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Stevenson ZC, Moerdyk-Schauwecker MJ, Banse SA, Patel DS, Lu H, Phillips PC. High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS). eLife 2023; 12:RP84831. [PMID: 37401921 PMCID: PMC10328503 DOI: 10.7554/elife.84831] [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] [Indexed: 07/05/2023] Open
Abstract
High-throughput transgenesis using synthetic DNA libraries is a powerful method for systematically exploring genetic function. Diverse synthesized libraries have been used for protein engineering, identification of protein-protein interactions, characterization of promoter libraries, developmental and evolutionary lineage tracking, and various other exploratory assays. However, the need for library transgenesis has effectively restricted these approaches to single-cell models. Here, we present Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS), a simple yet powerful approach to large-scale transgenesis that overcomes typical limitations encountered in multicellular systems. TARDIS splits the transgenesis process into a two-step process: creation of individuals carrying experimentally introduced sequence libraries, followed by inducible extraction and integration of individual sequences/library components from the larger library cassette into engineered genomic sites. Thus, transformation of a single individual, followed by lineage expansion and functional transgenesis, gives rise to thousands of genetically unique transgenic individuals. We demonstrate the power of this system using engineered, split selectable TARDIS sites in Caenorhabditis elegans to generate (1) a large set of individually barcoded lineages and (2) transcriptional reporter lines from predefined promoter libraries. We find that this approach increases transformation yields up to approximately 1000-fold over current single-step methods. While we demonstrate the utility of TARDIS using C. elegans, in principle the process is adaptable to any system where experimentally generated genomic loci landing pads and diverse, heritable DNA elements can be generated.
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Affiliation(s)
| | | | - Stephen A Banse
- Institute of Ecology and Evolution, University of OregonEugeneUnited States
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of OregonEugeneUnited States
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2
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Lockery SR, Pop S, Jussila B. Microinjection in C. elegans by direct penetration of elastomeric membranes. BIOMICROFLUIDICS 2023; 17:014103. [PMID: 36647539 PMCID: PMC9840533 DOI: 10.1063/5.0130806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The nematode worm C. elegans is widely used in basic and translational research. The creation of transgenic strains by injecting DNA constructs into the worm's gonad is an essential step in many C. elegans research projects. This paper describes the fabrication and use of a minimalist microfluidic chip for performing microinjections. The worm is immobilized in a tight-fitting microchannel, one sidewall of which is a thin elastomeric membrane through which the injection pipet penetrates to reach the worm. The pipet is neither broken nor clogged by passing through the membrane, and the membrane reseals when the pipet is withdrawn. Rates of survival and transgenesis are similar to those in the conventional method. Novice users found injections using the device easier to learn than the conventional method. The principle of direct penetration of elastomeric membranes is adaptable to microinjections in a wide range of organisms including cells, embryos, and other small animal models. It could, therefore, lead to a new generation of microinjection systems for basic, translational, and industrial applications.
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Affiliation(s)
| | - Stelian Pop
- InVivo Biosystems, Inc., Eugene, Oregon 97402, USA
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3
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Ghaemi R, Tong J, Gupta BP, Selvaganapathy PR. Microfluidic Device for Microinjection of Caenorhabditis elegans. MICROMACHINES 2020; 11:mi11030295. [PMID: 32168862 PMCID: PMC7143065 DOI: 10.3390/mi11030295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/26/2022]
Abstract
Microinjection is an established and reliable method to deliver transgenic constructs and other reagents to specific locations in C. elegans worms. Specifically, microinjection of a desired DNA construct into the distal gonad is the most widely used method to generate germ-line transformation of C. elegans. Although, current C. elegans microinjection method is effective to produce transgenic worms, it requires expensive multi degree of freedom (DOF) micromanipulator, careful injection alignment procedure and skilled operator, all of which make it slow and not suitable for scaling to high throughput. A few microfabricated microinjectors have been developed recently to address these issues. However, none of them are capable of immobilizing a freely mobile animal such as C. elegans worm using a passive immobilization mechanism. Here, a microfluidic microinjector was developed to passively immobilize a freely mobile animal such as C. elegans and simultaneously perform microinjection by using a simple and fast mechanism for needle actuation. The entire process of the microinjection takes ~30 s which includes 10 s for worm loading and aligning, 5 s needle penetration, 5 s reagent injection and 5 s worm unloading. The device is suitable for high-throughput and can be potentially used for creating transgenic C. elegans.
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Affiliation(s)
- Reza Ghaemi
- Department of Mechanical Engineering, McMaster University, Hamilton, ON L8S 4L8, Canada;
| | - Justin Tong
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (J.T.); (B.P.G.)
| | - Bhagwati P. Gupta
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (J.T.); (B.P.G.)
| | - P. Ravi Selvaganapathy
- Department of Mechanical Engineering, McMaster University, Hamilton, ON L8S 4L8, Canada;
- Correspondence: ; Tel.: +1-905-525-9140 (ext. 27435)
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Kleinfeld D, Luan L, Mitra PP, Robinson JT, Sarpeshkar R, Shepard K, Xie C, Harris TD. Can One Concurrently Record Electrical Spikes from Every Neuron in a Mammalian Brain? Neuron 2019; 103:1005-1015. [PMID: 31495645 PMCID: PMC6763354 DOI: 10.1016/j.neuron.2019.08.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/30/2019] [Accepted: 08/03/2019] [Indexed: 12/26/2022]
Abstract
The classic approach to measure the spiking response of neurons involves the use of metal electrodes to record extracellular potentials. Starting over 60 years ago with a single recording site, this technology now extends to ever larger numbers and densities of sites. We argue, based on the mechanical and electrical properties of existing materials, estimates of signal-to-noise ratios, assumptions regarding extracellular space in the brain, and estimates of heat generation by the electronic interface, that it should be possible to fabricate rigid electrodes to concurrently record from essentially every neuron in the cortical mantle. This will involve fabrication with existing yet nontraditional materials and procedures. We further emphasize the need to advance materials for improved flexible electrodes as an essential advance to record from neurons in brainstem and spinal cord in moving animals.
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Affiliation(s)
- David Kleinfeld
- Section of Neurobiology, University of California, San Diego, CA, USA; Department of Physics, University of California, San Diego, CA, USA.
| | - Lan Luan
- Department of Biomedical Engineering, University of Texas, Austin, TX, USA
| | - Partha P Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jacob T Robinson
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Rahul Sarpeshkar
- Department of Engineering, Dartmouth, Hanover, NH, USA; Department of Microbiology and Immunology, Dartmouth, Hanover, NH, USA; Department of Molecular and Systems Biology, Dartmouth, Hanover, NH, USA; Department of Physics, Dartmouth, Hanover, NH, USA
| | - Kenneth Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Chong Xie
- Department of Biomedical Engineering, University of Texas, Austin, TX, USA
| | - Timothy D Harris
- Howard Hughes Medical Institutes, Janelia Research Campus, Ashburn, VA, USA; Department of Bioengineering, Johns Hopkins University, Baltimore, MD, USA.
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Low IIC, Williams CR, Chong MK, McLachlan IG, Wierbowski BM, Kolotuev I, Heiman MG. Morphogenesis of neurons and glia within an epithelium. Development 2019; 146:dev171124. [PMID: 30683663 PMCID: PMC6398450 DOI: 10.1242/dev.171124] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022]
Abstract
To sense the outside world, some neurons protrude across epithelia, the cellular barriers that line every surface of our bodies. To study the morphogenesis of such neurons, we examined the C. elegans amphid, in which dendrites protrude through a glial channel at the nose. During development, amphid dendrites extend by attaching to the nose via DYF-7, a type of protein typically found in epithelial apical ECM. Here, we show that amphid neurons and glia exhibit epithelial properties, including tight junctions and apical-basal polarity, and develop in a manner resembling other epithelia. We find that DYF-7 is a fibril-forming apical ECM component that promotes formation of the tube-shaped glial channel, reminiscent of roles for apical ECM in other narrow epithelial tubes. We also identify a requirement for FRM-2, a homolog of EPBL15/moe/Yurt that promotes epithelial integrity in other systems. Finally, we show that other environmentally exposed neurons share a requirement for DYF-7. Together, our results suggest that these neurons and glia can be viewed as part of an epithelium continuous with the skin, and are shaped by mechanisms shared with other epithelia.
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Affiliation(s)
- Isabel I C Low
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Claire R Williams
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Megan K Chong
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Ian G McLachlan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Bradley M Wierbowski
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Irina Kolotuev
- Université de Rennes 1, Plateforme microscopie électronique, 35043 Rennes, France
| | - Maxwell G Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
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Worms on a Chip. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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7
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Farboud B. Targeted genome editing in Caenorhabditis elegans using CRISPR/Cas9. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28810059 DOI: 10.1002/wdev.287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/04/2017] [Accepted: 07/05/2017] [Indexed: 12/26/2022]
Abstract
Utilization of programmable nucleases to generate DNA lesions at precise endogenous sequences has transformed the ability to edit genomes from microbes to plants and animals. This is especially true in organisms that previously lacked the means to engineer precise genomic changes, like Caenorhabditis elegans. C. elegans is a 1 mm long free-living, nonparasitic, nematode worm, which is easily cultivated in a laboratory. Its detailed genetic map and relatively compact genome (~100 megabases) helped make it the first metazoan to have its entire genome sequenced. With detailed sequence information came development of numerous molecular tools to dissect gene function. Initially absent from this toolbox, however, were methods to make precise edits at chosen endogenous loci. Adapting site-specific nucleases for use in C. elegans, revolutionized studies of C. elegans biology. Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and then CRISPR-associated protein 9 (Cas9) were used to target specific endogenous DNA sequences to make double-strand DNA breaks (DSBs). Precise changes could be engineered by providing repair templates targeting the DSB in trans. The ease of programming Cas9 to bind and cleave DNA sequences with few limitations has led to its widespread use in C. elegans research and sped the development of strategies to facilitate mutant recovery. Numerous innovative CRISPR/Cas9 methodologies are now primed for use in C. elegans. WIREs Dev Biol 2017, 6:e287. doi: 10.1002/wdev.287 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Behnom Farboud
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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Kinser HE, Pincus Z. High-throughput screening in the C. elegans nervous system. Mol Cell Neurosci 2017; 80:192-197. [PMID: 27265309 PMCID: PMC5136351 DOI: 10.1016/j.mcn.2016.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 05/24/2016] [Accepted: 06/01/2016] [Indexed: 11/23/2022] Open
Abstract
The nematode Caenorhabditis elegans is widely used as a model organism in the field of neurobiology. The wiring of the C. elegans nervous system has been entirely mapped, and the animal's optical transparency allows for in vivo observation of neuronal activity. The nematode is also small in size, self-fertilizing, and inexpensive to cultivate and maintain, greatly lending to its utility as a whole-animal model for high-throughput screening (HTS) in the nervous system. However, the use of this organism in large-scale screens presents unique technical challenges, including reversible immobilization of the animal, parallel single-animal culture and containment, automation of laser surgery, and high-throughput image acquisition and phenotyping. These obstacles require significant modification of existing techniques and the creation of new C. elegans-based HTS platforms. In this review, we outline these challenges in detail and survey the novel technologies and methods that have been developed to address them.
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Affiliation(s)
- Holly E Kinser
- Department of Biomedical Engineering, Washington University in St. Louis, United States
| | - Zachary Pincus
- Department of Developmental Biology, Department of Genetics, Washington University, St. Louis, United States
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Kaymak E, Farley BM, Hay SA, Li C, Ho S, Hartman DJ, Ryder SP. Efficient generation of transgenic reporter strains and analysis of expression patterns in Caenorhabditis elegans using library MosSCI. Dev Dyn 2016; 245:925-36. [PMID: 27294288 PMCID: PMC4981527 DOI: 10.1002/dvdy.24426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/09/2016] [Accepted: 06/03/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND In C. elegans, germline development and early embryogenesis rely on posttranscriptional regulation of maternally transcribed mRNAs. In many cases, the 3' untranslated region (UTR) is sufficient to govern the expression patterns of these transcripts. Several RNA-binding proteins are required to regulate maternal mRNAs through the 3'UTR. Despite intensive efforts to map RNA-binding protein-mRNA interactions in vivo, the biological impact of most binding events remains unknown. Reporter studies using single copy integrated transgenes are essential to evaluate the functional consequences of interactions between RNA-binding proteins and their associated mRNAs. RESULTS In this report, we present an efficient method of generating reporter strains with improved throughput by using a library variant of MosSCI transgenesis. Furthermore, using RNA interference, we identify the suite of RNA-binding proteins that control the expression pattern of five different maternal mRNAs. CONCLUSIONS The results provide a generalizable and efficient strategy to assess the functional relevance of protein-RNA interactions in vivo, and reveal new regulatory connections between key RNA-binding proteins and their maternal mRNA targets. Developmental Dynamics 245:925-936, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Brian M. Farley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Samantha A. Hay
- Virginia Commonwealth University School of Medicine, VA, USA
| | - Chihua Li
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Samantha Ho
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | | | - Sean P. Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
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Schwartz ML, Jorgensen EM. SapTrap, a Toolkit for High-Throughput CRISPR/Cas9 Gene Modification in Caenorhabditis elegans. Genetics 2016; 202:1277-88. [PMID: 26837755 PMCID: PMC4905529 DOI: 10.1534/genetics.115.184275] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/20/2016] [Indexed: 01/16/2023] Open
Abstract
In principle, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 allows genetic tags to be inserted at any locus. However, throughput is limited by the laborious construction of repair templates and guide RNA constructs and by the identification of modified strains. We have developed a reagent toolkit and plasmid assembly pipeline, called "SapTrap," that streamlines the production of targeting vectors for tag insertion, as well as the selection of modified Caenorhabditis elegans strains. SapTrap is a high-efficiency modular plasmid assembly pipeline that produces single plasmid targeting vectors, each of which encodes both a guide RNA transcript and a repair template for a particular tagging event. The plasmid is generated in a single tube by cutting modular components with the restriction enzyme SapI, which are then "trapped" in a fixed order by ligation to generate the targeting vector. A library of donor plasmids supplies a variety of protein tags, a selectable marker, and regulatory sequences that allow cell-specific tagging at either the N or the C termini. All site-specific sequences, such as guide RNA targeting sequences and homology arms, are supplied as annealed synthetic oligonucleotides, eliminating the need for PCR or molecular cloning during plasmid assembly. Each tag includes an embedded Cbr-unc-119 selectable marker that is positioned to allow concurrent expression of both the tag and the marker. We demonstrate that SapTrap targeting vectors direct insertion of 3- to 4-kb tags at six different loci in 10-37% of injected animals. Thus SapTrap vectors introduce the possibility for high-throughput generation of CRISPR/Cas9 genome modifications.
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Affiliation(s)
- Matthew L Schwartz
- Department of Biology, University of Utah, Salt Lake City, Utah 84112-0840 Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah 84112-0840
| | - Erik M Jorgensen
- Department of Biology, University of Utah, Salt Lake City, Utah 84112-0840 Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah 84112-0840
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Song P, Dong X, Liu X. A microfluidic device for automated, high-speed microinjection of Caenorhabditis elegans. BIOMICROFLUIDICS 2016; 10:011912. [PMID: 26958099 PMCID: PMC4769256 DOI: 10.1063/1.4941984] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 02/03/2016] [Indexed: 05/22/2023]
Abstract
The nematode worm Caenorhabditis elegans has been widely used as a model organism in biological studies because of its short and prolific life cycle, relatively simple body structure, significant genetic overlap with human, and facile/inexpensive cultivation. Microinjection, as an established and versatile tool for delivering liquid substances into cellular/organismal objects, plays an important role in C. elegans research. However, the conventional manual procedure of C. elegans microinjection is labor-intensive and time-consuming and thus hinders large-scale C. elegans studies involving microinjection of a large number of C. elegans on a daily basis. In this paper, we report a novel microfluidic device that enables, for the first time, fully automated, high-speed microinjection of C. elegans. The device is automatically regulated by on-chip pneumatic valves and allows rapid loading, immobilization, injection, and downstream sorting of single C. elegans. For demonstration, we performed microinjection experiments on 200 C. elegans worms and demonstrated an average injection speed of 6.6 worm/min (average worm handling time: 9.45 s/worm) and a success rate of 77.5% (post-sorting success rate: 100%), both much higher than the performance of manual operation (speed: 1 worm/4 min and success rate: 30%). We conducted typical viability tests on the injected C. elegans and confirmed that the automated injection system does not impose significant adverse effect on the physiological condition of the injected C. elegans. We believe that the developed microfluidic device holds great potential to become a useful tool for facilitating high-throughput, large-scale worm biology research.
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Affiliation(s)
- Pengfei Song
- Department of Mechanical Engineering, McGill University , Montreal, Quebec H3A 0C3, Canada
| | - Xianke Dong
- Department of Mechanical Engineering, McGill University , Montreal, Quebec H3A 0C3, Canada
| | - Xinyu Liu
- Department of Mechanical Engineering, McGill University , Montreal, Quebec H3A 0C3, Canada
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