Figure 1. Transcription‐translation feedback loops of the circadian clock mechanism. In the positive loop, BMAL1 and CLOCK heterodimerize to activate transcription of the genes encoding proteins that function in the feedback loops as well as tissue‐specific target genes. In the negative loop, PER and CRY act to inhibit BMAL1/CLOCK transcriptional activity thereby decreasing their own expression. In an ancillary loop, ROR and REV‐ERB mediate opposing action on the expression of the Bmal1 gene.

Figure 2. The mammalian circadian system and its crosstalk with physiology. (A) The circadian system includes the hierarchical multi‐oscillator network, the input pathways for entrainment, and rhythmic outputs in genes, metabolism, physiology, and behavior. The SCN directly receives photic cues for entrainment to the light/dark cycle. In turn, the SCN functions to synchronize extra‐SCN and peripheral clocks. While the SCN is responsive to photic cues, the peripheral oscillators are more responsive to nonphotic cues such as feeding. (B) Several major organs and pathways that provide inputs to the circadian clock. The molecular clock is based on a transcriptional/translational negative feedback mechanism. The core loop consists of positive (BMAL1, CLOCK) and negative (PER, CRY) factors, which act on the E‐box cis‐element. In particular, the Per genes contain other regulatory elements including cAMP response element (CRE) and glucocorticoid response element (GRE). Melanopsin in the retina mediates photic transmission through cAMP production and the CRE‐binding protein (CREB) pathway. The hypothalamus (SCN to CRH neurons)‐pituitary‐adrenal axis regulates glucocorticoid secretion. Glucagon, insulin, and IGF‐1 provide metabolic and growth signal inputs to the clock via the master nutrient/energy sensors AMPK and mTOR. In the case of insulin and IGF‐1, the pathways lead to the upregulation of PER2 and CRY1, thereby affecting the clock function.

Figure 3. Definitions for genomic tools.

Figure 4. Transcriptional repressors and activators in the mouse liver. Correlating data from ChIP‐seq using antibodies against the proteins depicted in this figure, Takahashi and colleagues developed a model demonstrating how clock target gene promoter occupancy of the activator complex (in shades of green) peaks during the light phase (day) whereas occupancy of the repressor complex (shades of red) peaks during the dark phase (night). Occupancy of the activators coincides with H3K9ac (histone 3 lysine 9 acetylation), a marker of open chromatin, in contrast to the presence of H3K4me3 (histone 3 lysine 4 trimethylation), a marker of closed chromatin, which coincides with occupancy of the repressor complex. Reused, with permission, from Cox KH and Takahashi JS, 2019 54.

Figure 5. Model of neuro‐immune axis signaling contributing to cardiovascular disease through clock‐mediated signaling pathways. Soluble factors and cellular mediators contribute to the inflammatory milieu leading to pro‐fibrotic signaling in the heart. Together with arrhythmogenesis due to sympathetic activity, these conditions may contribute to cardiovascular disease. Diagram was created using Biorender.com.

Figure 6. Skeletal muscle circadian clock signaling. (A) The transcription‐translation feedback loop in muscle regulates muscle‐specific genes including MyoD1. (B) Despite differences in diurnality in humans and nocturnality in mice, the expression patterns of Bmal1 and Per2 are quite similar between these two species.

Figure 7. Circadian clock effects on physiological function. Circadian proteins in parentheses represent the known proteins that are implicated in the regulation of the process examined. Additional proteins not listed may not have been tested and could also be involved. Diagram was created using Biorender.com.