Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans

Abstract

A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.

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Figure 1
Figure 2: Distribution of phenotypes identified in the C. elegans genome-wide RNAi screen.
Figure 3: Systematic analysis of DIC time-lapse recordings monitoring the first two rounds of cell division in C. elegans embryos yields defect patterns or phenotypes that group into 23 different classes.
Figure 4: Genes in phenotype classes are associated with distinctive biochemical pathways and key events in the first cell divisions of C. elegans embryos.

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Acknowledgements

We thank M. Srayko, C. Cowan, L. Pelletier and W. B. Wood for critical reading of the manuscript, and M. Volkmer and S. Schloissnig for their help on the completion of the online Phenobank database. This work was supported in part by the German government through a DLR grant. A.C. was supported by the MRC, UK.

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Correspondence to B. Sönnichsen.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Table 1

Phenotypic and functional classification of all genes with early embryonic (DIC) phenotypes. (XLS 337 kb)

Supplementary Table 2

Comparison between RNAi and conventional genetics. (XLS 26 kb)

Supplementary Table 3

Comparison of screening coverage and detection accuracy for early embryonic phenotypes in the present study versus Zipperlen et al. and Piano et al. (XLS 25 kb)

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Sönnichsen, B., Koski, L., Walsh, A. et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462–469 (2005). https://doi.org/10.1038/nature03353

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