Functional annotation of extensively and divergently expressed miRNAs in suprachiasmatic nucleus of Clock ∆19 mutant mice.

Circadian locomotor output cycles kaput protein (CLOCK) is a core transcription factor of complex integrated feedback loops in mammalian circadian clock. More genes have been reported to be regulated by CLOCK, however little is known about the role of CLOCK-mediated miRNAs. To dissect this, we used microarray analysis to measure miRNAs expression in suprachiasmatic nuclei (SCN) of wild type (WT) and Clock Δ19 mutant mice at two different time points. We found that miRNAs regulation in two time points was extensive (nearly 75% of the miRNAs expressed at each time point), and very little overlap, with only 6 miRNAs in common. Besides this, the predicted CLOCK regulated miRNAs at two time points participated in extremely diverse pathways. We validated nine miRNAs (miR-125a-3p, miR-144, miR-199a-5p, miR-199b*, miR-200a, miR-200b, miR-203, miR-449a and miR-96), which were involved in the same signaling pathway-hippo signaling pathway. The rhythms of these miRNAs showed a broad distribution of phase, amplitude and waveform in Clock mutation. And further analysis indicated that there may be three models of miRNAs-mediated circadian rhythms and hippo signaling pathway. MiRNAs, the small player, may play a hub role in connecting circadian rhythms and other pathways via its multiple target genes networks.