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

Genome Biol. 2009;10(3):R26. doi: 10.1186/gb-2009-10-3-r26. Epub 2009 Mar 5.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actins / metabolism*
  • Animals
  • Cell Line
  • Cell Shape*
  • Cell Surface Extensions
  • Central Nervous System / cytology
  • Central Nervous System / enzymology
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / cytology*
  • Drosophila melanogaster / enzymology
  • Drosophila melanogaster / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Genes, Insect
  • Genetic Testing*
  • Hemocytes / cytology
  • Hemocytes / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Organ Specificity
  • Phenotype
  • Protein-Serine-Threonine Kinases / metabolism
  • RNA Interference*

Substances

  • Actins
  • Drosophila Proteins
  • mnb protein, Drosophila
  • Protein-Serine-Threonine Kinases