Research

Whole genome functional analysis identifies novel components required for mitotic spindle integrity in human cells

Daniel R Rines¹ , Maria Ana Gomez-Ferreria² , Yingyao Zhou¹ , Paul DeJesus¹ , Seanna Grob¹ , Serge Batalov¹ , Marc Labow³ , Dieter Huesken⁴ , Craig Mickanin³ , Jonathan Hall⁴ , Mischa Reinhardt⁴ , Francois Natt⁴ , Joerg Lange⁴ , David J Sharp² , Sumit K Chanda^1,5 and Jeremy S Caldwell¹

¹Genomics Institute of Novartis Research Foundation, John Jay Hopkins Drive, San Diego, California 92121, USA

²Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Marris Park Avenue, Bronx, New York 10461, USA

³Novartis Institute for Biomedical Research Inc., Mass Avenue, Cambridge, Massachusetts 02139, USA

⁴Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland

⁵Infectious & Inflammatory Disease Center, Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, California 92037, USA

author email corresponding author email

Genome Biology 2008, 9:R44doi:10.1186/gb-2008-9-2-r44

Published:	26 February 2008

Subject areas: Cancer, Cell biology, Genetics

Abstract

Background

The mitotic spindle is a complex mechanical apparatus required for accurate segregation of sister chromosomes during mitosis. We designed a genetic screen using automated microscopy to discover factors essential for mitotic progression. Using a RNA interference library of 49,164 double-stranded RNAs targeting 23,835 human genes, we performed a loss of function screen to look for small interfering RNAs that arrest cells in metaphase.

Results

Here we report the identification of genes that, when suppressed, result in structural defects in the mitotic spindle leading to bent, twisted, monopolar, or multipolar spindles, and cause cell cycle arrest. We further describe a novel analysis methodology for large-scale RNA interference datasets that relies on supervised clustering of these genes based on Gene Ontology, protein families, tissue expression, and protein-protein interactions.

Conclusion

This approach was utilized to classify functionally the identified genes in discrete mitotic processes. We confirmed the identity for a subset of these genes and examined more closely their mechanical role in spindle architecture.