The Ontogeny of Rhythms in Circadian Clock Gene Expression in Mouse Brain and Neuroimmune Tissues

The circadian system coordinates daily physiology across nearly all tissues to temporally organize metabolism and maintain homeostasis. In the brain, circadian timing regulates neural activity, cellular function, and neuroimmune signaling, which is especially important during development. Yet, the ontogeny of circadian regulation during neurodevelopment remains poorly defined. Here, we characterized time-of-day variation in core clock and neuroimmune genes across multiple brain structures during early postnatal development, alongside circulating corticosterone concentrations. Using male and female C57BL mice housed in a standard light-dark cycle [12:12 light (150 lux)/dark (0 lux)], we measured the expression of Per1 , Per2 , and Rev-erbα in the suprachiasmatic nucleus, hippocampus, and medial prefrontal cortex, as well as in neuroimmune tissues (choroid plexus, meninges, and isolated microglia) across postnatal days (PND) 1-24. Across development, rhythms were seen in corticosterone concentrations and all brain regions, with increased amplitudes and gene-specific phase maturation toward adult-like timing by PND 24. Notably, the choroid plexus and meninges exhibited time-of-day differences in clock gene expression by PND 10-24. In contrast, isolated microglia did not display detectable time-of-day differences in clock gene expression; however, microglial phagocytic activity varied by time of day. Together, these findings demonstrate that circadian regulation of the brain emerges during the neonatal period, and the parameters of time-of-day differences are tissue- and gene-specific during development. In addition, functional rhythms may precede or occur independent of detectable transcriptional differences. This work establishes a developmental framework for circadian-neuroimmune interactions, with important implications for neuroimmune development and vulnerability. Given the neuroimmune system’s role in shaping brain development, disruptions in these temporal processes may contribute to neurodevelopmental or mood disorders.