A Genome-wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells

• Published in: Cell Vol. 139; no. 1; pp. 199 - 210
• Main Authors: Zhang, Eric E., Liu, Andrew C., Hirota, Tsuyoshi, Miraglia, Loren J., Welch, Genevieve, Pongsawakul, Pagkapol Y., Liu, Xianzhong, Atwood, Ann, Huss, Jon W., Janes, Jeff, Su, Andrew I., Hogenesch, John B., Kay, Steve A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 02.10.2009
• Subjects: Biological Clocks; Cell cycle; Cell Line; Circadian Rhythm; Circadian rhythms; CLOCK protein; Data processing; DEVBIO; Feedback; Folic acid; Gene Knockdown Techniques; Genome-Wide Association Study; Hedgehog protein; Humans; Insulin; Metabolism; Oscillators; Protein interaction; RNA Interference; RNA, Small Interfering - metabolism; RNA-mediated interference; Signal transduction; SIGNALING; siRNA; SYSBIO; SYSBIO; DEVBIO; SIGNALING
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2009.08.031

Two decades of research identified more than a dozen clock genes and defined a biochemical feedback mechanism of circadian oscillator function. To identify additional clock genes and modifiers, we conducted a genome-wide small interfering RNA screen in a human cellular clock model. Knockdown of nearly 1000 genes reduced rhythm amplitude. Potent effects on period length or increased amplitude were less frequent; we found hundreds of these and confirmed them in secondary screens. Characterization of a subset of these genes demonstrated a dosage-dependent effect on oscillator function. Protein interaction network analysis showed that dozens of gene products directly or indirectly associate with known clock components. Pathway analysis revealed these genes are overrepresented for components of insulin and hedgehog signaling, the cell cycle, and the folate metabolism. Coupled with data showing many of these pathways are clock regulated, we conclude the clock is interconnected with many aspects of cellular function.