The Genetics of Circadian Rhythm

Table of Contents

The Genetics of Circadian Rhythm

Date of Content: September 9, 2023
Written by: Avanthika Nityanand
Reviewed by: Maarit Tiirikainen, PhD


What Is Circadian Rhythm?

Circadian rhythms are internal 24-hour cycles that control important body functions and processes, including the well-known sleep-wake pattern. This internal timing mechanism is shaped by environmental factors, most notably light, linking circadian rhythms to the day-night cycle. The circadian rhythm also enables the body to forecast external conditions, such as sunrise and sunset, and to pre-determine optimal periods for sleep, wakefulness, eating, and activity.

How Does Circadian Rhythm Work?

The suprachiasmatic nucleus (SCN) in the hypothalamus in the brain is the primary timekeeper for circadian rhythms. The SCN regulates these rhythms at the cellular level and influences various organs, such as the liver, adrenal glands, and the pineal gland.

Zeitgebers (Time-givers)

Our inherent circadian rhythm tends to be longer than a 24-hour cycle, and it varies between individuals. Therefore, it relies on external cues, called zeitgebers or “time-givers,” for constant synchronization with the surrounding environment.  Light is the most potent zeitgeber affecting the SCN. Specialized cells in the retina, known as melanopsin-expressing retinal ganglion cells, communicate directly with the SCN. These cells are particularly susceptible to blue light.

Although light remains the predominant zeitgeber, other elements like physical activity and eating patterns can also influence the SCN. For example, morning and early afternoon exercise advances the circadian clock, and evening exercise delays it.


Chronotype is a person’s natural inclination towards a particular daily activity pattern. Depending on the chronotype, you can be a “morning person,” an “evening person,” or somewhere in between, called an “intermediate type.” Your chronotype is largely influenced by the internal circadian rhythms regulated by your biological clock. However, genetic, environmental, and lifestyle factors can also shape it. While chronotype tendencies are often stable traits, they can change throughout a person’s life. For example, children and older adults tend to be more morning-oriented, while teenagers and young adults often shift towards evening types.

Evolutionary Significance

The circadian rhythm has allowed organisms to adapt to the predictable changes in their environment that are, in turn, linked to the rotation of the Earth. 

  • The circadian clock helps to synchronize an organism’s internal processes with external environmental cues such as light and temperature. 
  • By restricting certain activities to specific times of the day, circadian rhythms help in energy conservation.
  • Ultimately, the circadian rhythm offers a significant survival advantage. Organisms with a well-tuned circadian rhythm are better adapted to their environments, have more efficient energy usage, and have better reproductive success.

Can Your Genetics Influence Circadian Rhythm?

Genetics can play a significant role in influencing your circadian rhythm. Specific genes, often called “clock genes,” help regulate the internal mechanisms responsible for your daily sleep cycles, wakefulness, and other physiological processes. Variants in these genes can lead to individual differences in circadian rhythms, including sleep timing, duration, and tolerance to disruptions like jet lag or shift work.


Studies have identified specific genes, such as CLOCK, PER1, PER2, and PER3, closely associated with regulating circadian rhythms. These genes interact in complex ways to maintain the body’s internal clock and can vary in their function from person to person, leading to individual differences. For example, some people are naturally “morning people” and find it easier to wake up early and be productive. In contrast, others are “night owls” whose energy levels peak in the evenings.


Genetic predispositions can also make some individuals more susceptible to circadian rhythm disorders, such as Delayed Sleep Phase Syndrome (DSPS) or Advanced Sleep Phase Syndrome (ASPS). These disorders result in sleep-wake cycles misaligned with societal norms, making it challenging for affected individuals to adhere to conventional schedules.

Molecular Clock

The molecular clock is an intricate system of genes, proteins, and other cellular components that regulate the circadian rhythm in living organisms. The molecular clock comprises genes like CLOCK, BMAL1 (ARNTL), PER1-3, and CRY1-2 that work together to control time-related processes in the body. The CLOCK and BMAL1 genes help activate other genes, PER1-3 and CRY1-2, which in turn switch off the activity of CLOCK and BMAL1. This creates a loop that helps keep our internal clock running. Some of the most well-studied genes and polymorphisms related to circadian rhythms are described below.


Individuals with the T allele experienced significantly shorter sleep durations compared to those without the allele, even after accounting for socio-economic status, body mass index, alcohol consumption, and smoking habits

Another widely researched variant of the CLOCK gene with multiple impacts is rs1801260 (also known as CLOCK 3111T/C). Individuals carrying the C allele tend to be more active in the evening, experience delayed sleep initiation, and generally have shorter sleep durations.  A study from 2015 analyzed changes in body temperature, activity level, and posture among women who carry this allele. The research discovered that women with the minor allele C showed increased activity in the evening and distinct daily variations in body temperature, leading researchers to conclude that these individuals exhibit a ‘less stable circadian rhythm.’

PER2 Gene

A genetic variant of the PER2 gene, identified as rs35333999 (p.Val903Ile), was recently linked to chronotype preferences in a comprehensive genome-wide association study (GWAS). This variant is more prevalent among individuals of European descent and is uncommon in African and East Asian groups. The study found that people carrying the minor allele (T) tended to be evening types compared to those with the non-T alleles (C/C).

Other Genes

The PER1 gene produces a protein known as ‘period circadian protein homolog 1.’ This protein, in tandem with CRY (Cryptochrome Circadian Regulator), constitutes the second set of key genes that regulate our body’s internal clock. A 2013 study identified a specific variant, rs7221412, that impacts one’s natural activity timing. Individuals with the A/A genotype are likely to wake up approximately an hour earlier than those with the G/G genotype, with A/G individuals showing an intermediate waking time.


The BMAL1 (ARNTL) gene interacts with CLOCK to enhance the expression of other circadian genes PER and CRY. A specific variant of BMAL1, rs3816358 (with A being the minor allele), has also been investigated for its potential connections to the risk of developing breast cancer, cardiovascular disease, and diabetes.

Non-Genetic Factors Influencing Circadian Rhythm

Several factors can disrupt your circadian rhythm, leading to potential health issues, including sleep disorders, impaired cognitive function, and more. Here’s a list of some everyday disruptors:

Environmental Factors

  • Light Exposure: Artificial light in the evenings, especially from screens, can trick your brain into thinking it’s still daytime.
  • Noise Pollution: Loud or inconsistent noise can interrupt sleep patterns.
  • Temperature Fluctuations: An overly warm or cold environment can affect your body’s internal clock.

Lifestyle Factors

  • Irregular Sleep Schedule: Going to bed and waking up at different times each day can desynchronize your circadian rhythm.
  • Shift Work: Working nights or rotating shifts can severely disrupt your internal clock.
  • Jet Lag: Traveling across multiple time zones can interrupt your circadian rhythm.
  • Meal Timing: Eating irregularly can interfere with your body’s metabolic processes, which are regulated by your circadian rhythm.
  • Lack of Exercise: Physical activity can help regulate your circadian rhythm, while a sedentary lifestyle can disrupt it.

Psychological Factors

  • Stress and Anxiety: Stress and anxiety can lead to insomnia and other sleep problems, disrupting your natural circadian rhythm.
  • Depression: Mood disorders can alter your sleep-wake cycles and hormone regulation.

Medical Conditions

  • Sleep Disorders: Conditions like insomnia, sleep apnea, or restless leg syndrome can affect your quality of sleep and, in turn, your circadian rhythm.
  • Hormonal Imbalances: Endocrine system disorders, such as hyperthyroidism or diabetes, can disrupt circadian rhythms.
  • Medications: Some medications, particularly stimulants and certain antidepressants, can alter your circadian rhythm.

Substance Use

  • Alcohol: While it may seem to help you fall asleep, alcohol can disrupt the quality of your sleep.
  • Caffeine: Consuming caffeinated products in the afternoon or evening can make it difficult to fall asleep.
  • Recreational Drugs: Substances like marijuana and hallucinogens can disrupt your circadian rhythm and sleep quality.

How Is Circadian Rhythm Different From Biological Clock?

The terms “circadian rhythm” and “biological clock” are often used interchangeably, but they refer to distinct yet interconnected concepts in the field of chronobiology. 

The “biological clock” refers to an internal timing mechanism that regulates biological processes in an organism. It serves as the master control for generating circadian rhythms and is located in the brain, specifically in the SCN of the hypothalamus in the brain in mammals. This clock is influenced by external cues such as light and temperature, which help synchronize it with the environment. It doesn’t only control sleep-wake cycles but also various other physiological processes like hormone secretion, metabolism, and cell regeneration. 

Other Systems Affected By Circadian Rhythms

Although the sleep-wake pattern is perhaps the most well-known example of circadian rhythms, these 24-hour cycles are crucial to nearly all bodily systems.


Ongoing research reveals more about circadian rhythms’ role in various health aspects. For instance, studies have linked them to regulating metabolic functions, including blood sugar levels and cholesterol. They are also connected to mental health, affecting the likelihood of depression, bipolar disorder, and even neurodegenerative conditions like dementia.


Emerging evidence suggests that circadian rhythms may significantly impact the immune system and DNA repair mechanisms, critical for cancer prevention. Preliminary studies indicate that the timing of anti-cancer medications may be optimized based on circadian cycles, offering a potential avenue for more effective treatments.

What Happens When Your Circadian Rhythm Goes Out Of Sync?

When your circadian rhythm is out of sync, the body’s internal systems fail to operate at their peak efficiency. One of the most immediate consequences is a disruption in the sleep-wake cycle. Absent the proper cues from the internal clock can reduce the total amount of sleep, low-quality, fragmented sleep, and increase the risk of insomnia and excessive daytime fatigue.


Research indicates circadian rhythm imbalances may also be implicated in specific sleep disorders, such as obstructive sleep apnea (OSA). This disorder is characterized by repeated interruptions in breathing during sleep, leading to decreased oxygen levels and multiple awakenings throughout the night.

How To Optimize Your Circadian Rhythm?

Maintaining a healthy circadian rhythm is essential for optimal physical and mental well-being. Here are some tips to keep your circadian rhythm in control:

  • Stick to a Schedule: Try to wake up and sleep at the same time every day, even on weekends, to help regulate your internal clock.
  • Limit Blue Light Exposure: Reduce exposure to blue light from phones, tablets, and computer screens in the evening. This can help increase melatonin production, signaling your body that it’s time to wind down.
  • Get Morning Sunlight: Exposure to natural light in the morning helps reset your circadian rhythm and improves mood and alertness.
  • Avoid Caffeine and Alcohol Before Bed: Consuming caffeine or alcohol can disrupt sleep quality and the circadian rhythm.
  • Eat at Regular Times: Eating meals consistently daily can help synchronize your body’s internal clock.
  • Exercise Regularly: Physical activity, particularly in the morning or early afternoon, can help you fall asleep more easily and improve the quality of your sleep.
  • Create a Restful Environment: Keep your bedroom cool, dark, and quiet to signal to your body that it’s time for sleep. Consider using blackout curtains and white noise machines if necessary.
  • Limit Naps: While napping can be refreshing, keep them short (20-30 minutes) and not too close to bedtime to avoid disrupting your circadian rhythm.
  • Stay Hydrated but Not Too Much: While it’s essential to stay hydrated, try not to drink a lot of fluids right before bed to minimize nighttime waking for bathroom trips, which can disrupt your sleep cycle.
  • Consult with Professionals: If you’re having persistent sleep issues or circadian rhythm issues, consult a healthcare provider for personalized advice, which may include sleep studies or other diagnostic tests.

About The LifeDNA Sleep Report

Sleep is essential for everyone’s health and well-being. LifeDNA’s Sleep Report gives an insight into several traits that can help you optimize your sleep at night.

LifeDNA’s Sleep report covers an analysis of Circadian Rhythm (Chronotype). Get yours here.


What Are Circadian Rhythms?

  • 24-hour internal cycles for bodily functions.
  • Governed by a brain-based biological clock.
  • Light is the main synchronizer; disruptions can affect sleep and health.

How Circadian Rhythm Works

  • Controlled by the suprachiasmatic nucleus (SCN) in the hypothalamus.
  • Light cues from retina cells adjust the clock.
  • Other cues like exercise and eating can also influence the SCN.

Difference Between Circadian Rhythm and Biological Clock

  • The biological clock is the internal timing mechanism.
  • Circadian rhythm is a 24-hour cycle controlled by the biological clock.

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*Understanding your genetics can offer valuable insights into your well-being, but it is not deterministic. Your traits can be influenced by the complex interplay involving nature, lifestyle, family history, and others.

Our reports and suggestions do not diagnose or treat any health conditions or provide any medical advice. Consult with a healthcare professional before making any major lifestyle changes or if you have any other concerns about your results.



*Understanding your genetics can offer valuable insights into your well-being, but it is not deterministic. Your traits can be influenced by the complex interplay involving nature, lifestyle, family history, and others.

Our reports have not been evaluated by the Food and Drug Administration. The contents on our website and our reports are for informational purposes only, and are not intended to diagnose any medical condition, replace the advice of a healthcare professional, or provide any medical advice, diagnosis, or treatment. Consult with a healthcare professional before making any major lifestyle changes or if you have any other concerns about your results. The testimonials featured may have used more than one LifeDNA or LifeDNA vendors’ product or reports.