CLOCK
CLOCK is a gene, and its name is a backronym: circadian locomotor output cycles kaput. That word kaput hints at how it was found, by deliberately breaking it. In 1997, a team led by Joseph Takahashi fed mice a chemical that scrambles DNA, then watched their daily rhythms drift. Some mice stretched their internal day far past 24 hours. Others lost any sense of time entirely after a few days in the dark. From that broken behavior, a gene emerged that helps set the tempo of living things. What does this gene actually do inside a cell? Why does the same logic appear in a fruit fly and a mouse? And how did a timekeeper trace back to bacteria that lived before complex life existed? Those are the questions ahead.
CLOCK encodes a basic helix-loop-helix-PAS transcription factor, a protein that switches other genes on. It sits at the center of the circadian pacemaker, acting as an activator of the downstream elements that generate daily rhythms. In a fruit fly, newly made CLOCK starts out hypophosphorylated in the cytoplasm before it slips into the nucleus. Once inside, it gathers into nuclear foci, then spreads out evenly. A partner protein called CYCLE, known as dBMAL because it matches the mammalian BMAL1, locks onto CLOCK through their shared PAS domains. The joined pair then pulls in a co-activator, CREB-binding protein, and picks up phosphate groups. Now phosphorylated, the CLK-CYC complex grips the E-box stretches in the promoters of two genes, period and timeless, switching both on. The proteins they make, PER and TIM, eventually flood the cell. They pair into a PER-TIM heterodimer that blocks CLK-CYC from reaching those E-boxes, shutting the same genes back off. A kinase named doubletime then over-phosphorylates the complex in a PER-dependent way, destabilizing both CLK and PER until they degrade. Fresh hypophosphorylated CLK accumulates and starts the cycle again, so the rhythm of phosphorylation becomes the rhythm of the clock.
In mice, BMAL1 takes the role that CYCLE plays in flies, dimerizing with CLOCK to switch on period and a gene called cryptochrome. The PER and CRY proteins build up and pair off during subjective night, then move into the nucleus. There they press against the CLOCK:BMAL1 complex and shut down their own genes, a feedback loop confirmed through crystallographic analysis. CLOCK also carries histone acetyltransferase activity, a chemical tagging that loosens DNA, and dimerizing with BMAL1 makes that activity stronger. Working in vitro, Paolo Sassone-Corsi and colleagues showed this tagging activity is required to restore rhythms in Clock mutants. So CLOCK does not just bind DNA; it physically remodels the packaging around it.
SIRT1, an enzyme, latches onto the CLOCK-BMAL complex and dampens it, likely by stripping acetyl tags from BMAL1 and nearby histones. Its role stays controversial, and it may also strip tags from PER protein to mark it for destruction. Beyond the core rhythm, CLOCK-BMAL switches on a gene called Nampt, opening a second loop that runs on metabolism. The Nampt gene builds NAMPT protein, which sits in a chain of reactions converting niacin into NAD. SIRT1 needs that NAD to work, so rising NAD lets SIRT1 suppress BMAL1 by deacetylation. Less BMAL1 activity means less Nampt, less NAMPT, less NAD, and finally less SIRT1, which lifts the suppression and lets CLOCK-BMAL fire up Nampt once more. This second oscillator shows how tightly the clock and the cell's energy chemistry are wound together.
The earliest circadian rhythms were probably light-driven cell-division cycles in ancestral prokaryotes, only later becoming self-sustaining clocks through gene duplication. The oldest known clock genes are the kaiA, kaiB, and kaiC clusters found in cyanobacteria, with kaiC likely the ancestor of the other two. Their first job may have been chromosome maintenance rather than timekeeping, and kaiA and kaiB appeared only after cyanobacteria split from other prokaryotes. Harsh early-Earth conditions, including UV irradiation, may have pushed clock genes to diversify. Cryptochromes, the light-sensitive proteins that negatively regulate the clock, likely descend from kaiC through a genome duplication that predates the Cambrian explosion. BMAL1 is paralogous to CLOCK, and their common ancestor probably came before the insect-vertebrate split, roughly 500 million years ago. A fungal gene called WC1 is proposed as a candidate ancestor predating the fungi-animal split. A BLAST search in a 2004 review suggested CLOCK may have arisen from a duplication of BMAL1, though that idea stays speculative, while another theory points to NPAS2 as the paralog doing a parallel job in different tissues.
Allelic variation in the Clock1a gene, studied in 2014 in cyprinid fishes, may shape seasonal timing. The polymorphisms mostly change the length of the PolyQ domain, which is tied to how strongly CLOCK is transcribed. Longer alleles tended to track recently derived and earlier-spawning species, probably a response to seasonal water temperature, while every other amino acid stayed identical across native species. A 2017 study knocked down CLOCK in human neurons grown in vitro to probe its place in brain evolution. Disrupting CLOCK increased neuronal migration in the neocortex, hinting at a mechanism for the cortical expansion unique to human brains. A separate study tied a polymorphism in the gene's 3-prime flanking region to morning or evening preference, with the 3111C allele linked to a leaning toward evening hours. That region is well conserved between mice and humans and affects mRNA stability, so its variants could disrupt circadian patterns and feed into insomnia or other sleep disorders.
A mutant fly form of Clock called Jrk was identified by Allada, Hall, and Rosbash in 1998 using forward genetics. Jrk comes from a premature stop codon that strips away the protein's activation domain, and its effects are dominant. Half of heterozygous Jrk flies run a lengthened period of 24.8 hours; the other half go arrhythmic, while homozygous flies lose rhythm entirely. Those mutant flies make low levels of PER and TIM, proof that Clock acts as a positive element, yet they show no physical or behavioral defects. The mouse counterpart, ClockΔ19, carries a deletion in exon 19 and acts as a dominant-negative, crippling the CLOCK-BMAL dimer's ability to switch on period. Heterozygous ClockΔ19 mice lengthen their periods in constant darkness, and homozygous ClockΔ19/Δ19 mice go arrhythmic, both at the whole-animal and single-cell level. Then came the surprise: Clock-null mice, with the gene fully knocked out, kept completely normal rhythms. That result directly challenged the belief that Clock is necessary for normal circadian function. The paralog NPAS2 can stand in for CLOCK in those null mice, though mice with one NPAS2 allele started with shorter periods and drifted into arrhythmic behavior.
In humans, a polymorphism in Clock called rs6832769 may relate to the personality trait of agreeableness. The 3111C variant, tied to diurnal preference, also links to greater insomnia, trouble losing weight, and recurring major depressive episodes in people with bipolar disorder. In mice, Clock reaches into sleep, metabolism, pregnancy, and mood. Clock mutant mice sleep less, show altered plasma glucose and food-intake rhythms, and develop metabolic syndrome over time. They also suffer disrupted estrous cycles and higher rates of full-term pregnancy failure. The same mutation produces bipolar-like mania and euphoria, alongside more excitable dopamine neurons in the brain's reward centers, which led Colleen McClung to propose these mice as a model for human mood disorders. The clock's reach extends to cancer too: women with breast cancer showed significantly less methylation of the Clock promoter, an effect stronger in estrogen and progesterone receptor-negative tumors. In one study, 53 percent of microsatellite-instability colorectal cancers carried somatic CLOCK mutations, and nascent work in adipose tissue suggests suppressing CLOCK may causally tie into obesity and type 2 diabetes.
Common questions
What is the CLOCK gene and what does it do?
CLOCK is a gene encoding a basic helix-loop-helix-PAS transcription factor that affects both the persistence and period of circadian rhythms. It acts as an activator of downstream elements in the pathway that generates circadian rhythms. Its name is a backronym for circadian locomotor output cycles kaput.
Who discovered the CLOCK gene and when?
The CLOCK gene was first identified in 1997 by Joseph Takahashi and his colleagues. They used forward mutagenesis screening of mice treated with N-ethyl-N-nitrosourea to create and identify mutations affecting circadian activity. The mutant mice displayed an abnormally long period of daily activity that proved heritable.
How does the CLOCK protein control circadian rhythms?
CLOCK dimerizes with a partner protein, CYCLE in flies or BMAL1 in mice, and binds E-box elements to switch on genes such as period, timeless, and cryptochrome. The proteins those genes make accumulate and form complexes that block CLOCK, shutting the genes off. Cycles of phosphorylation and degradation then restart the loop, creating the daily rhythm.
What happens when the CLOCK gene is mutated in mice and flies?
In flies, the dominant Jrk mutation lengthens the period to 24.8 hours in half of heterozygotes and makes the rest arrhythmic, while homozygotes lose rhythm entirely. In mice, the dominant-negative ClockΔ19 mutation lengthens periods in heterozygotes and causes arrhythmicity in homozygotes. Surprisingly, Clock-null mice with the gene fully knocked out display completely normal circadian rhythms.
How is the CLOCK gene linked to human health and disease?
The 3111C variant of CLOCK is associated with evening preference, increased insomnia, difficulty losing weight, and recurrence of major depressive episodes in bipolar disorder. Less methylation of the Clock promoter is linked to breast cancer, and 53 percent of microsatellite-instability colorectal cancers in one study carried somatic CLOCK mutations. Suppression of CLOCK may also correlate with obesity and type 2 diabetes.
How did the CLOCK gene evolve?
The earliest circadian rhythms likely arose from light-driven cell-division cycles in ancestral prokaryotes, with the kaiA, kaiB, and kaiC gene clusters in cyanobacteria the oldest known clock genes. BMAL1 is paralogous to CLOCK, and their common ancestor probably predated the insect-vertebrate split roughly 500 million years ago. A 2004 review suggested CLOCK may have arisen from a duplication of the BMAL1 gene, though this remains speculative.