Evolution of a Length Polymorphism in the Human PER3 Gene, a Component of the Circadian System
Abstract
Period homologue 3 ( PER3) is a component of the mammalian circa-dian system, although its precise role is unknown. A biallelic variable number tandem repeat (VNTR) polymorphism exists in human PER3, consisting of 4 or 5 repeats of a 54-bp sequence in a region encoding a putative phosphorylation domain. This polymorphism has previously been reported to associate with diurnal preference (“morningness” and “eveningness”) and delayed sleep-phase syndrome. We have investigated the global allele frequencies of this variant in ethnically distinct indigenous populations. All populations were polymorphic, with the shorter (4-repeat) allele ranging in frequency from 0.19 (Papua New Guinea) to 0.89 (Mongolia). To investigate if allele frequency has been influenced by natural selection, the authors 1) tested for a correlation with latitude and mean annual insolation (incident sunlight energy), using classical markers to correct for historical population differentiation; and they 2) compared allele-frequency difference between European American, African American, and East Asian populations, as measured using F ST , to an empirical null distribution of F ST values based on a genome-wide dataset of single nucleotide polymorphisms (SNPs) of presumed neutral loci that were previously typed by The SNP Consortium. The variation in allele frequencies between indigenous populations did not show a pattern that would indicate selective pressure on PER3resulting from day-length variation or mean annual insolation, and the allele-frequency difference between European Americans, African Americans, and East Asians was not an outlier when compared to the distribution for presumed neutral SNPs. We therefore find no evidence for differential or balancing selection in the contemporary pattern of global PER3allele frequencies.
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The derived allele frequencies of all three pigmentation-associated SNPs increased between ancient Eneolithic/Bronze Age and modern Ukrainian samples from the same geographic region.
“We also genotyped the three pigmentation-associated SNPs in a sample of 60 modern Ukrainians (28) and observed an increase in frequency of all derived alleles between the ancient and modern samples from the same geographic region (Table 1 and Fig. S1).”
From Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y (2014) · cites this paper as [28]
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“PERIOD3 VNTR Polymorphism: Role of a Circadian Gene in Differential Vulnerability to Acute TSD and Chronic PSD Three related studies investigated the role of the variable number tandem repeat (VNTR) polymorphism of the circadian gene PERIOD3(PER3)—which shows similar allelic frequencies in African Americans and Caucas…”
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BackgroundDo Caucasian and Asian clocks tick differently?
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“(16) could not provide evidence that the day length or the mean annual isolation contributed as selective pressures to the VNTR polymorphism of the PER3 gene in humans.”
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“For example, although the PER3(4) allele is thought to be more common than the PER3(5) allele (Ciarleglio et al., 2008; Nadkarni et al., 2005), the PER3(5) allele was more common in the athletes assessed by Kunorozva et al.”
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“different countries and latitudes is needed because there is a considerable variation for four-/five-repeat allele frequencies of hPer3 among global populations (Nadkarni et al. 2005).”
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“39 Although the population distribution of PER3 genotypes in night shift workers has not been adequately established, the distribu - tion of PER3 genotypes in our sample matches that of a prior study with approximately twice the sample size of police of - ficers engaged in shift work (approximately…”
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Genetic Ancestry for Sleep Research
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Pereira, D., van der Veen, D. R., Gonçalves, B. S. B., Tufik, S., von Schantz, M., Archer, S. N., & Pedrazzoli, M. (2014) · BioMed Research International · doi:10.1155/2014/170795 · Cited by 12 · see citing works
“It has also been proposed that, in humans, the PER3 gene could be involved in the entrainment to differential seasonal light signals created by latitude [7, 12].”
Hansen, M. V., Rasmussen, L. S., Jespersgaard, C., Rosenberg, J., & Gögenür, I. (2012) · Anesthesia & Analgesia · doi:10.1213/ane.0b013e318253d6b3 · Cited by 10 · see citing works
“There is considerable variation in PER3 repeat-allele frequencies among different populations, but our findings on the distributions of the genotypes correspond well with previous reports.(6,9,10) Our allele frequencies of 0.”
BackgroundMethodResultInfluentialHida, A., Kitamura, S., Kadotani, H., Uchiyama, M., Ebisawa, T., Inoue, Y., Kamei, Y., & Mishima, K. (2018) · Human Genome Variation · doi:10.1038/s41439-018-0017-7 · Cited by 9 · see citing works
Is Period3 Genotype Associated With Sleep and Recovery in Patients With Disorders of Consciousness?
Bedini, G., Bersano, A., Sebastiano, D. R., Sattin, D., Ciaraffa, F., Tosetti, V., Brenna, G., Franceschetti, S., Ciusani, E., Leonardi, M., et al. (2015) · Neurorehabilitation and neural repair · doi:10.1177/1545968315604398 · Cited by 9 · see citing works
“275 GCS 3 (3-10) 3 (3-8) 3 (3-8) 3 (3-10) .”
InfluentialMagee, M., Sletten, T. L., Murray, J. M., Gordon, C. J., Lovato, N., Bartlett, D. J., Kennaway, D. J., Lockley, S. W., Lack, L. C., Grunstein, R. R., et al. (2020) · Journal of Pineal Research · doi:10.1111/jpi.12684 · Cited by 9 · see citing works
Dagmura, H., Yığıt, S., Nursal, A. F., Duman, E., & Gümüşay, Ö. (2021) · Genetic Testing and Molecular Biomarkers · doi:10.1089/gtmb.2020.0179 · Cited by 7 · see citing works
Per3 VNTR polymorphism and chronic heart failure
Lipková, J., Vašků, J. B., Špinarová, L., Bienert, P., Hlavna, M., Goldbergová, M. P., Pařenica, J., Špinar, J., & Vašků, A. (2012) · Biomedical Papers · doi:10.5507/bp.2012.069 · Cited by 7 · see citing works
Sleep Under Preindustrial Conditions: What We Can Learn from It
Casiraghi, L. P., & de la Iglesia, H. O. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2249-0_1 · Cited by 5 · see citing works
Period3: um gene relacionado com a sincronização de ritmos circadianos pela luz
Pereira, D. S., Sabino, F. C., & Umemura, G. S. (2012) · Revista da Biologia · doi:10.7594/revbio.09.03.05 · Cited by 5 · see citing works
Investigation of circadian rhythm gene Per3 in diabetic neuropathy
Rüstemoğlu, H., Acı, R., Kaya, S. U., Yığıt, S., & Rüstemoğlu, A. (2023) · Nucleosides Nucleotides & Nucleic Acids · doi:10.1080/15257770.2023.2286996 · Cited by 4 · see citing works
“[21] Indeed, when we examined the limited number of studies conducted for the PER3 VNTR locus in the Turkish population, we observed that the frequency of 5/5 genotype varied between 16% and 22.3% in healthy groups.”
BackgroundInfluentialOn the issue of adaptive fitness of chronotypes in high latitudes
Borisenkov, M. F., Gubin, D. G., & Sergey, K. (2024) · Biological Rhythm Research · doi:10.1080/09291016.2024.2363742 · Cited by 3 · see citing works
“Nadkarni et al. (2005) studied human PER3 allele distribution worldwide and found no evidence for differential or balancing selection in the contemporary pattern of global PER3 allele frequencies.”
Genetics of Sleep Timing, Duration, and Homeostasis in Humans
Goel, N. (2012) · Sleep Medicine Clinics · doi:10.1016/j.jsmc.2012.06.013 · Cited by 3 · see citing works
PERIOD3 gene P415A/H417R polymorphism-linked familial advanced sleep phase
Okechukwu, C. E. (2021) · Egyptian Journal of Medical Human Genetics · doi:10.1186/s43042-021-00177-6 · Cited by 2 · see citing works
Kunorozva, L., Rae, D. E., & Roden, L. C. (2022) · Chronobiology International · doi:10.1080/07420528.2022.2139184 · Cited by 1 · see citing works
“…in various ethnic groups around the world have reported no significant differences in the distribution of this genotype (An et al. 2014; Bedini et al. 2016; Dagmura et al. 2021; Ozsoy et al. 2021; Voinescu and Coogan 2012) except in the Papua New Guinea population (Nadkarni et al. 2005).”
BackgroundAssociation Study between Per3 Gene Polymorphism and Diurnal Preference
Kang, S., Choi, T., Yoon, H., Park, Y., Kim, L., & Lee, H. (2011) · Sleep Medicine and Psychophysiology · doi:10.14401/kasmed.2011.18.1.035 · Cited by 1 · see citing works
CLOCK GENES, CIRCADIAN RHYTHMS, AND MOOD DISORDERS: THE ROLE OF POSITIVE AFFECT
Miller, M. A. (2014) · D-Scholarship@Pitt (University of Pittsburgh)
Avaliação de componentes biológicos associados à sonolência em jovens universitários trabalhadores
Teixeira, L. R., Pedrazzoli, M., da Luz, A. A., Turte, S. L., de Paula, L. P., Valente, D. L., Tufik, S., & Fischer, F. M. (2012) · Arca - Repositório Institucional da Fiocruz
Kolomeichuk, S. N., Korneva, V. A., Илюха, В. В., & Kuznetsova, T. Y. (2015) · Современные проблемы науки и образования
Cerliani, M. B., & Richard, S. M. (2013) · Americanae (AECID Library)
Do, K., & Cho, B.-W. (2015) · Journal of Life Science · doi:10.5352/jls.2015.25.11.1304
“A numbers of studies on PER3 have been conducted in humans, mice and horses [2, 5, 12], however the functional association of PER3 has not vastly been study in horse.”
BackgroundPER3 VNTR circadian gene is associated with arterial stiffness variable in healthy subjects
Kolomeichuk, S. N., Ilyukha, V., Korneva, V. A., & Kuznetsova, T. Y. (2016) · Biological Rhythm Research · doi:10.1080/09291016.2016.1251948
Assessment of biological components associated with sleepiness in young working college students
Teixeira, L. R., Pedrazzoli, M., da Luz, A. A., Turte, S. L., de Paula, L. P., Valente, D. L., Tufik, S., & Fischer, F. M. (2012) · Sleep Science · doi:10.1055/s-0046-1820331
“Nadkarni et al.(32) demonstrated that the 4 repetitions allele was the most common in 25 different ethnic groups in Africa, Europe, and Asia.”
BackgroundDelayed Sleep Phase Syndrome – A Case Report
Bihari, S., & Ramakrishnan, N. (2006) · Indian Journal of Sleep Medicine · doi:10.5005/ijsm-1-3-154
Coloring inside the lines: genomic architecture and evolution of a widespread color pattern in frogsPreprint
Goutte, S., Hariyani, I. E., Utzinger, K. D., Bourgeois, Y., & Boissinot, S. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.28.466315
Deboer, T. (2009) · Sleep Medicine Reviews · doi:10.1016/j.smrv.2009.10.001
Clock genes and biological rhythms. Effects of psychotropic drugs
Osland, T. M. (2012) · NORA - Norwegian Open Research Archives
KADOTANI, H., Hida, A., Kitamura, S., Uchiyama, M., Ebisawa, T., Inoue, Y., Kamei, Y., & Mishima, K. (2018) · Institutional Repositories DataBase (IRDB)
- Authors
- Nadkarni, N. A., Weale, M. E., von Schantz, M., & Thomas, M. G.
- Affiliations
- Hammersmith Hospital (GB)
- University College London (GB)
- Centre for Chronobiology, School of Biomedical and Molecular Sciences, University of Surrey, Guildford, United Kingdom
- Venue
- Journal of Biological Rhythms
- Publisher
- SAGE Publications
- Published
- 2005-12
- Volume
- 20
- Issue
- 6
- Pages
- 490-499
- ISSN
- 0748-7304 (ISSN-L)
- 1552-4531
- OpenAlex
- W1967981583
- Cited by
- 76
- References
- 30
- Citations by year
- 2024: 1 · 2023: 1 · 2022: 2 · 2021: 3 · 2020: 1 · 2019: 1 · 2018: 5 · 2017: 5 · 2016: 2 · 2015: 5 · 2014: 9 · 2013: 1 · 2012: 12
- FWCI
- 1.33
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Biological Rhythms (publishedVersion)
- PubMed (publishedVersion)
- Open Research (University of Surrey) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Surrey Research Insight Open Access (The University of Surrey) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Topics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- Per3, variable number tandem repeats, circadian system, allele frequency, natural selection, diurnal preference, delayed sleep phase syndrome, latitude, solar irradiation, genetic differentiation, F(ST), indigenous peoples, human genetic variation
- MeSH terms
- Circadian Rhythm, Gene Frequency, Humans, Nuclear Proteins, Polymorphism, Genetic, Selection, Genetic, Transcription Factors, Evolution, Molecular, Period Circadian Proteins
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