What are circadian clocks, where are they, and how can we nurture them?

Author: Satchin Panda, PhD

Circadian rhythms – such as daily rhythm in sleep-wake, heart rate, blood pressure etc. – are generated by circadian clocks. A few decades ago it was assumed that there was a master circadian clock somewhere in the brain that dictated time-of-day to the rest of the body. But slowly, as scientists unraveled mechanisms driving the clock, they discovered that the body keeps track of time in a highly sophisticated way.

To understand how our bodies keep track of time, I would like to briefly introduce the pioneering work of Jeff Hall, Michael Rosbash, and Michael Young, who shared the Nobel Prize in Physiology and Medicine in 2017 for figuring out how the circadian clock works in fruit flies. They identified a gene that is critical for the fruit fly clock, called Period (Per for short). A version of Per is found in all living organisms and they demonstrated that the Per gene slowly turns on and then turns off, with the whole cycle taking about 24 hours. This daily rise and fall of the Per gene provided the fly clues as to when to sleep and when to wake up even when the fly was kept in complete darkness. If the Per gene cycled too fast – for example, completing the whole rhythm in 22 hours – the fly’s sleep-wake cycle would also be 22 hours. Similarly, a Per cycle of 26 hours would cause the fly to sleep and wake up  every 26 hours. Finally, if the Per gene was completely silenced, the fly would not have any sense of time and would sleep at random times. This convinced the scientists that the Per gene is an integral part of a circadian clock that is found in all living organisms. Just like our ancestors tracked the rise and set times of the sun and moon to keep track of time, the fruit fly was tracking the rise and fall of the Per gene to deduce the time of day.

Scientists studying how frogs maintain a circadian rhythm discovered that they produce a daily rhythm in the sleep hormone melatonin. Rhythms in this hormone are also seen in rats and humans. However, in rats and humans the hormone is secreted by the pineal gland in the brain, whereas in frogs the eye produces copious amounts of melatonin. When scientists removed a frog’s eye and kept it alive in an experimental dish (by providing vital nutrients), the eye continued to make melatonin. Not only that, but the amount of hormone it produced rose and fell with a 24-hour rhythm. This experiment convinced the scientists that the frog’s eye is capable of producing a daily rhythm without input from the brain. In other words, the eye contains its own circadian clock.

A few years later, Jeff Plautz, a graduate student in Steve Kay’s lab at The Scripps Research Institute in La Jolla, performed another intriguing experiment. Plautz generated an interesting strain of fruit flies in which Per was fused to a glow-in-the-dark protein. Thus, the whole fly glowed brightly when the Per gene was turned on, and then dimmed as the Per gene turned off. Using this strain, Plautz could monitor the fly’s internal clock simply by using a camera. He designed a system for measuring the brightness of hundreds of fruit flies throughout the day, taking snapshots every 30 minutes. One day, instead of placing whole flies into his camera set-up, he dissected them and placed different bits (wings, antennae, abdomens, etc.) in front of the camera. To his surprise, almost every bit of tissue continued to glow and dim with a 24-hour rhythm. This simple experiment revealed circadian clocks in lots of different parts of the body, all of which, like the frog’s eye, functioned just fine without a brain.

In subsequent years, the laboratories of Ueli Schibler in Geneva and Michael Menaker in Virginia found that in mice and humans, every organ, every tissue, and almost every cell has its own circadian clock. Even when individual skin cells are placed into an experimental dish, their circadian clock continues to tick for days. Numerous other labs have contributed to our understanding of how circadian clocks operate in individual cells and organs.

Is there a Master Clock? In an orchestra, each musician reads their own notes and plays their own instrument, but they take cues from the conductor to play in a synchronized manner. With so many clocks in the body, even a small deviation in a small percentage of clocks would create chaos.  One solution would be to have a master clock that synchronized all the individual clocks. Indeed, in the early 1970s, scientists located the master circadian clock. At the bottom of the brain, where the nerve fibers from our eyes criss-cross and enter our brain, there is a small cluster of only 20,000 neurons called the suprachiasmatic nucleus (SCN). Neurons within the SCN are directly or indirectly linked to many other parts of the brain. The SCN is so crucial that when an animal does not have one, it sleeps and wakes up at random times during the day. In fact, scientists suspect that the SCN becomes compromised in late stages of neurodegenerative diseases, like Alzheimer’s disease, causing the patients to lose sense of time and to sleep and wake up at random times. For animals that have had their SCN surgically removed, inserting an SCN from another animal re-establishes daily rhythms in sleep and wakefulness.

The location of the master circadian clock is very interesting, as these neurons have a dedicated link to the eye. This ensures that outside information concerning light and darkness is directly transferred from the eye to the master clock. Once the master clock is in sync with the outside day:night cycle, it can communicate this day:night information to the rest of the body. Another structure at the base of the brain (called the hypothalamus) regulates hunger, thirst, sleep, body temperature, and levels of various hormones. Being close to the hypothalamus as well, the SCN can coordinate daily rhythms in sleep-wake, hunger-satiety, body temperature, and hormones, which in turn synchronizes the individual clocks in each cell to form the grand orchestra that is the circadian rhythm.

We need to delve a bit deeper if we are to understand precisely what constitutes a circadian clock. We know that the Per gene slowly rises and falls like the hand of a clock. The hand of the clock goes around because tens or hundreds of parts inside the clock move with precise speed to nudge or slow down each other. Similarly, there are dozens of different genes that work together to ultimately turn the Per gene on or off every 24 hours. Just like in a watch, each of these genes is essential for the clock to work with precision. They are generally called clock genes, and include Cry, Clock (yes, there is a gene named clock), Bmal1, Rev-Erb, Ror, etc. All of these genes are critical for our health, and mutations in these circadian clock genes slow down or speed up our circadian rhythms. These individuals are programmed to go to bed earlier or later than is considered normal.

The circadian clock is composed of many genes, and most clock genes perform many jobs; they are not just part of the clock. For example, some clock genes dictate when to store or burn glucose, cholesterol, fat, or amino acids. This means that when certain clock genes turn on, they also wake up the fat-burning machinery; other clock genes turn off the fat storing genes at the same time. Similarly, clock genes are involved in processes that repair damaged parts of the cell, detoxify the cell, etc. Just like everyone on the planet is connected to Kevin Bacon by 6 degrees of separation, it is reasonable to say that almost every gene lined to a human disease is connected to the circadian clock genes by 3 degree of separation. In this way, almost every cellular function takes its timing cue from the circadian clock, ensuring and enabling the body to function optimally.

These interactions between the clock and other functions of the cell raises one more important issue. Suppose a clock gene is turned on in the morning (around 9 am) and at 6 pm it begins to decline, reaching its lowest level of functionality around 9 pm, which is maintained until 9 am the next morning. Imagine that the same gene also helps to store sugar. Thus, between 9 am and 6 pm, this clock gene can help store extra sugar, keeping blood sugar levels low. This works fine as long as the person eats between 9 am and 6 pm. If this person changes her/his eating schedule and starts to eat breakfast at 7 am, the body will not be well equipped to handle this rush of sugar because the clock/sugar gene has not yet been turned on. This will last for a few days, however the clock gene slowly “learns” that breakfast time has changed, and adjusts itself to turn on by 7 am instead. Accordingly, the timing of the clock is also changed. Beginning the day 2 hours earlier means the clock winds down in the evening two hours earlier as well (from 6 pm to 4 pm). As long as the person finishes dinner by 4 pm, blood sugar will be perfectly controlled, but if dinner is delayed, the resulting dysynchrony between the clock and eating pattern will cause problems.

Just like the timing of our meals affects clocks in our gut, liver, muscle, and fat cells (i.e., cells that directly handle glucose and other forms of nutrition), the time we choose to wake up or go to sleep can affect the clocks in our brain and other organs. This is why our circadian clock is not a rigid timing system. Rather, it does its best to adapt to our daily routine to keep us healthy. However, if we randomly change our daily routine from day to day, our circadian clocks get confused and we feel tired.  On the other hand, keeping regular routines of sleeping and eating is the most powerful way to nurture and sustain robust circadian clocks in our brain and body. Once the clocks are functioning at a high level, the multi-tasking clock genes similarly optimize almost all other functions of our body, promoting our health and well-being.


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