Genome-Wide Functional Analysis of Human Cell-Cycle Regulators

• Published in: Proceedings of the National Academy of Sciences - PNAS 2006-10, Vol.103 (40), p.14819-14824
• Main Authors: Mukherji, Mridul, Bell, Russell, Supekova, Lubica, Wang, Yan, Orth, Anthony P., Batalov, Serge, Miraglia, Loren, Huesken, Dieter, Lange, Joerg, Martin, Christopher, Sahasrabudhe, Sudhir, Reinhardt, Mischa, Natt, Francois, Hall, Jonathan, Mickanin, Craig, Labow, Mark, Chanda, Sumit K., Cho, Charles Y., Schultz, Peter G.
• Format: Article
• Language: English
• Subjects: Biological Sciences; Cell cycle; Cell cycle proteins; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; Cell lines; Cell nucleus; Cluster Analysis; Cytokinesis - genetics; DNA; Gene Expression; Gene expression regulation; Genes; Genes, cdc; Genetic screening; Genome, Human - genetics; Genomic Library; Genomics; Humans; Microscopy; Mitosis - genetics; Neoplasms - genetics; Phenotype; Protein Interaction Mapping; Proteins; Regulator genes; Ribonucleic acid; RNA; RNA Interference; RNA, Small Interfering - metabolism; Small interfering RNA
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0604320103

Human cells have evolved complex signaling networks to coordinate the cell cycle. A detailed understanding of the global regulation of this fundamental process requires comprehensive identification of the genes and pathways involved in the various stages of cell-cycle progression. To this end, we report a genome-wide analysis of the human cell cycle, cell size, and proliferation by targeting >95% of the protein-coding genes in the human genome using small interfering RNAs (siRNAs). Analysis of >2 million images, acquired by quantitative fluorescence microscopy, showed that depletion of 1,152 genes strongly affected cell-cycle progression. These genes clustered into eight distinct phenotypic categories based on phase of arrest, nuclear area, and nuclear morphology. Phase-specific networks were built by interrogating knowledge-based and physical interaction databases with identified genes. Genome-wide analysis of cell-cycle regulators revealed a number of kinase, phosphatase, and proteolytic proteins and also suggests that processes thought to regulate Gi-S phase progression like receptor-mediated signaling, nutrient status, and translation also play important roles in the regulation of G₂/M phase transition. Moreover, 15 genes that are integral to TNF/NF-KB signaling were found to regulate G₂/M, a previously unanticipated role for this pathway. These analyses provide systems-level insight into both known and novel genes as well as pathways that regulate cell-cycle progression, a number of which may provide new therapeutic approaches for the treatment of cancer.