Destruction of the SCN leads to a complete loss of circadian rhythm. Rats with damage to the SCN have no circadian rhythms, i.e., they sleep the same total amount, but polyphasically for random lengths at a time.
The SCN also controls 'slave oscillators' in the peripheral tissues, which exhibit their own ~24 hour rhythms, but are crucially synchronized by the SCN.
The importance of entraining our bodies to an exogenous cue, such as daylight, is reflected by several circadian rhythm sleep disorders, where this process does not function normally.
Neurons in the ventrolateral SCN (vlSCN) have the ability for light-induced gene expression. If light is turned on at night, the vlSCN relays this information throughout the SCN, in a process called entrainment.
Neurons in the dorsomedial SCN (dmSCN) are believed to make an endogenous 24-hour rhythm that can persist under constant darkness (in humans averaging about 24h 11min). Melanopsin-containing ganglion cells in the retina have a direct connection to the SCN via the retinohypothalamic tract.
The circadian rhythm in the SCN is generated by a gene expression cycle in individual SCN neurons. This cycle has been well conserved through evolution, and is essentially similar in cells from many widely different organisms that show circadian rhythms.
These genes encode various transcription factors that trigger expression of other proteins. The products of clock and cycle, called CLK and CYC, belong to the PAS-containing subfamily of the basic-helix-loop-helix (bHLH) family of transcription factors, and form a heterodimer . This heterodimer (CLK-CYC) initiates the transcription of per and tim, whose protein products dimerize and then inhibit their own expression by disrupting CLK-CYC-mediated transcription. This negative feedback mechanism gives a 24-hour rhythm in the expression of the clock genes. Many genes are suspected to be linked to circadian control by "E-box elements" in their promoters, as CLK-CYC and its homologs bind to these elements.
The 24-hr rhythm could be reset by light via the protein CRYPTOCHROME (CRY), which is involved in the circadian photoreception in Drosophila. CRY associates with TIM in a light-dependent manner that leads to the destruction of TIM. Without the presence of TIM for stabilization, PER is eventually destroyed during the day. As a result, the repression of CLK-CYC is reduced and the whole cycle reinitiates again.
CLOCK (circadian locomotor output cycles kaput) was first cloned in mouse and BMAL1 (brain and muscle aryl hydrocarbon receptor nuclear translocator (ARNT)-like 1) is the primary homolog of Drosophila CYC.
TIM has been identified in mammals, however, its function is still not determined.
Recent research suggests that, outside the SCN clock, genes may have other important roles as well, including their influence on the effects of drugs of abuse such as cocaine.
Neurons in the SCN fire action potentials in a 24-hour rhythm. At mid-day, the firing rate reaches a maximum, and, during the night, it falls again. How the gene expression cycle (so-called the core clock) connects to the neural firing remains unknown.
Many SCN neurons are sensitive to light stimulation via the retina, and sustainedly firing action potentials during a light pulse (~30 seconds) in rodents. The photic response is likely linked to effects of light on circadian rhythms. In addition, focal application of melatonin can decrease firing activity of these neurons, suggesting that melatonin receptors present in the SCN mediate phase-shifting effects through the SCN.
Two contradictory reports exist about circadian variation of the cell calcium concentration. However, both reports agree that the resting calcium level is slightly higher during the day than at night.
A member of the American Psychiatric Association, Professor D.F.Swaab carried out research into this particular hypothalamic component whilst trying to find evidence of an organic basis for homosexuality in humans. He found the suprachiasmatic nucleus to be nearly twice the size in male homosexual subjects as in their heterosexual counterparts. This research was further confirmed by Laura S. Allen, who found the midsagittal plane of the anterior commissure of the hypothalamus to be one third larger in male homosexual subjects than in male heterosexuals. As suggested by the author of the article: "This anatomical difference, which correlates with gender and sexual orientation, may, in part, underlie differences in cognitive function and cerebral lateralization among homosexual men, heterosexual men, and heterosexual women". However, as it is put by Jeffrey Satinover, M.D “The specifics of these findings are not as important as realizing that unless group differences are dramatic, individual studies of such differences mean almost nothing. It would take hundreds, perhaps thousands of such studies before meaningful trend emerges”. It is also true that the brain may reconfigure itself in response to certain experiences. Research by G. Gabbard published in the American Journal of Psychiatry 149, no. 8 points that the establishment of new connections between cells, dramatically increase or decreases in the thickness of connections between cells in response to training, trauma and especially traumatic experience altering brain and body of monkeys in measurable ways.