A genome-wide RNAi screen for modifiers of the circadian clock in human cells

Cell. 2009 Oct 2;139(1):199-210. doi: 10.1016/j.cell.2009.08.031. Epub 2009 Sep 17.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biological Clocks*
  • Cell Line
  • Circadian Rhythm*
  • Gene Knockdown Techniques
  • Genome-Wide Association Study*
  • Humans
  • RNA Interference
  • RNA, Small Interfering / metabolism


  • RNA, Small Interfering