Research

Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology

Tao Liu¹, David Sims² and Buzz Baum^1*

• * Corresponding author: Buzz Baum b.baum@ucl.ac.uk

Author Affiliations

¹ MRC Laboratory of Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK

² The Institute of Cancer Research, Chester Beatty Laboratories, Fulham Road, London SW3 6JB, UK

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Genome Biology 2009, 10:R26 doi:10.1186/gb-2009-10-3-r26

Published: 5 March 2009

Abstract

Background

In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems.

Results

Here, to dissect generic and cell type-specific mechanisms underlying cell morphology, we have performed identical kinome RNAi screens in six different Drosophila cell lines, derived from two distinct tissues of origin. This analysis identified a core set of kinases required for normal cell morphology in all lines tested, together with a number of kinases with cell type-specific functions. Most significantly, the screen identified a role for minibrain (mnb/DYRK1A), a kinase associated with Down's syndrome, in the regulation of actin-based protrusions in CNS-derived cell lines. This cell type-specific requirement was not due to the peculiarities in the morphology of CNS-derived cells and could not be attributed to differences in mnb expression. Instead, it likely reflects differences in gene expression that constitute the cell type-specific functional context in which mnb/DYRK1A acts.

Conclusions

Using parallel RNAi screens and gene expression analyses across cell types we have identified generic and cell type-specific regulators of cell morphology, which include mnb/DYRK1A in the regulation of protrusion morphology in CNS-derived cell lines. This analysis reveals the importance of using different cell types to gain a thorough understanding of gene function across the genome and, in the case of kinases, the difficulties of using the differential gene expression to predict function.