The suprachiasmatic nucleus (SCN) is the master clock that orchestrates circadian clocks across the body to synchronize with and anticipate the earth’s light/dark cycles. Although post-transcriptional regulators called microRNAs have been implicated in physiological SCN function, how the absence of the entire mature miRNome impacts SCN output has not yet been explored. Here, we have generated an SCN-specific Dicer knockout mouse model by crossing Syt10Cre mice with Dicerflox mice to study behavioral consequences of miRNA depletion in the SCN. We show that loss of all mature miRNAs in the SCN shortens the circadian period length by ~40 minutes at the tissue level, and by ~50 minutes at the locomotor activity level. Knockout animals also showed arrythmicity or ultradian locomotor activities with no light masking under constant light, a condition which usually caused lengthening of the circadian period length and reduced activities, i.e. light masking, in nocturnal animals. Moreover, induction of Dicer knockout by Cre injection into the SCN of adult Dicerflox mice eventually resulted in loss of behavioral rhythms. Finally, we show suggestive evidence that SCN desynchronization might be one mechanism underlying the behavioral phenotypes of SCN-specific Dicer knockout animals.

While it is generally known that metabolic disorders and circadian dysfunction are intertwined, how the two systems affect each other is not well understood, nor are the genetic factors that might exacerbate this pathological interaction. Blood chemistry is profoundly changed in metabolic disorders, and we have previously shown that serum factors change cellular clock properties. To investigate if circulating factors altered in metabolic disorders have circadian modifying effects, and whether these effects are of genetic origin, we measured circadian rhythms in U2OS cell in the presence of serum collected from diabetic, obese, or control subjects. We observed that circadian period lengthening in U2OS cells was associated with serum chemistry that is characteristic of insulin resistance. Characterizing the genetic variants that altered circadian period length by genome-wide association analysis, we found that one of the top variants mapped to the E3 ubiquitin ligase MARCH1 involved in insulin sensitivity. Confirming our data, the serum circadian modifying variants were also enriched in type 2 diabetes and chronotype variants identified in the UK Biobank cohort. Finally, to identify serum factors that might be involved in period lengthening, we performed detailed metabolomics, and found that the circadian modifying variants are particularly associated with branched chain amino acids, whose levels are known to correlate with diabetes and insulin resistance. Overall, our multi-omics data showed comprehensively that systemic factors serve as a path through which metabolic disorders influence circadian system, and these can be examined in human populations directly by simple cellular assays in common cultured cells.