Site- and cell-type-specific miRNA and mRNA genes and networks across the cortex, striatum, and hypothalamus

Biological rhythms control gene expression, but effects on central nervous system (CNS) cells and structures remain poorly defined. While circadian (24-hour) rhythms are most studied, many genes have periods of greater and less than 24-hours; these fluctuations can be both site- and cell-specific. Identifying patterns of gene rhythmicity across the CNS is necessary for both the study of chronobiology and to make sense of data obtained in the laboratory. We now identify cycling mRNAs, miRNAs, gene networks and mRNA-miRNA co-expression pairs in the cortex, hypothalamus, and corpus striatum of male C57BL/6J mice using high-dimensional datasets. A searchable catalogue ( https://www.ghasemloulab.ca/chronoCNS ) helps refine the analysis of cellular and molecular rhythmicity across the CNS (using the liver as a control). Immunofluorescence confirms the rhythmicity of key targets across cells in these structures, with strong cycling signatures in resting oligodendrocytes. Our study sheds light on the contribution of diurnal, ultradian, and infradian rhythms and mRNA-miRNA interactions to CNS function.