What Is the Suprachiasmatic Nucleus? How Your Body Clock Works

There are two clusters of cells in our brain that play a key role in controlling our circadian rhythm. These are called the suprachiasmatic nucleus (SCN). The light-sensitive cells in our eyes pass information to these, which allows them to know when the sun is out and control our clocks. Once these know that, they can then help control other messages throughout our body, one being when our pineal gland should release melatonin.

Many people think of the SCN as the clock that controls whether we will sleep or not. While it does control our body to sleep, it isn’t all that controls if we sleep or not. Once you learn what the SCN does, it becomes easier to understand the body’s clock. It just controls different things than the pineal gland.

What stands out to me is how the body clock connects something as ordinary as light entering the eyes to the timing of rhythms throughout the body. The SCN is small, but learning what it does makes circadian timing easier to understand.

Key Takeaways

• The SCN consists of two groups of neurons located in the hypothalamus, just superior to the optic chiasm.
• They receive input from light-sensitive cells that help regulate its circadian rhythm.
• The SCN sends out time signals to other parts of the body. There are also other clock systems within organs and tissue.
• The SCN controls the secretion of melatonin by sending signals, through multiple synapses, to the pineal gland.
• This allows you to be more prone to sleeping at certain times, but other factors will cause you to fall asleep as well.

Medical Disclaimer: This article is for general education and is not a substitute for medical advice, diagnosis, or treatment. If you have ongoing concerns about sleep, speak with a qualified health professional.

What Is the Suprachiasmatic Nucleus?

The suprachiasmatic nucleus consists of two clusters of neurons located on either side of the brain. Together, they make up the SCN. As the name suggests, “supra” refers to its position above the optic chiasm. Some axons from our eyes cross over at the chiasm, hence its name.

The SCN is a region within our brain that makes up a portion of the hypothalamus. Our hypothalamus controls many functions that allow us to operate and maintain homeostasis. The SCN is responsible for controlling our body clock. The cells in the SCN exhibit periods of activity every day, even without changes in light. A change in light allows our SCN to calibrate to a time period closer to our daily schedule.

Circadian Rhythm is a term used to describe something that happens approximately every 24 hours. “Circa” means “around” and “dies” means “day.” While we may think that our body’s clock is set by our daily habits, it actually isn’t. Our bodies can develop these clocks biologically, and they can be affected by the habits we create.

Where Is the SCN Located?

Our SCN is located in the lower portion of our brain and within the anterior hypothalamus. As stated before, the SCN is above our optic chiasm. There isn’t anything we as humans can feel to determine where our SCN is.

Its location allows it to receive input from our eyes via a direct neural pathway and enables the SCN to send information to other areas of the brain to control our daily clocks. The SCN is not near our pineal gland and does not have a direct wire to it. Many neurons are located between the SCN and the pineal gland.

Why Is the SCN Called the Body’s Master Clock?

Because it controls many of our body’s clocks. However, this can lead people to believe that everything in our body relies on our SCN. Many of our organs have molecular clocks that can tell our bodies what time it is. These clocks can help regulate activity within our organs. Our SCN can also control these clocks through various types of communication. Habits that we build into our lives can also help set some of these clocks.

Think of it like an orchestra. Our SCN can help give all the instruments a common beat. But each instrument can have its own clock and receive signals that allow it to know when to play. When there is no consistency in time signals, some of these clocks will fall out of sync. This does not mean that our SCN controls everything that happens throughout the day.

For an overview of the research on circadian-clock inputs and outputs, see this review, “Inputs and Outputs of the Mammalian Circadian Clock”.

How Does Light Travel From the Eyes to the SCN?

Our eyes aren’t only able to create visual information; they also gather data about light exposure, which can help our body understand what time of day it is.

There are many types of cells in the retina that are sensitive to light. Some of these cells are called intrinsically photosensitive retinal ganglion cells, or ipRGCs. These contain a protein called melanopsin, which allows them to detect light. They are also fed by rod and cone cells, which are the cells in the retina associated with night vision and color/vision acuity.

Axons from some retinal ganglion cells travel to the SCN via the retinohypothalamic tract. “Retino” means retina, and “hypothalamic” means hypothalamus. The eyes send information to the SCN without the need to perceive an image.

Once the SCN has this information, it can begin to change its phase. Light can affect the SCN at different phases of the biological clock, which is why light is considered a zeitgeber. It all depends on when you are exposed to light and your internal clock.

When an organism is adjusting to an external time giver, it is known as entertainment. Light is just one zeitgeber that can affect our circadian clocks. There are many other things that can influence our body clock, such as other areas of the brain sending signals to the SCN and our body’s ability to sense movement and meals.

How Does the SCN Coordinate Daily Rhythms?

The SCN allows us to regulate our rhythms by relaying time to the rest of our bodies and regulating behavior. This can include times we want to be awake or sleepy and certain rhythms in our body going up and down. Everyone will differ on how these times and rhythms fluctuate. There are many factors that can affect your body clock, such as age and habits.

There are many different neurons within the SCN, each having its own rhythm. They all interact with each other, which allows them to have a better coordinated rhythm to send out to the rest of our brain. There are many theories about what exactly happens within the SCN. It has been said that it’s more of an input/output rather than just controlling one thing.

The SCN does not directly control all the body clocks. It plays a role in helping to keep everything regulated. As stated before, light can regulate your SCN. Other cues can regulate other clocks throughout your body, such as meal times. Again, this can play a factor in your rhythms being on time, but not always.

This leads me to my next question. How is a circadian rhythm not the same as your habits? You may have a habit of waking up at the same time every day due to a job or kids. However, your SCN is still producing a time signal that you should wake up. Your habits can affect this but are not the same thing.

How Does the SCN Influence Melatonin Timing?

Our SCN plays a role in releasing melatonin from the pineal gland. Melatonin is released at higher concentrations during your body clock’s nighttime. This allows your body to know it’s in its night cycle. It does not force you to sleep, nor is it what tells the SCN that it’s dark.

There are many steps that take place when the SCN talks to our pineal gland. One could simply say that:

SCN → paraventricular nucleus → spinal cord → superior cervical ganglion → pineal gland

These arrows are not direct connections to each other. There are many synapses involved in this pathway. It involves the PVN in your hypothalamus, neurons in the top of your spine, and the superior cervical ganglion, which consists of neurons located in your neck. These can help regulate the pineal gland.

Therefore, the pineal gland is another output of our SCN, not the master clock.

Feature	Suprachiasmatic nucleus	Pineal gland
What it is	A pair of neuron clusters in the hypothalamus	A small hormone-producing gland
Main role in this topic	Helps organize circadian timing	Releases melatonin in a daily pattern
Relationship to light	Receives light-related signals from the eyes	Does not receive the eye’s light signal directly
Relationship to the other	Helps regulate the timing of pineal activity	Acts as one target in the SCN-linked pathway

If you want a little more background on the gland itself, the site’s pineal gland function guide covers its role and melatonin in more detail.

Does the SCN Make You Fall Asleep?

The SCN can make you more prone to sleeping; however, it will not put you to sleep. Many factors can contribute to your sleep time. Circadian time, time awake, and your environment are just some of those factors.

There are two processes commonly used to describe sleep. One is Process C, which is driven by circadian time. Process C can make you sleepier at certain times of the day and more awake at others. The second is called Process S, or sleep drive. Process S increases as you stay awake and typically decreases while you are sleeping. Processes C and S go hand-in-hand but are not identical.

You can be tired from staying awake too long and not fall asleep due to your circadian rhythm. Or you can be at a time when you would normally be sleepy and not fall asleep due to outside stimuli. These are simply examples and should not be used to self-diagnose a sleep disorder.

As you can see, the SCN can affect when you sleep. It is just one aspect that affects sleep/wake time. It does not control when you will fall asleep.

What Might Happen When SCN Signals Are Disrupted?

It has been shown that when your SCN is affected, your circadian time can be altered. Studies done on animals show that when the SCN is damaged, it can lead to the disruption of diurnal rhythms. Studies have also looked at light exposure and feeding that occur at incorrect times of the day. This article gives an in-depth explanation of these relationships: “Circadian Rhythms Disrupted by Light at Night and Mistimed Food Intake Alter Hormonal Rhythms and Metabolism.”

This does not mean that light exposure at night will cause you to become ill or that eating one meal off schedule will damage your SCN. Some studies use laboratory settings or test on animals, which cannot always be translated to humans. There are correlations between circadian disruption and disease in humans, but these do not directly link to SCN signaling causing the disease.

Melatonin has also played a role in research regarding circadian disruption. Depending on the species or strain of animal, results can vary. Be sure to read this article about various strains of mice and take it with the understanding that it is animal research: “The Role of the Melatoninergic System in Circadian and Seasonal Rhythms.”

The science here states that the SCN is a factor that can influence our body’s clock. If the signals from the SCN are altered, our biological clocks can be affected. It should not be used as the sole cause of all sleep problems or diseases.

Frequently Asked Questions

Is the suprachiasmatic nucleus a gland?

No, there is no such thing as the suprachiasmatic gland. The SCN consists of two nuclei located in your hypothalamus. Your pineal gland secretes melatonin. The SCN affects the pineal gland, but it does so through multiple synapses.

Does the SCN connect to the pineal gland?

In the context of circadian biology, it is known as the primary pathway that leads to your pineal gland. It travels through many synapses, including ones in the brainstem and spinal cord, to reach the pineal gland via sympathetic nerves. Stating it is a direct pathway from the SCN to the pineal gland would not be accurate.

Can light entrain the SCN?

Light can affect your SCN by traveling from the eye to your hypothalamus. The timing of light exposure will determine whether your SCN becomes more or less entrained. This is not medical advice for an individual.

Is the SCN responsible for all our circadian rhythms?

No. Your SCN is just one of many clocks we have throughout our bodies. Other clocks can also be affected by zeitgebers. The SCN is just one piece of the puzzle when it comes to circadian biology.

Will my SCN determine when I wake up?

Your SCN will affect when you wake up, but it is not the only factor that plays into waking you up. Your circadian rhythm is just one aspect of why you may wake up at certain times.

Conclusion

As we know, the suprachiasmatic nucleus plays a role in our circadian rhythms. It helps receive information from our eyes about light exposure and affects when our pineal gland secretes melatonin. Through many synapses, the SCN controls our circadian rhythm.

Although it may be called the master clock, it is not the only clock we have in our body. There are many things that can affect when you wake up.

The idea I’m taking away is that the SCN is a coordinator, not a sleep switch. That distinction makes the science more interesting to me, and it helps explain why sleep timing involves more than one part of the body.

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