Autophagy is a highly conserved intracellular degradation system, and recently 
was shown to display circadian rhythms in mice. The mechanisms underlying 
circadian regulation of autophagy, however, are still unclear. Here, we observed 
that numbers of autophagosomes and autolysosomes exhibit daily rhythms in the 
zebrafish liver, and cebpb/(c/ebpβ) and various autophagy genes are rhythmically 
expressed in zebrafish larvae but significantly upregulated in per1b and 
TALEN-generated nr1d1/rev-erbα mutant fish, indicating that both Per1b and Nr1d1 
play critical roles in autophagy rhythms. Luciferase reporter and ChIP assays 
show that the circadian clock directly regulates autophagy genes through Nr1d1, 
and also regulates transcription of cebpb through Per1b. We also found that 
fasting leads to altered expression of both circadian clock genes and autophagy 
genes in zebrafish adult peripheral organs. Further, transcriptome analysis 
reveals multiple functions of Nr1d1 in zebrafish. Taken together, these findings 
provide evidence for how the circadian clock regulates autophagy, imply that 
nutritional signaling affects both circadian regulation and autophagy activities 
in peripheral organs, and shed light on how circadian gene mutations act through 
autophagy to contribute to common metabolic diseases such as obesity.