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Automated analysis of embryonic gene expression with cellular resolution in C. elegans

Nature Methods volume 5, pages 703–709 (2008)Cite this article

Abstract

We describe a system that permits the automated analysis of reporter gene expression in Caenorhabditis elegans with cellular resolution continuously during embryogenesis. We demonstrate its utility by defining the expression patterns of reporters for several embryonically expressed transcription factors. The invariant cell lineage permits the automated alignment of multiple expression profiles, allowing direct comparison of the expression of different genes' reporters. We also used this system to monitor perturbations to normal development involving changes both in cell-division timing and in cell fate. Systematic application of this system could reveal the gene activity of each cell throughout development.

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Figure 1: Lineage-based expression data display.
Figure 2: Comparison of expression patterns.
Figure 3: Expression changes after RNAi.

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Acknowledgements

We thank J. Thomas, J. Priess and members of their labs for helpful discussions. We also thank J. Thomas for critical comments on the manuscript. We thank A. Audhya (University of Wisconsin, Madison) for providing worm-optimized mCherry before publication and J. Waddle (Southern Methodist University) for providing unpublished HIS-24 protein fusion vectors. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the US National Institutes of Health National Center for Research Resources. This work was partially supported by funding from the National Institutes of Health. J.I.M. is a fellow of the Jane Coffin Childs Memorial Fund for Medical Research. Z.B. is a Damon Runyon Fellow supported by Damon Runyon Cancer Research Fellowship (DRG-1813-04).

Author information

Author notes

  1. Zhirong Bao

    Present address: Present address: Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10065, USA.,

  2. John Isaac Murray and Zhirong Bao: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, 98195, Washington, USA

    John Isaac Murray, Zhirong Bao, Thomas J Boyle, Max E Boeck, Barbara L Mericle, Thomas J Nicholas, Zhongying Zhao, Matthew J Sandel & Robert H Waterston

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  1. John Isaac Murray
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Contributions

R.H.W., Z.B. and J.I.M. conceived the experiments. J.I.M., Z.B., M.E.B., T.J.N., B.L.M., Z.Z. and M.J.S. performed the experiments. T.J.B., Z.B. and J.I.M. wrote software for data analysis. J.I.M., Z.B., T.J.B. and J.I.M. analyzed the data. J.I.M. and R.H.W. wrote the paper with input from the other authors.

Corresponding author

Correspondence to Robert H Waterston.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Tables 1–2; Supplementary Methods (PDF 458 kb)

Supplementary Data (XLS 10082 kb)

Supplementary Video 1.

3D projection for pha-4 reporter image series. A 3D projection of a single pha-4 image series showing ubiquitous GFP (green) and pha-4 driven H1-DsRed.T1 (red). (MOV 5332 kb)

Supplementary Video 2.

3D model of pha-4 reporter expression. A 3D model of development derived from our analysis showing expressing cells as spheres colored by lineage identity as in Figure 1B and nonexpressing cells as semitransparent spheres. (MOV 3557 kb)

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Murray, J., Bao, Z., Boyle, T. et al. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat Methods 5, 703–709 (2008). https://doi.org/10.1038/nmeth.1228

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