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Originally published as MBC in Press, 10.1091/mbc.E06-04-0340 on September 6, 2006

Vol. 17, Issue 11, 4837-4845, November 2006

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Targeted Comparative RNA Interference Analysis Reveals Differential Requirement of Genes Essential for Cell ProliferationFormula

Yuichi J. Machida*, Yuefeng Chen*, Yuka Machida*, Ankit Malhotra*,{dagger}, Sukumar Sarkar*, and Anindya Dutta*

*Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908; and {dagger}Department of Computer Sciences, University of Virginia School of Engineering and Applied Science, Charlottesville, VA 22904

Submitted April 24, 2006; Accepted August 28, 2006
Monitoring Editor: Charles Boone

Differences in the genetic and epigenetic make up of cell lines have been very useful for dissecting the roles of specific genes in the biology of a cell. Targeted comparative RNAi (TARCOR) analysis uses high throughput RNA interference (RNAi) against a targeted gene set and rigorous quantitation of the phenotype to identify genes with a differential requirement for proliferation between cell lines of different genetic backgrounds. To demonstrate the utility of such an analysis, we examined 257 growth-regulated genes in parallel in a breast epithelial cell line, MCF10A, and a prostate cancer cell line, PC3. Depletion of an unexpectedly high number of genes (25%) differentially affected proliferation of the two cell lines. Knockdown of many genes that spare PC3 (p53–) but inhibit MCF10A (p53+) proliferation induces p53 in MCF10A cells. EBNA1BP2, involved in ribosome biogenesis, is an example of such a gene, with its depletion arresting MCF10A at G1/S in a p53-dependent manner. TARCOR is thus useful for identifying cell type–specific genes and pathways involved in proliferation and also for exploring the heterogeneity of cell lines. In particular, our data emphasize the importance of considering the genetic status, when performing siRNA screens in mammalian cells.

Formula The online version of this contains supplemental material at MBC Online (http://www.molbiolcell.org).

This article was published online ahead of print in MBC in Press (http://www.molbiolcell.org/cgi/doi/10.1091/mbc.E06-04-0340) on September 6, 2006.

Address correspondence to: Anindya Dutta (ad8q{at}virginia.edu)

Abbreviations used: RNAi, RNA interference; siRNA, small interfering RNA; TARCOR, targeted comparative RNAi




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