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The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit

Nature Reviews Genetics volume 12, pages 793–801 (2011)Cite this article

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Key Points

  • The nematode worm Caenorhabitis elegans is ideal as a model organism for scientific research owing to its simplicity and arsenal of available tools. New technologies increase the usefulness of the worm as a model.

  • Loss-of-function experiments used to rely on untargeted mutagenesis techniques, such as chemical or transposon-based mutagenesis. Recent techniques allow for targeted mutagenesis using Mos-transposon-directed or zinc finger nuclease (ZFN)- or transcription activator-like effector nuclease (TALEN)-site-directed mutagenesis.

  • Loss-of-function experiments using RNAi have been refined so that knockdown only occurs in a tissue of interest rather than in the whole body.

  • Gain-of-function experiments have been improved in multiple facets by recent developments: recombineering technology and a fosmid DNA library have facilitated the generation and modification of DNA constructions, Mos transposition has allowed for single-copy insertion of a transgene into a defined locus, and using antibiotics as a selection marker has made it easier to screen for positive transgenesis events.

  • Gain-of-function experiments have been enhanced by the introduction of the FLP–FRT (flippase and flippase recognition target) system for inducible gene expression. In combination with other inducible systems, such as Cre–loxP and the heat shock promoter, FLP–FRT should allow for more refined control over gene expression.

  • Flow-cytometry technology can be used to ameliorate difficult or labour-intensive processes, including sorting synchronous-stage embryos and screening for genetic mutants.

  • Microfluidic technology can semi-automate procedures that require considerable labour or precision. Recent developments use microfluidic setups in order to semi-automate lifespan analysis and neurosurgery.

  • Imaging techniques have allowed for studies on the level of single cells or single molecules. Recent developments include methods to quantify gene expression in single cells, trace expression through cellular lineages during embryogenesis and detect single mRNA molecules in single cells.

  • Optogenetics, a method that uses light to activate or inactivate specific neurons, is ideally suited for C. elegans owing to the worm's transparent body and fairly simple nervous system of only 302 neurons. Recent methods that allow for optogenetics in freely moving worms permit the examination of the neural networks underlying movement and other behaviours, which could not be examined in immobilized worms.

Abstract

The inherent simplicity of Caenorhabditis elegans and its extensive genetic toolkit make it ideal for studying complex biological processes. Recent developments further increase the usefulness of the worm, including new methods for: altering gene expression, altering physiology using optogenetics, manipulating large numbers of worms, automating laborious processes and processing high-resolution images. These developments both enhance the worm as a model for studying processes such as development and ageing and make it an attractive model in areas such as neurobiology and behaviour.

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Figure 1: New genetic methods in Caenorhabditis elegans.
Figure 2: Caenorhabditis elegans microfluidics.
Figure 3: Using imaging in Caenorhabditis elegans to study cell lineages.
Figure 4: Using optogenetics in Caenorhabditis elegans.

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Acknowledgements

We thank members of the worm research community and apologize for the numerous works we could not cite owing to space limitations. We thank D. Sagi, M. Schvarzstein and members of the Kim laboratory for helpful discussion. We thank A. Sánchez-Blanco, A. Friedland and the anonymous reviewers for their suggestions and improvements and for their critical reading of the manuscript. X.X. is supported by the Cancer Biology Training Grant at Stanford University, California, USA. Research in the laboratory of S.K.K. is supported by the US National Human Genome Research Institute, the US National Institute of General Medical Sciences, the US National Institute on Aging and the Glenn Foundation.

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  1. Cancer Biology Program and Department of Developmental Biology, Stanford University School of Medicine, Stanford, 94305, California, USA

    Xiao Xu & Stuart K. Kim

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Correspondence to Stuart K. Kim.

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FURTHER INFORMATION

Stuart K. Kim's homepage

C. elegans fosmid library

C. elegans Gene Knockout Consortium

C. elegans RNAi library

Caenorhabditis Genetics Center

Cell lineaging information from the Waterston laboratory

Kim laboratory Automatic Cell Lineage Analyzer information

National BioResource Project of Japan

NemaGENETAG

Stanford Microfluidics Foundry

WormBase

WormBook

Wormatlas

Glossary

Biolistic bombardment

A technique for delivering nucleic acids into the cells, in which small metal particles coated with nucleic acid are fired into the target tissue under high pressure.

Recombineering

Molecular genetic engineering technique that uses homologous recombination to manipulate and/or alter DNA.

Fosmid

A low-copy vector for the construction of stable genomic libraries that uses the Escherichia coli F factor origin for replication. Each fosmid can store ~40 kb of library DNA, and these sequences are more stable in fosmids than in multi-copy vectors.

Florescence-activated cell sorting

(FACS). An experimental technology that can separate cells by their fluorescence and light-scattering properties.

Fluorescent in situ hybridization

(FISH). A microscopic technique that uses fluorescently tagged DNA probes to detect the cytological localization of specific RNA by in situ hybridization.

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Xu, X., Kim, S. The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit. Nat Rev Genet 12, 793–801 (2011). https://doi.org/10.1038/nrg3050

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