Surreal illustration of a clockwork brain in a starry night, representing the complexity of circadian rhythms.

Decoding Your Sleep: Why a Single Gene Isn't the Whole Story

Mira Elwood in Health & Wellness December 2025 • 4 min read.

"Exploring the complexities of circadian rhythm disorders and the search for universal genetic markers."

Ever wonder why some people are early birds while others are night owls? Our bodies operate on internal clocks, known as circadian rhythms, that regulate everything from sleep and wakefulness to hormone release and body temperature. These rhythms are influenced by a complex interplay of genes, proteins, and environmental cues.

Circadian rhythm sleep-wake disorders (CRSWDs) disrupt these natural patterns, leading to significant difficulties in daily life. Scientists have been working hard to pinpoint the genetic factors that contribute to these disorders, hoping to develop targeted treatments and interventions.

One gene that has received a lot of attention is PER3, which plays a crucial role in the circadian clock. Studies have linked a specific variation in this gene, called a variable number tandem repeat (VNTR), to sleep preferences and disorders. But is PER3 the key to unlocking the mysteries of sleep, or is the story more complicated than that?

The PER3 Gene: A Promising Lead That Didn't Pan Out?

Surreal illustration of a clockwork brain in a starry night, representing the complexity of circadian rhythms.

Previous research suggested that the PER3 VNTR could be a significant factor in determining whether someone is a morning person or an evening person. The 4-repeat allele of the VNTR was associated with extreme evening preference and delayed sleep-wake phase disorder (DSWPD), while the 5-repeat allele was linked to extreme morning preference and greater sleep propensity. However, a new study challenges these findings.

Researchers in Japan investigated the relationship between the PER3 VNTR and CRSWDs in a large cohort of Japanese individuals. The study included 248 people with CRSWDs (180 with DSWPD and 68 with non-24-hour sleep-wake disorder) and 925 controls. The researchers genotyped the PER3 VNTR in all participants and looked for associations with CRSWD phenotypes and diurnal preferences.

Here's what they discovered:

No significant association between the PER3 VNTR and CRSWDs.
No significant association between the PER3 VNTR and morningness-eveningness preferences.
The frequency of the VNTR polymorphism differed from previous studies in other populations.

These findings suggest that the PER3 VNTR may not be a universal genetic marker for circadian rhythm and sleep-wake disorders. While the VNTR has been associated with sleep phenotypes in some populations, it may not play the same role in others. The researchers propose that the genetic architecture of circadian rhythms and sleep regulation may vary across different ethnic groups.

The Big Picture: Why Sleep is More Than Just One Gene

While the PER3 VNTR may not be the holy grail of sleep genetics, this study highlights the complexity of circadian rhythm regulation. Numerous genes, proteins, and environmental factors contribute to our sleep-wake patterns. Future research should focus on exploring these interactions to gain a more comprehensive understanding of sleep disorders.

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This article is based on research published under:

DOI-LINK: 10.1038/s41439-018-0017-7, Alternate LINK

Title: Lack Of Association Between Per3 Variable Number Tandem Repeat And Circadian Rhythm Sleep–Wake Disorders

Subject: Genetics

Journal: Human Genome Variation

Publisher: Springer Science and Business Media LLC

Authors: Akiko Hida, Shingo Kitamura, Hiroshi Kadotani, Makoto Uchiyama, Takashi Ebisawa, Yuichi Inoue, Yuichi Kamei, Kazuo Mishima

Published: 2018-07-12

Everything You Need To Know

What are circadian rhythms and why are they important?

Circadian rhythms are internal biological clocks that regulate various bodily functions, including sleep-wake cycles, hormone release, and body temperature. These rhythms are influenced by a complex interplay of genes, proteins, and environmental factors. They are significant because disruptions to these rhythms, known as Circadian Rhythm Sleep-Wake Disorders (CRSWDs), can lead to difficulties in daily life. The implications are that understanding these rhythms is key to diagnosing and treating sleep disorders.

What is the PER3 gene and what role does it play in sleep?

The PER3 gene is a gene that plays a crucial role in the circadian clock. Scientists have investigated a specific variation within the PER3 gene, called a variable number tandem repeat (VNTR), to understand its link to sleep preferences and disorders. Previous research suggested that the PER3 VNTR could be a significant factor in determining someone's sleep schedule. However, a new study suggests the role of the PER3 VNTR in CRSWDs may not be universal across different populations.

What is a VNTR in the context of this research?

A Variable Number Tandem Repeat (VNTR) is a specific type of genetic variation, within the PER3 gene, that researchers have studied in relation to sleep patterns. In the context of this research, the PER3 VNTR has been investigated to see if it is linked to Circadian Rhythm Sleep-Wake Disorders (CRSWDs) and morningness-eveningness preferences. The findings of a recent study challenge previous associations between the PER3 VNTR and specific sleep phenotypes, indicating that the relationship may be more complex than previously thought.

What are Circadian Rhythm Sleep-Wake Disorders, and what are their implications?

Circadian Rhythm Sleep-Wake Disorders (CRSWDs) are a group of sleep disorders that disrupt the natural patterns of the circadian rhythms. This can lead to significant difficulties in daily life, such as problems with work, school, or social activities. One example of a CRSWD mentioned is Delayed Sleep-Wake Phase Disorder (DSWPD). The implications of CRSWDs include the potential for impaired cognitive function, mood disorders, and increased risk of other health problems. Understanding the genetic and environmental factors that contribute to CRSWDs is critical for developing effective treatments.

What did the study conclude about the PER3 VNTR and its impact on sleep?

The study suggests that the PER3 VNTR may not be a universal genetic marker for sleep disorders and diurnal preferences. The results indicate that the association between the PER3 VNTR and sleep phenotypes may vary across different ethnic groups. The study highlights the complexity of the genetic architecture underlying circadian rhythms. The implications are that scientists need to explore other genetic and environmental factors that influence sleep-wake patterns. This could lead to more personalized and effective interventions for sleep disorders, which are not solely determined by the PER3 VNTR, but a combination of factors.