ease and efficiency of genetic methods for C. elegans genome manipulation, there have not been comparable advances in the physical process of microinjection. Here, we report a simple and inexpensive method for handling worms using a paintbrush during the injection process that nearly tripled average microinjection rates compared to traditional worm handling methods. We found that the paintbrush increased injection throughput by substantially increasing both injection speeds and post-injection survival rates. In addition to dramatically and universally increasing injection efficiency for experienced personnel, the paintbrush method also significantly improved the abilities of novice investigators to perform key steps in the microinjection process. We expect that this method will benefit the C. elegans community by increasing the speed at which new strains can be generated and will also make microinjection-based approaches less challenging and more accessible to personnel and labs without extensive experience.
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Affiliation(s)
- Theresa V Gibney
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
| | - Michelle Favichia
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Laila Latifi
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - David Q Matus
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Daniel C McIntyre
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Angelo B Arrigo
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Kendall R Branham
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Louis T Bubrig
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Abbas Ghaddar
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Juliana A Jiranek
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Kendra E Liu
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | - Charles G Marcucci
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Robert J Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Ariel M Pani
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.
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16
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Price IF, Wagner JA, Pastore B, Hertz HL, Tang W. C. elegans germ granules sculpt both germline and somatic RNAome. Nat Commun 2023; 14:5965. [PMID: 37749091 PMCID: PMC10520050 DOI: 10.1038/s41467-023-41556-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
Germ granules are membrane-less organelles essential for small RNA biogenesis and germline development. Among the conserved properties of germ granules is their association with the nuclear membrane. Recent studies demonstrated that LOTUS domain proteins, EGGD-1 and EGGD-2 (also known as MIP-1 and MIP-2 respectively), promote the formation of perinuclear germ granules in C. elegans. This finding presents a unique opportunity to evaluate the significance of perinuclear localization of germ granules. Here we show that loss of eggd-1 causes the coalescence of germ granules and formation of abnormal cytoplasmic aggregates. Impairment of perinuclear granules affects certain germline classes of small RNAs including Piwi-interacting RNAs. Transcriptome profiling reveals overexpression of spermatogenic and cuticle-related genes in eggd-1 hermaphrodites. We further demonstrate that disruption of germ granules activates HLH-30-mediated transcriptional program in somatic tissues. Collectively, our findings underscore the essential role of EGGD-1 in germ granule organization and reveal an unexpected germ granule-to-soma communication.
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Affiliation(s)
- Ian F Price
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Jillian A Wagner
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hannah L Hertz
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
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17
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Wit J, Dilks CM, Zhang G, Guisbert KSK, Zdraljevic S, Guisbert E, Andersen EC. Praziquantel inhibits Caenorhabditis elegans development and species-wide differences might be cct-8-dependent. PLoS One 2023; 18:e0286473. [PMID: 37561720 PMCID: PMC10414639 DOI: 10.1371/journal.pone.0286473] [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: 04/24/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Anthelmintic drugs are used to treat parasitic roundworm and flatworm infections in humans and other animals. Caenorhabditis elegans is an established model to investigate anthelmintics used to treat roundworms. In this study, we use C. elegans to examine the mode of action and the mechanisms of resistance against the flatworm anthelmintic drug praziquantel (PZQ), used to treat trematode and cestode infections. We found that PZQ inhibited development and that this developmental delay varies by genetic background. Interestingly, both enantiomers of PZQ are equally effective against C. elegans, but the right-handed PZQ (R-PZQ) is most effective against schistosome infections. We conducted a genome-wide association mapping with 74 wild C. elegans strains to identify a region on chromosome IV that is correlated with differential PZQ susceptibility. Five candidate genes in this region: cct-8, znf-782, Y104H12D.4, Y104H12D.2, and cox-18, might underlie this variation. The gene cct-8, a subunit of the protein folding complex TRiC, has variation that causes a putative protein coding change (G226V), which is correlated with reduced developmental delay. Gene expression analysis suggests that this variant correlates with slightly increased expression of both cct-8 and hsp-70. Acute exposure to PZQ caused increased expression of hsp-70, indicating that altered TRiC function might be involved in PZQ responses. To test if this variant affects development upon exposure to PZQ, we used CRISPR-Cas9 genome editing to introduce the V226 allele into the N2 genetic background (G226) and the G226 allele into the JU775 genetic background (V226). These experiments revealed that this variant was not sufficient to explain the effects of PZQ on development. Nevertheless, this study shows that C. elegans can be used to study PZQ mode of action and resistance mechanisms. Additionally, we show that the TRiC complex requires further evaluation for PZQ responses in C. elegans.
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Affiliation(s)
- Janneke Wit
- Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
| | - Clayton M. Dilks
- Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States of America
| | - Gaotian Zhang
- Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
| | - Karen S. Kim Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Stefan Zdraljevic
- Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States of America
| | - Eric Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Erik C. Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
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18
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Brocal-Ruiz R, Esteve-Serrano A, Mora-Martínez C, Franco-Rivadeneira ML, Swoboda P, Tena JJ, Vilar M, Flames N. Forkhead transcription factor FKH-8 cooperates with RFX in the direct regulation of sensory cilia in Caenorhabditis elegans. eLife 2023; 12:e89702. [PMID: 37449480 PMCID: PMC10393296 DOI: 10.7554/elife.89702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Cilia, either motile or non-motile (a.k.a primary or sensory), are complex evolutionarily conserved eukaryotic structures composed of hundreds of proteins required for their assembly, structure and function that are collectively known as the ciliome. Ciliome gene mutations underlie a group of pleiotropic genetic diseases known as ciliopathies. Proper cilium function requires the tight coregulation of ciliome gene transcription, which is only fragmentarily understood. RFX transcription factors (TF) have an evolutionarily conserved role in the direct activation of ciliome genes both in motile and non-motile cilia cell-types. In vertebrates, FoxJ1 and FoxN4 Forkhead (FKH) TFs work with RFX in the direct activation of ciliome genes, exclusively in motile cilia cell-types. No additional TFs have been described to act together with RFX in primary cilia cell-types in any organism. Here we describe FKH-8, a FKH TF, as a direct regulator of the sensory ciliome genes in Caenorhabditis elegans. FKH-8 is expressed in all ciliated neurons in C. elegans, binds the regulatory regions of ciliome genes, regulates ciliome gene expression, cilium morphology and a wide range of behaviors mediated by sensory ciliated neurons. FKH-8 and DAF-19 (C. elegans RFX) physically interact and synergistically regulate ciliome gene expression. C. elegans FKH-8 function can be replaced by mouse FOXJ1 and FOXN4 but not by other members of other mouse FKH subfamilies. In conclusion, RFX and FKH TF families act jointly as direct regulators of ciliome genes also in sensory ciliated cell types suggesting that this regulatory logic could be an ancient trait predating functional cilia sub-specialization.
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Affiliation(s)
- Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Ainara Esteve-Serrano
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | | | - Peter Swoboda
- Department of Biosciences and Nutrition. Karolinska Institute. Campus FlemingsbergStockholmSweden
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de OlavideSevilleSpain
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
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19
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Kukhtar D, Fussenegger M. Synthetic biology in multicellular organisms: Opportunities in nematodes. Biotechnol Bioeng 2023. [PMID: 37448225 DOI: 10.1002/bit.28497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/27/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has mainly focused on introducing new or altered functionality in single cell systems: primarily bacteria, yeast, or mammalian cells. Here, we describe the extension of synthetic biology to nematodes, in particular the well-studied model organism Caenorhabditis elegans, as a convenient platform for developing applications in a multicellular setting. We review transgenesis techniques for nematodes, as well as the application of synthetic biology principles to construct nematode gene switches and genetic devices to control motility. Finally, we discuss potential applications of engineered nematodes.
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Affiliation(s)
- Dmytro Kukhtar
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Faculty of Life Science, University of Basel, Basel, Switzerland
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20
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Nonet ML. Rapid generation of Caenorhabditis elegans single-copy transgenes combining recombination-mediated cassette exchange and drug selection. Genetics 2023; 224:iyad072. [PMID: 37079426 PMCID: PMC10324946 DOI: 10.1093/genetics/iyad072] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
I outline a streamlined method to insert large, single-copy transgenes into the Caenorhabditis elegans genome using recombination-mediated cassette exchange (RMCE) that relies solely on drug selection yielding a homozygous fluorescent protein (FP) marked transgene in 3 generations (8 days) at high efficiency (>1 insertion per 2 injected P0 animals). Landing sites for this approach are available on four chromosomes in several configurations which yield lines marked in distinct cell types. An array of vectors permit creating transgenes using a variety of selection methods (HygR, NeoR, PuroR, and unc-119) that yield lines expressing different colored FPs (BFP, GFP, mNG, and Scarlet). Although these transgenes retain a plasmid backbone and a selection marker, the inclusion of these sequences typically does not alter the expression of several cell-specific promoters tested. However, in certain orientations, promoters exhibit crosstalk with adjacent transcription units. In cases where crosstalk is problematic, the loxP-flanked fluorescent marker, plasmid backbone, and hygR gene can be excised by crossing through germline Cre expressing lines also created using this technique. Finally, genetic and molecular reagents designed to facilitate customization of both targeting vectors and landing sites are also described. Together, the rapid RMCE toolbox provides a platform for developing further innovative uses of RMCE to create complex genetically engineered tools.
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Affiliation(s)
- Michael L Nonet
- Department of Neuroscience, Washington University Medical School, St. Louis, MO 63110, USA
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21
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Mikkelsen NS, Bak RO. Enrichment strategies to enhance genome editing. J Biomed Sci 2023; 30:51. [PMID: 37393268 PMCID: PMC10315055 DOI: 10.1186/s12929-023-00943-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Genome editing technologies hold great promise for numerous applications including the understanding of cellular and disease mechanisms and the development of gene and cellular therapies. Achieving high editing frequencies is critical to these research areas and to achieve the overall goal of being able to manipulate any target with any desired genetic outcome. However, gene editing technologies sometimes suffer from low editing efficiencies due to several challenges. This is often the case for emerging gene editing technologies, which require assistance for translation into broader applications. Enrichment strategies can support this goal by selecting gene edited cells from non-edited cells. In this review, we elucidate the different enrichment strategies, their many applications in non-clinical and clinical settings, and the remaining need for novel strategies to further improve genome research and gene and cellular therapy studies.
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Affiliation(s)
- Nanna S Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark.
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22
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Lins J, Brock TJ, Hopkins CE, Hart AC. Generation of a C. elegans tdp-1 null allele and humanized TARDBP containing human disease-variants. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000693. [PMID: 37351305 PMCID: PMC10282831 DOI: 10.17912/micropub.biology.000693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023]
Abstract
Clinical variants of TARDBP are associated with frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS) and other degenerative diseases. The predicted C. elegans ortholog of TARDBP is encoded by tdp-1 , but functional orthology has not been demonstrated in vivo. We undertook CRISPR/Cas9-based genome editing of the tdp-1 locus to create a complete loss of function allele; all tdp-1 exons and introns were deleted, creating tdp-1(tgx58) , which resulted in neurodegeneration after oxidative stress. Next, we undertook CRISPR-based genome editing to replace tdp-1 exons with human TARDBP coding sequences, creating humanized ( hTARDBP ) C. elegans expressing TDP-43 . Based on the efficiency of this genome editing, we suggest that iterative genome editing of the tdp-1 target locus using linked coCRISPR markers, like dpy-10 , would be a more efficient strategy for sequential assembly of the large engineered transgenes. hTARDBP decreased the neurodegeneration defect of tdp-1(tgx58) , demonstrating functional cross-species orthology. To develop C. elegans models of FTD and ALS, we inserted five different patient TARDBP variants in the C. elegans hTARDBP locus. Only one clinical variant increased stress-induced neurodegeneration; other variants caused inconsistent or negligible defects under these conditions. Combined, this work yielded an unambiguous null allele for tdp-1 , a validated, humanized hTARDBP, and multiple ALS/FTD patient-associated variant models that can be used for future studies.
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Affiliation(s)
- Jeremy Lins
- Department of Neuroscience, Brown University, Providence, RI 02912
| | | | | | - Anne C Hart
- Department of Neuroscience, Brown University, Providence, RI 02912
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23
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Han WK, Tang FX, Gao HL, Wang Y, Yu N, Jiang JJ, Liu ZW. Co-CRISPR: A valuable toolkit for mutation enrichment in the gene editing of Spodoptera frugiperda. INSECT SCIENCE 2023; 30:625-636. [PMID: 36169087 DOI: 10.1111/1744-7917.13122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/28/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
The CRISPR/Cas9 system has been successfully applied in dozens of diverse species; although the screening of successful CRISPR/Cas9 editing events remains particularly laborious, especially for those that occur at relatively low frequency. Recently, a co-CRISPR strategy was proved to enrich the desired CRISPR events. Here, the co-CRISPR strategy was developed in the Fall armyworm, Spodoptera frugiperda, with kynurenine 3-monooxygenase gene (kmo) as a marker. The kmo mosaics induced by single-guide RNAs (sgRNAs)/Cas9 displayed the darker green color phenotype in larvae, compared with wild type (brown), and mosaic-eye adults were significantly acquired from the mosaic larvae group. In the kmo knockout strain, no significant difference was observed in larval development and adult reproduction. Acetylcholinesterase 2 (ace2) and Wnt1 were selected as target genes to construct the co-CRISPR strategy using kmo marker. By co-injection of kmo and ace2 sgRNAs, the mutant efficiency of ace2 was significantly increased in the kmo mosaic (larvae or adults) groups. Similarly, more malformed pupae with Wnt1 mutations were observed in the darker green larvae group. Taken together, these results demonstrated that kmo was a suitable visible marker gene for the application and extension of co-CRISPR strategy in Fall armyworm. Using darker green color in larvae or mosaic-eye in adults from kmo knockout as a marker, the mutant efficiency of a target gene could be enriched in a Fall armyworm group consisting of marked individuals. The co-CRISPR strategy is helpful for gene function studies by the knockout technique with no or lethal phenotypes.
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Affiliation(s)
- Wei-Kang Han
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Feng-Xian Tang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hao-Li Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yan Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Na Yu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jian-Jun Jiang
- Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, China
| | - Ze-Wen Liu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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24
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Higurashi S, Tsukada S, Aleogho BM, Park JH, Al-Hebri Y, Tanaka M, Nakano S, Mori I, Noma K. Bacterial diet affects the age-dependent decline of associative learning in Caenorhabditis elegans. eLife 2023; 12:81418. [PMID: 37252859 DOI: 10.7554/elife.81418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 04/27/2023] [Indexed: 06/01/2023] Open
Abstract
The causality and mechanism of dietary effects on brain aging are still unclear due to the long time scales of aging. The nematode Caenorhabditis elegans has contributed to aging research because of its short lifespan and easy genetic manipulation. When fed the standard laboratory diet, Escherichia coli, C. elegans experiences an age-dependent decline in temperature-food associative learning, called thermotaxis. To address if diet affects this decline, we screened 35 lactic acid bacteria as alternative diet and found that animals maintained high thermotaxis ability when fed a clade of Lactobacilli enriched with heterofermentative bacteria. Among them, Lactobacillus reuteri maintained the thermotaxis of aged animals without affecting their lifespan and motility. The effect of Lb. reuteri depends on the DAF-16 transcription factor functioning in neurons. Furthermore, RNA sequencing analysis revealed that differentially expressed genes between aged animals fed different bacteria were enriched with DAF-16 targets. Our results demonstrate that diet can impact brain aging in a daf-16-dependent manner without changing the lifespan.
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Affiliation(s)
- Satoshi Higurashi
- Milk Science Research Institute, Megmilk Snow Brand Co. Ltd., Saitama, Japan
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Sachio Tsukada
- Milk Science Research Institute, Megmilk Snow Brand Co. Ltd., Saitama, Japan
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Binta Maria Aleogho
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Group of Microbial Motility, Department of Biological Science, Division of Natural Science, Graduate school of Science, Nagoya University, Nagoya, Japan
| | - Joo Hyun Park
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yana Al-Hebri
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Masaru Tanaka
- Milk Science Research Institute, Megmilk Snow Brand Co. Ltd., Saitama, Japan
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Shunji Nakano
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Ikue Mori
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kentaro Noma
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Group of Microbial Motility, Department of Biological Science, Division of Natural Science, Graduate school of Science, Nagoya University, Nagoya, Japan
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25
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Malaiwong N, Porta-de-la-Riva M, Krieg M. FLInt: single shot safe harbor transgene integration via Fluorescent Landmark Interference. G3 (BETHESDA, MD.) 2023; 13:jkad041. [PMID: 36805659 PMCID: PMC10151404 DOI: 10.1093/g3journal/jkad041] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023]
Abstract
The stable incorporation of transgenes and recombinant DNA material into the host genome is a bottleneck in many bioengineering applications. Due to the low efficiency, identifying the transgenic animals is often a needle in the haystack. Thus, optimal conditions require efficient screening procedures, but also known and safe landing sites that do not interfere with host expression, low input material and strong expression from the new locus. Here, we leverage an existing library of ≈300 different loci coding for fluorescent markers that are distributed over all 6 chromosomes in Caenorhabditis elegans as safe harbors for versatile transgene integration sites using CRISPR/Cas9. We demonstrated that a single crRNA was sufficient for cleavage of the target region and integration of the transgene of interest, which can be easily followed by loss of the fluorescent marker. The same loci can also be used for extrachromosomal landing sites and as co-CRISPR markers without affecting body morphology or animal behavior. Thus, our method overcomes the uncertainty of transgene location during random mutagenesis, facilitates easy screening through fluorescence interference and can be used as co-CRISPR markers without further influence in phenotypes.
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Affiliation(s)
| | | | - Michael Krieg
- Corresponding author: Institut de Ciències Fotòniques (ICFO), 08860 Castelldefels, Spain.
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26
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Fok A, Brissette B, Hallacy T, Ahamed H, Ho E, Ramanathan S, Ringstad N. High-fidelity encoding of mechanostimuli by tactile food-sensing neurons requires an ensemble of ion channels. Cell Rep 2023; 42:112452. [PMID: 37119137 DOI: 10.1016/j.celrep.2023.112452] [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: 02/15/2022] [Revised: 02/07/2023] [Accepted: 04/14/2023] [Indexed: 04/30/2023] Open
Abstract
The nematode C. elegans uses mechanosensitive neurons to detect bacteria, which are food for worms. These neurons release dopamine to suppress foraging and promote dwelling. Through a screen of genes highly expressed in dopaminergic food-sensing neurons, we identify a K2P-family potassium channel-TWK-2-that damps their activity. Strikingly, loss of TWK-2 restores mechanosensation to neurons lacking the NOMPC-like channel transient receptor potential 4 (TRP-4), which was thought to be the primary mechanoreceptor for tactile food sensing. The alternate mechanoreceptor mechanism uncovered by TWK-2 mutation requires three Deg/ENaC channel subunits: ASIC-1, DEL-3, and UNC-8. Analysis of cell-physiological responses to mechanostimuli indicates that TRP and Deg/ENaC channels work together to set the range of analog encoding of stimulus intensity and to improve signal-to-noise characteristics and temporal fidelity of food-sensing neurons. We conclude that a specialized mechanosensory modality-tactile food sensing-emerges from coordination of distinct force-sensing mechanisms housed in one type of sensory neuron.
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Affiliation(s)
- Alice Fok
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, and Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Benjamin Brissette
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, and Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Tim Hallacy
- Harvard University, Departments of Molecular and Cell Biology, Stem Cell and Regenerative Biology and Applied Physics, Cambridge, MA 10238, USA
| | - Hassan Ahamed
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, and Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Elver Ho
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, and Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Sharad Ramanathan
- Harvard University, Departments of Molecular and Cell Biology, Stem Cell and Regenerative Biology and Applied Physics, Cambridge, MA 10238, USA
| | - Niels Ringstad
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, and Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA.
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27
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Chen SAA, Kern AF, Ang RML, Xie Y, Fraser HB. Gene-by-environment interactions are pervasive among natural genetic variants. CELL GENOMICS 2023; 3:100273. [PMID: 37082145 PMCID: PMC10112290 DOI: 10.1016/j.xgen.2023.100273] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 10/09/2022] [Accepted: 01/31/2023] [Indexed: 04/22/2023]
Abstract
Gene-by-environment (GxE) interactions, in which a genetic variant's phenotypic effect is condition specific, are fundamental for understanding fitness landscapes and evolution but have been difficult to identify at the single-nucleotide level. Although many condition-specific quantitative trait loci (QTLs) have been mapped, these typically contain numerous inconsequential variants in linkage, precluding understanding of the causal GxE variants. Here, we introduce BARcoded Cas9 retron precise parallel editing via homology (CRISPEY-BAR), a high-throughput precision genome editing strategy, and use it to map GxE interactions of naturally occurring genetic polymorphisms impacting yeast growth. We identified hundreds of GxE variants within condition-specific QTLs, revealing unexpected genetic complexity. Moreover, we found that 93.7% of non-neutral natural variants within ergosterol biosynthesis pathway genes showed GxE interactions, including many impacting antifungal drug resistance through diverse molecular mechanisms. In sum, our results suggest an extremely complex, context-dependent fitness landscape characterized by pervasive GxE interactions while also demonstrating massively parallel genome editing as an effective means for investigating this complexity.
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Affiliation(s)
- Shi-An A. Chen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Alexander F. Kern
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roy Moh Lik Ang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yihua Xie
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Corresponding author
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28
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Gibney TV, Favichia M, Latifi L, Medwig-Kinney TN, Matus DQ, McIntyre DC, Arrigo AB, Branham KR, Bubrig LT, Ghaddar A, Jiranek JA, Liu KE, Marcucci CG, Porter RJ, Pani AM. A simple method to dramatically increase C. elegans germline microinjection efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533855. [PMID: 36993165 PMCID: PMC10055348 DOI: 10.1101/2023.03.23.533855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Genome manipulation methods in C. elegans require microinjecting DNA or ribonucleoprotein complexes into the microscopic core of the gonadal syncytium. These microinjections are technically demanding and represent a key bottleneck for all genome engineering and transgenic approaches in C. elegans . While there have been steady improvements in the ease and efficiency of genetic methods for C. elegans genome manipulation, there have not been comparable advances in the physical process of microinjection. Here, we report a simple and inexpensive method for handling worms using a paintbrush during the injection process that nearly tripled average microinjection rates compared to traditional worm handling methods. We found that the paintbrush increased injection throughput by substantially increasing both injection speeds and post-injection survival rates. In addition to dramatically and universally increasing injection efficiency for experienced personnel, the paintbrush method also significantly improved the abilities of novice investigators to perform key steps in the microinjection process. We expect that this method will benefit the C. elegans community by increasing the speed at which new strains can be generated and will also make microinjection-based approaches less challenging and more accessible to personnel and labs without extensive experience.
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Affiliation(s)
- Theresa V. Gibney
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Michelle Favichia
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Laila Latifi
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - David Q. Matus
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
- David Matus is a paid consultant of Arcadia Science
| | | | - Angelo B. Arrigo
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Louis T. Bubrig
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Abbas Ghaddar
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Kendra E. Liu
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Charles G. Marcucci
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Robert J. Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Ariel M. Pani
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
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29
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Martínez-Fernández C, Jha S, Aliagas E, Holmberg CI, Nadal E, Cerón J. BAP1 Malignant Pleural Mesothelioma Mutations in Caenorhabditis elegans Reveal Synthetic Lethality between ubh-4/ BAP1 and the Proteasome Subunit rpn-9/ PSMD13. Cells 2023; 12:929. [PMID: 36980270 PMCID: PMC10047281 DOI: 10.3390/cells12060929] [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] [Received: 01/16/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
The deubiquitinase BAP1 (BRCA1-associated protein 1) is associated with BAP1 tumor predisposition syndrome (TPDS). BAP1 is a tumor suppressor gene whose alterations in cancer are commonly caused by gene mutations leading to protein loss of function. By CRISPR-Cas, we have generated mutations in ubh-4, the BAP1 ortholog in Caenorhabditis elegans, to model the functional impact of BAP1 mutations. We have found that a mimicked BAP1 cancer missense mutation (UBH-4 A87D; BAP1 A95D) resembles the phenotypes of ubh-4 deletion mutants. Despite ubh-4 being ubiquitously expressed, the gene is not essential for viability and its deletion causes only mild phenotypes without affecting 20S proteasome levels. Such viability facilitated an RNAi screen for ubh-4 genetic interactors that identified rpn-9, the ortholog of human PSMD13, a gene encoding subunit of the regulatory particle of the 26S proteasome. ubh-4[A87D], similarly to ubh-4 deletion, cause a synthetic genetic interaction with rpn-9 inactivation affecting body size, lifespan, and the development of germ cells. Finally, we show how ubh-4 inactivation sensitizes animals to the chemotherapeutic agent Bortezomib, which is a proteasome inhibitor. Thus, we have established a model to study BAP1 cancer-related mutations in C. elegans, and our data points toward vulnerabilities that should be studied to explore therapeutic opportunities within the complexity of BAP1 tumors.
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Affiliation(s)
- Carmen Martínez-Fernández
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Sweta Jha
- Medicum, Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Elisabet Aliagas
- Department of Medical Oncology, Institut Català d’Oncologia (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Carina I. Holmberg
- Medicum, Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Ernest Nadal
- Department of Medical Oncology, Institut Català d’Oncologia (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Preclinical and Experimental Research in Thoracic Tumors (PReTT), Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Julián Cerón
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
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30
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Fung W, Tan TM, Kolotuev I, Heiman MG. A sex-specific switch in a single glial cell patterns the apical extracellular matrix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533199. [PMID: 36993293 PMCID: PMC10055199 DOI: 10.1101/2023.03.17.533199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Apical extracellular matrix (aECM) constitutes the interface between every tissue and the outside world. It is patterned into diverse tissue-specific structures through unknown mechanisms. Here, we show that a male-specific genetic switch in a single C. elegans glial cell patterns the aECM into a ∼200 nm pore, allowing a male sensory neuron to access the environment. We find that this glial sex difference is controlled by factors shared with neurons ( mab-3, lep-2, lep-5 ) as well as previously unidentified regulators whose effects may be glia-specific ( nfya-1, bed-3, jmjd-3.1 ). The switch results in male-specific expression of a Hedgehog-related protein, GRL-18, that we discover localizes to transient nanoscale rings at sites of aECM pore formation. Blocking male-specific gene expression in glia prevents pore formation, whereas forcing male-specific expression induces an ectopic pore. Thus, a switch in gene expression in a single cell is necessary and sufficient to pattern aECM into a specific structure.
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Affiliation(s)
- Wendy Fung
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
| | - Taralyn M. Tan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, 1015 Lausanne, Switzerland
| | - Maxwell G. Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
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31
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Genome editing of the vermilion locus generates a visible eye color marker for Oncopeltus fasciatus. Sci Rep 2023; 13:4188. [PMID: 36918709 PMCID: PMC10015096 DOI: 10.1038/s41598-023-31145-2] [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: 12/20/2022] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Insects display a vast array of eye and body colors. Genes encoding products involved in biosynthesis and deposition of pigments are ideal genetic markers, contributing, for example, to the power of Drosophila genetics. Oncopeltus fasciatus is an emerging model for hemimetabolous insects, a member of the piercing-sucking feeding order Hemiptera, that includes pests and disease vectors. To identify candidate visible markers for O. fasciatus, we used parental and nymphal RNAi to identify genes that altered eye or body color while having no deleterious effects on viability. We selected Of-vermilion for CRISPR/Cas9 genome editing, generating three independent loss-of-function mutant lines. These studies mapped Of-vermilion to the X-chromosome, the first assignment of a gene to a chromosome in this species. Of-vermilion homozygotes have bright red, rather than black, eyes and are fully viable and fertile. We used these mutants to verify a role for Of-xdh1, ortholog of Drosophila rosy, in contributing to red pigmentation using RNAi. Rather than wild-type-like red bodies, bugs lacking both vermilion and xdh1 have bright yellow bodies, suggesting that ommochromes and pteridines contribute to O. fasciatus body color. Our studies generated the first gene-based visible marker for O. fasciatus and expanded the genetic toolkit for this model system.
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32
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Hellekes V, Claus D, Seiler J, Illner F, Schiffer PH, Kroiher M. CRISPR/Cas9 mediated gene editing in non-model nematode Panagrolaimus sp. PS1159. Front Genome Ed 2023; 5:1078359. [PMID: 36818277 PMCID: PMC9935820 DOI: 10.3389/fgeed.2023.1078359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The phylum Nematoda harbors a huge diversity of species in a broad range of ecosystems and habitats. Nematodes share a largely conserved Bauplan but major differences have been found in early developmental processes. The development of the nematode model organism Caenorhabditis elegans has been studied in great detail for decades. These efforts have provided the community with a large number of protocols and methods. Unfortunately, many of these tools are not easily applicable in non-Caenorhabditis nematodes. In recent years it has become clear that many crucial genes in the C. elegans developmental toolkit are absent in other nematode species. It is thus necessary to study the developmental program of other nematode species in detail to understand evolutionary conservation and novelty in the phylum. Panagrolaimus sp. PS1159 is a non-parasitic nematode exhibiting parthenogenetic reproduction and we are establishing the species to comparatively study evolution, biodiversity, and alternative reproduction and survival strategies. Here, we demonstrate the first successful application of the CRISPR/Cas9 system for genome editing in Panagrolaimus sp. PS1159 and the closely related hermaphroditic species Propanagrolaimus sp. JU765 applying the non-homologous end joining and the homology-directed repair (HDR) mechanisms. Using microinjections and modifying published protocols from C. elegans and P. pacificus we induced mutations in the orthologue of unc-22. This resulted in a visible uncoordinated twitching phenotype. We also compared the HDR efficiency following the delivery of different single-stranded oligodeoxynucleotides (ssODNs). Our work will expand the applicability for a wide range of non-model nematodes from across the tree and facilitate functional analysis into the evolution of parthenogenesis, changes in the developmental program of Nematoda, and cryptobiosis.
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Affiliation(s)
- Viktoria Hellekes
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany,Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany,*Correspondence: Viktoria Hellekes,
| | - Denise Claus
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Johanna Seiler
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Felix Illner
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Philipp H. Schiffer
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Michael Kroiher
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
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33
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Renaud MS, Seroussi U, Claycomb JM. Analysis of C. elegans Germline Small RNA Pathways. Methods Mol Biol 2023; 2677:37-59. [PMID: 37464234 DOI: 10.1007/978-1-0716-3259-8_2] [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
Sequence-specific gene regulation by small RNA (sRNA) pathways is essential for the development and function of organisms in all domains of life. These regulatory complexes, containing an Argonaute protein (AGO) guided by a bound sRNA, have the potential to regulate thousands of individual target transcripts at both the co- and post-transcriptional level. Determining the repertoire of transcripts that an AGO is capable of regulating in a particular context is essential to understanding the function of these regulatory modules. Immunoprecipitation (IP) of AGOs and subsequent RNA sequencing of their bound sRNAs allows for the inference of their target transcripts by mapping the sequences of the co-precipitated sRNAs back to their complementary target transcripts. This approach can be complemented by sequencing sRNAs from ago mutants as sRNA transcripts are degraded in the absence of their AGO binding partner. Here, we describe a framework for analyzing AGO/sRNA pathways in the germline, from using CRISPR-Cas9 to tag or mutate AGOs, through protocols for the extraction, sequencing, and analysis of sRNAs from AGO IPs and ago mutants.
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Affiliation(s)
- Mathias S Renaud
- Department of Molecular Genetics, University of Toronto, Toronto, ON, USA
| | - Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, USA
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, USA.
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34
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Kim HM, Hong Y, Chen J. A Decade of CRISPR-Cas Gnome Editing in C. elegans. Int J Mol Sci 2022; 23:ijms232415863. [PMID: 36555505 PMCID: PMC9781986 DOI: 10.3390/ijms232415863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas allows us to introduce desired genome editing, including mutations, epitopes, and deletions, with unprecedented efficiency. The development of CRISPR-Cas has progressed to such an extent that it is now applicable in various fields, with the help of model organisms. C. elegans is one of the pioneering animals in which numerous CRISPR-Cas strategies have been rapidly established over the past decade. Ironically, the emergence of numerous methods makes the choice of the correct method difficult. Choosing an appropriate selection or screening approach is the first step in planning a genome modification. This report summarizes the key features and applications of CRISPR-Cas methods using C. elegans, illustrating key strategies. Our overview of significant advances in CRISPR-Cas will help readers understand the current advances in genome editing and navigate various methods of CRISPR-Cas genome editing.
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35
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Mastrandreas P, Boglari C, Arnold A, Peter F, de Quervain DJF, Papassotiropoulos A, Stetak A. Phosphorylation of MSI-1 is implicated in the regulation of associative memory in Caenorhabditis elegans. PLoS Genet 2022; 18:e1010420. [PMID: 36223338 PMCID: PMC9555661 DOI: 10.1371/journal.pgen.1010420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022] Open
Abstract
The Musashi family of RNA-binding proteins controls several biological processes including stem cell maintenance, cell division and neural function. Previously, we demonstrated that the C. elegans Musashi ortholog, msi-1, regulates forgetting via translational repression of the Arp2/3 actin-branching complex. However, the mechanisms controlling MSI-1 activity during the regulation of forgetting are currently unknown. Here we investigated the effects of protein phosphorylation on MSI-1 activity. We showed that MSI-1 function is likely controlled by alterations of its activity rather than its expression levels. Furthermore, we found that MSI-1 is phosphorylated and using mass spectrometry we identified MSI-1 phosphorylation at three residues (T18, S19 and S34). CRISPR-based manipulations of MSI-1 phosphorylation sites revealed that phosphorylation is necessary for MSI-1 function in both short- and long-term aversive olfactory associative memory. Thus, our study provides insight into the mechanisms regulating memory-related MSI-1 activity and may facilitate the development of novel therapeutic approaches. Understanding neural circuits and molecular mechanisms underlying learning and memory are the major challenges of neuroscience. It is a generally accepted model that a learning event causes modification of synapses; strengthening some within a circuit and weakening others (termed “synaptic plasticity”). A plastic nervous system requires not only the ability to acquire and store but also to forget new inputs. While learning and memory is widely investigated, clear-cut evidence for mechanisms involved in forgetting is still sparse. Previously, we demonstrated the role of the protein Musashi (MSI-1) in the active regulation of forgetting in the nematode C. elegans. Here we investigated the role of protein modification (phosphorylation) as a possible regulatory mechanism of the MSI-1 protein activity. We found that MSI-1 protein is modified at different positions and all of these modifications at the protein level contribute to the correct activity of the protein leading to active forgetting of short and long-term memories.
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Affiliation(s)
- Pavlina Mastrandreas
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, Basel, Switzerland
- Division of Molecular Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland
- Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland
| | - Csaba Boglari
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, Basel, Switzerland
- Division of Molecular Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland
- Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland
| | - Andreas Arnold
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, Basel, Switzerland
- Division of Molecular Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland
- Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland
| | - Fabian Peter
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, Basel, Switzerland
- Division of Molecular Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland
- Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland
| | - Dominique J.-F. de Quervain
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, Basel, Switzerland
- Division of Cognitive Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland
- University Psychiatric Clinics, University of Basel, Basel, Switzerland
| | - Andreas Papassotiropoulos
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, Basel, Switzerland
- Division of Molecular Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland
- Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland
- University Psychiatric Clinics, University of Basel, Basel, Switzerland
| | - Attila Stetak
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, Basel, Switzerland
- Division of Molecular Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland
- Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland
- University Psychiatric Clinics, University of Basel, Basel, Switzerland
- * E-mail:
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36
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Marker-free co-selection for successive rounds of prime editing in human cells. Nat Commun 2022; 13:5909. [PMID: 36207338 PMCID: PMC9546848 DOI: 10.1038/s41467-022-33669-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. However, efficiency remains a key challenge in a broad range of human cell types. In this work, we design a robust co-selection strategy through coediting of the ubiquitous and essential sodium/potassium pump (Na+/K+ ATPase). We readily engineer highly modified pools of cells and clones with homozygous modifications for functional studies with minimal pegRNA optimization. This process reveals that nicking the non-edited strand stimulates multiallelic editing but often generates tandem duplications and large deletions at the target site, an outcome dictated by the relative orientation of the protospacer adjacent motifs. Our approach streamlines the production of cell lines with multiple genetic modifications to create cellular models for biological research and lays the foundation for the development of cell-type specific co-selection strategies. Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. Here the authors develop a co-selection strategy to facilitate prime editing in human cells and provide design principles to prevent the formation of undesired editing byproducts at the target site.
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Bacterial diet modulates tamoxifen-induced death via host fatty acid metabolism. Nat Commun 2022; 13:5595. [PMID: 36151093 PMCID: PMC9508336 DOI: 10.1038/s41467-022-33299-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Tamoxifen is a selective estrogen receptor (ER) modulator that is used to treat ER-positive breast cancer, but that at high doses kills both ER-positive and ER-negative breast cancer cells. We recapitulate this off-target effect in Caenorhabditis elegans, which does not have an ER ortholog. We find that different bacteria dramatically modulate tamoxifen toxicity in C. elegans, with a three-order of magnitude difference between animals fed Escherichia coli, Comamonas aquatica, and Bacillus subtilis. Remarkably, host fatty acid (FA) biosynthesis mitigates tamoxifen toxicity, and different bacteria provide the animal with different FAs, resulting in distinct FA profiles. Surprisingly these bacteria modulate tamoxifen toxicity by different death mechanisms, some of which are modulated by FA supplementation and others by antioxidants. Together, this work reveals a complex interplay between microbiota, FA metabolism and tamoxifen toxicity that may provide a blueprint for similar studies in more complex mammals. Here, Diot et al. use the nematode Caenorhabditis elegans as a model to identify off-target toxicity mechanisms for tamoxifen, and find that these include fatty acid metabolism and cell death, which can be modulated by different bacterial species.
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Huang W, Kew C, Fernandes SDA, Löhrke A, Han L, Demetriades C, Antebi A. Decreased spliceosome fidelity and egl-8 intron retention inhibit mTORC1 signaling to promote longevity. NATURE AGING 2022; 2:796-808. [PMID: 37118503 PMCID: PMC10154236 DOI: 10.1038/s43587-022-00275-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
AbstractChanges in splicing fidelity are associated with loss of homeostasis and aging, yet only a handful of splicing factors have been shown to be causally required to promote longevity, and the underlying mechanisms and downstream targets in these paradigms remain elusive. Surprisingly, we found a hypomorphic mutation within ribonucleoprotein RNP-6/poly(U)-binding factor 60 kDa (PUF60), a spliceosome component promoting weak 3′-splice site recognition, which causes aberrant splicing, elevates stress responses and enhances longevity in Caenorhabditis elegans. Through genetic suppressor screens, we identify a gain-of-function mutation within rbm-39, an RNP-6-interacting splicing factor, which increases nuclear speckle formation, alleviates splicing defects and curtails longevity caused by rnp-6 mutation. By leveraging the splicing changes induced by RNP-6/RBM-39 activities, we uncover intron retention in egl-8/phospholipase C β4 (PLCB4) as a key splicing target prolonging life. Genetic and biochemical evidence show that neuronal RNP-6/EGL-8 downregulates mammalian target of rapamycin complex 1 (mTORC1) signaling to control organismal lifespan. In mammalian cells, PUF60 downregulation also potently and specifically inhibits mTORC1 signaling. Altogether, our results reveal that splicing fidelity modulates lifespan through mTOR signaling.
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El Mouridi S, Alkhaldi F, Frøkjær-Jensen C. Modular safe-harbor transgene insertion for targeted single-copy and extrachromosomal array integration in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2022; 12:jkac184. [PMID: 35900171 PMCID: PMC9434227 DOI: 10.1093/g3journal/jkac184] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/29/2022] [Indexed: 12/02/2022]
Abstract
Efficient and reproducible transgenesis facilitates and accelerates research using genetic model organisms. Here, we describe a modular safe-harbor transgene insertion (MosTI) for use in Caenorhabditis elegans which improves targeted insertion of single-copy transgenes by homology directed repair and targeted integration of extrachromosomal arrays by nonhomologous end-joining. MosTI allows easy conversion between selection markers at insertion site and a collection of universal targeting vectors with commonly used promoters and fluorophores. Insertions are targeted at three permissive safe-harbor intergenic locations and transgenes are reproducibly expressed in somatic and germ cells. Chromosomal integration is mediated by CRISPR/Cas9, and positive selection is based on a set of split markers (unc-119, hygroR, and gfp) where only animals with chromosomal insertions are rescued, resistant to antibiotics, or fluorescent, respectively. Single-copy insertion is efficient using either constitutive or heat-shock inducible Cas9 expression (25-75%) and insertions can be generated from a multiplexed injection mix. Extrachromosomal array integration is also efficient (7-44%) at modular safe-harbor transgene insertion landing sites or at the endogenous unc-119 locus. We use short-read sequencing to estimate the plasmid copy numbers for 8 integrated arrays (6-37 copies) and long-read Nanopore sequencing to determine the structure and size (5.4 Mb) of 1 array. Using universal targeting vectors, standardized insertion strains, and optimized protocols, it is possible to construct complex transgenic strains which should facilitate the study of increasingly complex biological problems in C. elegans.
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Affiliation(s)
- Sonia El Mouridi
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Faisal Alkhaldi
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Christian Frøkjær-Jensen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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40
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Fakieh R, Duong T, Wu Y, Rasmussen N, Reiner D. A simple strategy for addition of degron tags to endogenous genes harboring prior insertions of fluorescent protein. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000622. [PMID: 36035777 PMCID: PMC9412190 DOI: 10.17912/micropub.biology.000622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/13/2022]
Abstract
There exist insufficient validated "entry portal" sites in the C. elegans genome for CRISPR/Cas9-dependent insertion into endogenous genes to confer diverse spatiotemporal patterns and levels of expression on exogenous sequences. Consequently, we recognized the most common potential "entry portal" sequences: genes previously tagged with fluorescent proteins using CRISPR/Cas9. As proof of concept, we used existing mKate2-encoding sequences inserted in the 5' end of genes as an insertion point for the auxin inducible degron, AID*. This sequence permits reasonably efficient insertion that can be employed using a variety of approaches for different end goals. Our strategy is thus generalizable to many needs.
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Affiliation(s)
| | | | | | | | - David Reiner
- Texas A&M University
,
Correspondence to: David Reiner (
)
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41
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Disease modeling by efficient genome editing using a near PAM-less base editor in vivo. Nat Commun 2022; 13:3435. [PMID: 35701478 PMCID: PMC9198099 DOI: 10.1038/s41467-022-31172-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 06/08/2022] [Indexed: 12/18/2022] Open
Abstract
Base Editors are emerging as an innovative technology to introduce point mutations in complex genomes. So far, the requirement of an NGG Protospacer Adjacent Motif (PAM) at a suitable position often limits the base editing possibility to model human pathological mutations in animals. Here we show that, using the CBE4max-SpRY variant recognizing nearly all PAM sequences, we could introduce point mutations for the first time in an animal model with high efficiency, thus drastically increasing the base editing possibilities. With this near PAM-less base editor we could simultaneously mutate several genes and we developed a co-selection method to identify the most edited embryos based on a simple visual screening. Finally, we apply our method to create a zebrafish model for melanoma predisposition based on the simultaneous base editing of multiple genes. Altogether, our results considerably expand the Base Editor application to introduce human disease-causing mutations in zebrafish. Base Editors are emerging as an innovative technology to introduce point mutations in complex genomes. Here the authors describe a near PAM-less base editor and its application in zebrafish to efficiently create disease models harbouring specific point mutations.
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42
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Costache V, Prigent Garcia S, Plancke CN, Li J, Begnaud S, Suman SK, Reymann AC, Kim T, Robin FB. Rapid assembly of a polar network architecture drives efficient actomyosin contractility. Cell Rep 2022; 39:110868. [PMID: 35649363 PMCID: PMC9210446 DOI: 10.1016/j.celrep.2022.110868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/13/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Actin network architecture and dynamics play a central role in cell contractility and tissue morphogenesis. RhoA-driven pulsed contractions are a generic mode of actomyosin contractility, but the mechanisms underlying how their specific architecture emerges and how this architecture supports the contractile function of the network remain unclear. Here we show that, during pulsed contractions, the actin network is assembled by two subpopulations of formins: a functionally inactive population (recruited) and formins actively participating in actin filament elongation (elongating). We then show that elongating formins assemble a polar actin network, with barbed ends pointing out of the pulse. Numerical simulations demonstrate that this geometry favors rapid network contraction. Our results show that formins convert a local RhoA activity gradient into a polar network architecture, causing efficient network contractility, underlying the key function of kinetic controls in the assembly and mechanics of cortical network architectures. RhoA-driven actomyosin contractility plays a key role in driving cell and tissue contractility during morphogenesis. Tracking individual formins, Costache et al. show that the network assembled downstream of RhoA displays a polar architecture, barbed ends pointing outward, a feature that supports efficient contractility and force transmission during pulsed contractions.
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Affiliation(s)
- Vlad Costache
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine IBPS, Laboratoire de Biologie du Développement, Paris, France
| | - Serena Prigent Garcia
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine IBPS, Laboratoire de Biologie du Développement, Paris, France
| | - Camille N Plancke
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine IBPS, Laboratoire de Biologie du Développement, Paris, France
| | - Jing Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Simon Begnaud
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine IBPS, Laboratoire de Biologie du Développement, Paris, France
| | - Shashi Kumar Suman
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine IBPS, Laboratoire de Biologie du Développement, Paris, France
| | - Anne-Cécile Reymann
- IGBMC, CNRS UMR7104, INSERM U1258, and Université de Strasbourg, Illkirch, France
| | - Taeyoon Kim
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - François B Robin
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine IBPS, Laboratoire de Biologie du Développement, Paris, France.
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Vicencio J, Sánchez-Bolaños C, Moreno-Sánchez I, Brena D, Vejnar CE, Kukhtar D, Ruiz-López M, Cots-Ponjoan M, Rubio A, Melero NR, Crespo-Cuadrado J, Carolis C, Pérez-Pulido AJ, Giráldez AJ, Kleinstiver BP, Cerón J, Moreno-Mateos MA. Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes. Nat Commun 2022; 13:2601. [PMID: 35552388 PMCID: PMC9098488 DOI: 10.1038/s41467-022-30228-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 04/22/2022] [Indexed: 01/21/2023] Open
Abstract
The requirement for Cas nucleases to recognize a specific PAM is a major restriction for genome editing. SpCas9 variants SpG and SpRY, recognizing NGN and NRN PAMs, respectively, have contributed to increase the number of editable genomic sites in cell cultures and plants. However, their use has not been demonstrated in animals. Here we study the nuclease activity of SpG and SpRY by targeting 40 sites in zebrafish and C. elegans. Delivered as mRNA-gRNA or ribonucleoprotein (RNP) complexes, SpG and SpRY were able to induce mutations in vivo, albeit at a lower rate than SpCas9 in equivalent formulations. This lower activity was overcome by optimizing mRNA-gRNA or RNP concentration, leading to mutagenesis at regions inaccessible to SpCas9. We also found that the CRISPRscan algorithm could help to predict SpG and SpRY targets with high activity in vivo. Finally, we applied SpG and SpRY to generate knock-ins by homology-directed repair. Altogether, our results expand the CRISPR-Cas targeting genomic landscape in animals.
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Affiliation(s)
- Jeremy Vicencio
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Carlos Sánchez-Bolaños
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ismael Moreno-Sánchez
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - David Brena
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Dmytro Kukhtar
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Miguel Ruiz-López
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Mariona Cots-Ponjoan
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Alejandro Rubio
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Natalia Rodrigo Melero
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Jesús Crespo-Cuadrado
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Carlo Carolis
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Antonio J Pérez-Pulido
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Antonio J Giráldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Julián Cerón
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
| | - Miguel A Moreno-Mateos
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain.
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain.
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44
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Zinc transporters ZIPT-2.4 and ZIPT-15 are required for normal C. elegans fecundity. J Assist Reprod Genet 2022; 39:1261-1276. [PMID: 35501415 DOI: 10.1007/s10815-022-02495-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/11/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE The requirement of zinc for the development and maturation of germ lines and reproductive systems is deeply conserved across evolution. The nematode Caenorhabditis elegans offers a tractable platform to study the complex system of distributing zinc to the germ line. We investigated several zinc importers to investigate how zinc transporters play a role in the reproductive system in nematodes, as well as establish a platform to study zinc transporter biology in germline and reproductive development. METHODS Previous high throughput transcriptional datasets as well as phylogenetic analysis identified several putative zinc transporters that have a function in reproduction in worms. Phenotypic analysis of CRISPR-generated knockouts and tags included characterization of offspring output, gonad development, and protein localization. Light and immunofluorescence microscopy allowed for visualization of physiological and molecular effects of zinc transporter mutations. RESULTS Disruption of two zinc transporters, ZIPT-2.4 and ZIPT-15, was shown to lead to defects in reproductive output. A mutation in zipt-2.4 has subtle effects on reproduction, while a mutation in zipt-15 has a clear impact on gonad and germline development that translates into a more pronounced defect in fecundity. Both transporters have germline expression, as well as additional expression in other cell types. CONCLUSIONS Two ZIP-family zinc transporter orthologs of human ZIP6/10 and ZIP1/2/3 proteins are important for full reproductive fecundity and participate in development of the gonad. Notably, these zinc transporters are present in gut and reproductive tissues in addition to the germ line, consistent with a complex zinc trafficking network important for reproductive success.
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45
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Shaffer JM, Greenwald I. SALSA, a genetically encoded biosensor for spatiotemporal quantification of Notch signal transduction in vivo. Dev Cell 2022; 57:930-944.e6. [PMID: 35413239 PMCID: PMC9473748 DOI: 10.1016/j.devcel.2022.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/14/2022] [Accepted: 03/14/2022] [Indexed: 12/26/2022]
Abstract
Notch-mediated lateral specification is a fundamental mechanism to resolve stochastic cell fate choices by amplifying initial differences between equivalent cells. To study how stochastic events impact Notch activity, we developed a biosensor, SALSA (sensor able to detect lateral signaling activity), consisting of an amplifying "switch"-Notch tagged with TEV protease-and a "reporter"-GFP fused to a nuclearly localized red fluorescent protein, separated by a TEVp cut site. When ligand activates Notch, TEVp enters the nucleus and releases GFP from its nuclear tether, allowing Notch activation to be quantified based on the changes in GFP subcellular localization. We show that SALSA accurately reports Notch activity in different signaling paradigms in Caenorhabditis elegans and use time-lapse imaging to test hypotheses about how stochastic elements ensure a reproducible and robust outcome in a canonical lin-12/Notch-mediated lateral signaling paradigm. SALSA should be generalizable to other experimental systems and be adaptable to increase options for bespoke "SynNotch" applications.
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Affiliation(s)
- Justin M Shaffer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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46
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Mathies LD, Blackwell G, Bettinger JC. New alleles of the SWI/SNF chromatin remodeling complex gene phf-10. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000533. [PMID: 35622521 PMCID: PMC9010112 DOI: 10.17912/micropub.biology.000533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022]
Abstract
SWI/SNF chromatin remodeling complexes regulate many aspects of metazoan development and mutations in SWI/SNF genes are associated with diverse human diseases including cancer and alcohol use disorder. In C. elegans, SWI/SNF subunits are required for viability, somatic gonad development, and normal behavioral responses to ethanol. SWI/SNF complexes can be classified as BAF (BRG1/Brm-associated factors) or PBAF (Polybromo-associated BAF) based on their subunit composition. While there are loss-of-function alleles for most SWI/SNF family members, strong loss of function mutations have not previously been reported for the PBAF gene phf-10. Here we describe two new alleles of phf-10 that we generated using CRISPR/Cas9 genome editing.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
,
Correspondence to: Laura D Mathies (
)
| | - GinaMari Blackwell
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
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47
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Binti S, Melinda RV, Joseph BB, Edeen PT, Miller SD, Fay DS. A life cycle alteration can correct molting defects in Caenorhabditis elegans. Dev Biol 2022; 483:143-156. [PMID: 35038442 PMCID: PMC8867747 DOI: 10.1016/j.ydbio.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 11/28/2022]
Abstract
Molting is a widespread feature in the development of many invertebrates, including nematodes and arthropods. In Caenorhabditis elegans, the highly conserved protein kinases NEKL-2/NEK8/9 and NEKL-3/NEK6/7 (NEKLs) promote molting through their involvement in the uptake and intracellular trafficking of epidermal cargos. We found that the relative requirements for NEKL-2 and NEKL-3 differed at different life-cycle stages and under different environmental conditions. Most notably, the transition from the second to the third larval stage (L2→L3 molt) required a higher level of NEKL function than during several other life stages or when animals had experienced starvation at the L1 stage. Specifically, larvae that entered the pre-dauer L2d stage could escape molting defects when transiting to the (non-dauer) L3 stage. Consistent with this, mutations that promote entry into L2d suppressed nekl-associated molting defects, whereas mutations that inhibit L2d entry reduced starvation-mediated suppression. We further showed that loss or reduction of NEKL functions led to defects in the transcription of cyclically expressed molting genes, many of which are under the control of systemic steroid hormone regulation. Moreover, the timing and severity of these transcriptional defects correlated closely with the strength of nekl alleles and with their stage of arrest. Interestingly, transit through L2d rescued nekl-associated expression defects in suppressed worms, providing an example of how life-cycle decisions can impact subsequent developmental events. Given that NEKLs are implicated in the uptake of sterols by the epidermis, we propose that loss of NEKLs leads to a physiological reduction in steroid-hormone signaling and consequent defects in the transcription of genes required for molting.
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Affiliation(s)
- Shaonil Binti
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Rosa V Melinda
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Braveen B Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Phillip T Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Sam D Miller
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA.
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48
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Rawsthorne-Manning H, Calahorro F, G. Izquierdo P, Tardy P, Boulin T, Holden-Dye L, O’Connor V, Dillon J. Confounds of using the unc-58 selection marker highlights the importance of genotyping co-CRISPR genes. PLoS One 2022; 17:e0253351. [PMID: 35041685 PMCID: PMC8765651 DOI: 10.1371/journal.pone.0253351] [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: 06/22/2021] [Accepted: 10/29/2021] [Indexed: 11/19/2022] Open
Abstract
Multiple advances have been made to increase the efficiency of CRISPR/Cas9 editing using the model genetic organism Caenorhabditis elegans (C. elegans). Here we report on the use of co-CRISPR 'marker' genes: worms in which co-CRISPR events have occurred have overt, visible phenotypes which facilitates the selection of worms that harbour CRISPR events in the target gene. Mutation in the co-CRISPR gene is then removed by outcrossing to wild type but this can be challenging if the CRISPR and co-CRISPR gene are hard to segregate. However, segregating away the co-CRISPR modified gene can be less challenging if the worms selected appear wild type and are selected from a jackpot brood. These are broods in which a high proportion of the progeny of a single injected worm display the co-CRISPR phenotype suggesting high CRISPR efficiency. This can deliver worms that harbour the desired mutation in the target gene locus without the co-CRISPR mutation. We have successfully generated a discrete mutation in the C. elegans nlg-1 gene using this method. However, in the process of sequencing to authenticate editing in the nlg-1 gene we discovered genomic rearrangements that arise at the co-CRISPR gene unc-58 that by visual observation were phenotypically silent but nonetheless resulted in a significant reduction in motility scored by thrashing behaviour. This highlights that careful consideration of the hidden consequences of co-CRISPR mediated genetic changes should be taken before downstream analysis of gene function. Given this, we suggest sequencing of co-CRISPR genes following CRISPR procedures that utilise phenotypic selection as part of the pipeline.
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Affiliation(s)
| | - Fernando Calahorro
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Patricia G. Izquierdo
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Philippe Tardy
- Institut NeuroMyoGène, Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon, France
| | - Thomas Boulin
- Institut NeuroMyoGène, Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon, France
| | - Lindy Holden-Dye
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Vincent O’Connor
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - James Dillon
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
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49
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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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50
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Pastore B, Hertz HL, Tang W. Comparative analysis of piRNA sequences, targets and functions in nematodes. RNA Biol 2022; 19:1276-1292. [PMID: 36412988 PMCID: PMC9683057 DOI: 10.1080/15476286.2022.2149170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. briggsae. piRNA sequences in C. briggsae are extremely divergent from their counterparts in C. elegans, yet both species adopt similar genomic organization that drive piRNA expression. By examining production of Piwi-mediated secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to C. elegans, small RNAs targeting ribosomal RNAs or histone transcripts are not hyper-accumulated in C. briggsae Piwi mutants. Instead, we found that transcripts with few introns are prone to small RNA overamplification. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
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Affiliation(s)
- Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, The Ohio State University,Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA,Center for RNA Biology, Ohio State University, Columbus, OH, USA
| | - Hannah L. Hertz
- Department of Biological Chemistry and Pharmacology, The Ohio State University,Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, The Ohio State University,Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA,CONTACT Wen Tang Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
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