Circadian clocks regulate many different physiological processes and synchronize these to environmental light:dark cycles. In Drosophila, light is transmitted to the clock by a circadian blue light photoreceptor CRYPTOCHROME (CRY). In response to light, CRY promotes the degradation of the circadian clock protein TIMELESS (TIM) and then is itself degraded. To identify novel genes involved in circadian entrainment, we performed an unbiased genome-wide screen in Drosophila cells using a sensitive and quantitative assay that measures light-induced degradation of CRY. We systematically knocked down the expression of ∼21,000 genes and identified those that regulate CRY stability. These genes include ubiquitin ligases, signal transduction molecules, and redox molecules. Many of the genes identified in the screen are specific for CRY degradation and do not affect degradation of the TIM protein in response to light, suggesting that, for the most part, these two pathways are distinct. We further validated the effect of three candidate genes on CRY stability in vivo by assaying flies mutant for each of these genes. This work identifies a novel regulatory network involved in light-dependent CRY degradation and demonstrates the power of a genome-wide RNAi approach for understanding circadian biology.[Keywords: RNAi; circadian rhythms; clock proteins; degradation; photoreceptors] Supplemental material is available at http://www.genesdev.org. The cycling of PER and TIM is essential for circadian rhythms and is thought to provide timekeeping cues for the organism. Consistent with the idea that levels of PER-TIM constitute time-of-day signals, light sets the time of the clock by altering levels of these molecules. Thus, entrainment of the molecular clock to light is mediated by light-induced degradation of the TIM protein.In response to light, TIM is targeted to the ubiquitinproteasome pathway by an E3 ubiquitin ligase complex containing the F-box protein JETLAG (JET) (Naidoo et al. 1999;Koh et al. 2006). The ubiquitin-proteasome pathway may also affect light-independent PER-TIM degradation, which maintains cycling under free-running conditions (Grima et al. 2002;Ko et al. 2002). Degradation of TIM in response to light, as well as in free-running conditions, is affected by its phosphorylation state (Zeng et al. 1996;Naidoo et al. 1999;Grima et al. 2002;Yuan et al. 2005).Photic signals are transmitted to TIM by a dedicated circadian photoreceptor, CRYPTOCHROME (CRY) (Cashmore 2003;Lin and Todo 2005). After signaling to TIM, CRY is itself degraded by the proteasome pathway (Lin et al. 2001), However the role of light-dependent CRY degradation in regulating circadian behavior and resetting is not clear. According to one report, clock neuron-specific overexpression of CRY increases circadian photo sensitivity (Emery et al. 2000), while another study found that overexpression of CRY reduces photo sensitivity (Ishikawa et al. 1999). A CRY mutant (CRY m ) lacking the C-terminal domain required for the regula-