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A functional genomic analysis of cell morphology using RNA interference

AA Kiger1, B Baum15, S Jones2, MR Jones3, A Coulson3, C Echeverri4 and N Perrimon1*

Author affiliations

1 Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA

2 Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver V5Z 4E6, Canada

3 MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK

4 Cenix BioScience GmbH, D-01307 Dresden, Germany

5 Current address: Ludwig Institute for Cancer Research, University College London W1W 7BS, UK

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Citation and License

Journal of Biology 2003, 2:27  doi:10.1186/1475-4924-2-27

Published: 1 October 2003



The diversity of metazoan cell shapes is influenced by the dynamic cytoskeletal network. With the advent of RNA-interference (RNAi) technology, it is now possible to screen systematically for genes controlling specific cell-biological processes, including those required to generate distinct morphologies.


We adapted existing RNAi technology in Drosophila cell culture for use in high-throughput screens to enable a comprehensive genetic dissection of cell morphogenesis. To identify genes responsible for the characteristic shape of two morphologically distinct cell lines, we performed RNAi screens in each line with a set of double-stranded RNAs (dsRNAs) targeting 994 predicted cell shape regulators. Using automated fluorescence microscopy to visualize actin filaments, microtubules and DNA, we detected morphological phenotypes for 160 genes, one-third of which have not been previously characterized in vivo. Genes with similar phenotypes corresponded to known components of pathways controlling cytoskeletal organization and cell shape, leading us to propose similar functions for previously uncharacterized genes. Furthermore, we were able to uncover genes acting within a specific pathway using a co-RNAi screen to identify dsRNA suppressors of a cell shape change induced by Pten dsRNA.


Using RNAi, we identified genes that influence cytoskeletal organization and morphology in two distinct cell types. Some genes exhibited similar RNAi phenotypes in both cell types, while others appeared to have cell-type-specific functions, in part reflecting the different mechanisms used to generate a round or a flat cell morphology.