Suprachiasmatic nucleus (SCN)

The suprachiasmatic nucleus (SCN) is a paired structure in your hypothalamus, sitting just above the optic chiasm, with about 20,000 neurons per side. It is the master circadian clock of mammals. It generates a near-24-hour rhythm through a self-regulating feedback loop of genes and proteins (CLOCK, BMAL1, PER, and CRY). Light input keeps it in sync. Special retinal cells (ipRGCs, carrying the pigment melanopsin) send signals along the retinohypothalamic tract to entrain the SCN to the day-night cycle. Its role as the pacemaker was nailed down by Ralph and colleagues (Science, 1990): grafting SCN tissue from a fast-clock mutant hamster into a hamster whose own SCN was removed restored rhythms, but on the donor's schedule. The SCN's outputs then synchronize the 'peripheral clocks' in your liver, muscle, fat, and other tissues, through nerve and hormonal signals.

Last reviewed: June 22, 2026

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