A Genome-wide microRNA screen identifies the microRNA-183/96/182 cluster as a modulator of circadian rhythms

Abstract

The regulatory mechanisms of circadian rhythms have been studied primarily at the level of the transcription-translation feedback loops of protein coding genes. Regulatory modules involving non-coding RNAs are less thoroughly understood. In particular, emerging evidence has revealed the important role of miRNAs in maintaining the robustness of the circadian system. To identify miRNAs that have the potential to modulate circadian rhythms, we conducted a genome-wide miRNA screen using U2OS luciferase reporter cells. Among 989 miRNAs in the library, 120 changed the period length in a dosage-dependent manner. We further validated the circadian regulatory function of a miRNA cluster, miR-183/96/182, both in vitro and in vivo. We found that all three members of this miRNA cluster can modulate circadian rhythms. Particularly, miR-96 directly targeted a core circadian clock gene, PER2. The knockout of the miR-183/96/182 cluster in mice showed tissue-specific effects on circadian parameters and altered circadian rhythms at the behavioral level. This study identified a large number of miRNAs, including the miR-183/96/182 cluster, as circadian modulators. We provide a resource for further understanding the role of miRNAs in the circadian network and highlight the importance of miRNAs as a novel genome-wide layer of circadian clock regulation. Significance StatementAlthough miRNAs are emerging as important regulators of diverse physiological and pathological processes, our knowledge of their potential role in regulation of circadian rhythms is still limited. We deployed a cell-based genome-wide screening approach, and successfully identified mature miRNAs as cell-autonomous circadian modulators. We then specifically focused on the miR-183/96/182 cluster among the candidate miRNA hits and revealed their circadian function both in vitro and in vivo from the unbiased screen. This study provides resources for further understanding the role of miRNAs in the circadian network. It also highlights the importance of miRNAs as a novel genome-wide layer of circadian clock regulation.