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MicroRNAs are important coordinators of circadian regulation that mediate the fine-tuning of gene expression. Although many studies have shown the effects of individual miRNAs on the circadian clock, the global functional miRNA-mRNA interaction network involved in the circadian system remains poorly understood. Here, we used CLEAR (Covalent Ligation of Endogenous Argonaute-bound RNAs)-CLIP (Cross-Linking and Immuno-Precipitation) to explore the regulatory functions of miRNAs in the circadian system by comparing the miRNA-mRNA interactions between Drosophila wild-type strain W(1118) and a mutant of the key circadian transcriptional regulator Clock (Clk(jrk)). This experimental approach unambiguously identified tens of thousands of miRNA-mRNA interactions in both the head and body. The miRNA-mRNA interactome showed dramatic changes in the Clk(jrk) flies. Particularly, among ~300 miRNA-mRNA circadian relevant interactions, multiple interactions involving core clock genes pdp1, tim and vri displayed distinct changes as a result of the Clk mutation. Based on the CLEAR-CLIP analysis, we found a novel regulation of the circadian rhythm and sleep by the miR-375-timeless interaction. The results indicated that Clk disruption abolished normal rhythmic expression of miR-375 and the functional regulation occurred in the l-LNv neurons, where miR-375 modulated circadian rhythm and sleep via targeting timeless. This work provides the first global view of miRNA regulation in the circadian rhythm.

MicroRNA is critical coordinator to circadian regulation by silencing gene expression. Although many circadian related miRNAs and some of its target are known, the global functional miRNA-mRNA interaction networks remain poorly understand which is hindered by imperfect base-pairing between miRNA and target mRNA. In this study, we used CLEAR (Covalent Ligation of Endogenous Argonaute-bound RNAs) -CLIP (Cross-Linking and Immuno-Precipitation) to explore the regulatory functions of miRNAs in the circadian system by comparing the miRNA-mRNA interactions between the Drosophila wild-type strain w1118 and the Clk mutant Clkjrk. We unambiguously identified thousands of miRNA-mRNA interactions from CLEAR-CLIP data set at unprecedented depth in vivo for the first time. Among them, about 300 miRNA-mRNA interactions were involved in the regulation of circadian, in which miRNAs targeting core clock genes pdp1, tim and vri presented distinct changes in response to Clkjrk. Particularly, the mir-375-timeless interaction from CLER-CLIP shows important effects on circadian, this functional event occurred in the l-LNv neurons. Overexpression of mir-375 in tim neurons caused decreases in TIM content resulting in arrhythmicity of daily locomotion and changes of sleep. This present work provides a global view of miRNA targeting in the circadian rhythm.