Body clock genes

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This text is part of: "Science of sleep" by Piotr Wozniak (2017)

Body clock

The suprachiasmatic nucleus (SCN) is the master oscillator at the root of our main circadian cycle. Individual cells in the SCN fire in synchrony on the basis of a genetic loop that takes roughly 24 hours to complete. The loop is very complex, it includes many genes, their transcripts and protein products. Individual components of this complex system inhibit, suppress, or activate other components. All the various interactions are not yet fully understood, however, a simplified model is presented below for the sake of hinting at the general principles behind the genetic clock.

Clock genes

The genetic circadian oscillator clock system forms a negative feedback loop, in which clock proteins built up in the cytoplasm are shunted to the nucleus to repress their own transcription. This mechanism is called a transcription-translation negative-feedback loop (TTFL) that is capable of pretty regular oscillations.

Feedback loop

The key genes of the circadian clock system are Clock, Bmal1, period (Per), and cryptochrome (Cry). Those components are highly conserved in all kingdoms of living organisms indicating their essential role in survival. The two transcriptional activators CLOCK and BMAL1 form a CLOCK:BMAL1 protein dimer at that start of the day. That dimer promotes the transcription of their transcriptional target genes: period (Per) and cryptochrome (Cry). The RNA of Per, Cry, Bmal1 and Clock is translated into proteins in the cytoplasm. PER and CRY proteins accumulate in the cytoplasm during the day, peak by the evening, and by sunset start building up in the nucleus as well. In the nucleus, PER and CRY function as negative regulators of CLOCK/BMAL1 activity, and repress their own transcription. As a result, PER and CRY plummet during the night and thus close the negative feedback loop. This restarts the cycle from the production of CLOCK:BMAL1, and so on. The loop formed by Clock/Bmal1 and Per/Cry oscillates in a roughly 24 hour cycle. Complexes that contain CRY inhibit the CLOCK:BMAL1 dimer production, and slow down the transcription of Per and Cry genes. The picture gets more complicated with the fact that there are at least three variants of Per (Per1, Per2, and Per3), and two of Cry (Cry1, and Cry2). Complexes that contain PER2 protein enhance the transcription of Bmal1. PER1 modestly inhibits transcription induced by the CLOCK/BMAL1 complex.

Clock gene mutations

Circadian role of individual genes is well illustrated by engineering knockout mice. For example, mice lacking Cry1 or Cry2 have altered free running circadian periods. If both genes are missing, the animals become arrhythmic in constant conditions with constant elevated levels of Per1 mRNA! Similarly, Per1/Per2 double mutants lose rhythmicity. Mutations to the Per2 gene can cause familial ASPS. The non-redundant role of Bmal1 can be shown by deletion, which leads to immediate arrhythmicity in constant darkness. The clock genes are affected by various hormonal, metabolic and immune inputs (e.g. adenosine).

Clock gene evolution

The circadian genetic machinery is so well conserved in the evolution that the study of Drosophila provides a cheap alternative to knockout experiments in rodents. Orthologs have been identified in mammals for most of the Drosophila circadian clock genes. In insects though, unlike in mammals, CRY1 function is light-dependent. Even cyanobacteria have a circadian genetic clock that can be reconstituted in vitro for detailed quantitative analysis and comparative simulations. One of the conclusions coming from studying cyanobacteria is that the TTFL clock may actually be a slave to a master biochemical oscillator called the PTO (post-translational oscillator) (Qin et al. 2010[1]). The initial suggestion on the role of biochemical oscillators came from the persistence of the circadian rhythm in conditions of inhibited transcription and translation (Iwasaki et al. 2005[2]). Beyond their circadian roles, the genes are also involved in other functions. Interestingly, cryptochromes have been shown to be involved in magnetoception in birds, and photoreception in plant growth.

It seems that many subcomponents of the oscillator system can run in 24 hour cycles, and even a simple theoretical three protein phosophorylation loop can be formed that is temperature compensated and whose stability may depend on minor regulatory adjustments to the properties of the proteins involved and/or their processing. This might mean that individual proteins must have been perfected and tuned up in the course of evolution to produce stable rhythms that can ideally match our lifestyles linked to the rotation of the Earth. No wonder then that scientists have identified numerous mutations that produce minor changes in the properties of the oscillator or its entrainment systems (Golombek and Rosenstein 2010[3])

Nobel Prize 2017

Jeffrey Hall, Michael Rosbash, and Michael Young won the 2017 Nobel prize for medicine for elucidating molecular mechanisms that control our internal clocks. Rosbash complained jokingly that the 5 am phone call from the Nobel Committee destroyed his circadian rhytm.


  1. Qin X., Byrne M., Xu Y., Mori T., and Johnson C.H. Coupling of a Core Post-Translational Pacemaker to a Slave Transcription/Translation Feedback Loop in a Circadian System," PLoS Biology / Volume 8 / Issue 6 (June 15, 2010): e1000394, doi:10.1371/journal.pbio.1000394
  2. Tomita J., Nakajima M., Kondo T., and Iwasaki H., No transcription-translation feedback in circadian rhythm of KaiC phosphorylation," Science / Volume 307 / Issue 5707 (January 14, 2005): 251–254
  3. Golombek D.A. and Rosenstein R.E., Physiology of Circadian Entrainment," Physiological Reviews / Volume 90 / Issue 3: 1063-1102, doi: 10.1152/physrev.00009.2009