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. 2016 Sep 28;35(1):21.
doi: 10.1186/s40101-016-0111-9.

A Comparative Study on the Regulatory Region of the PERIOD1 Gene Among Diurnal/Nocturnal Primates

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Free PMC article

A Comparative Study on the Regulatory Region of the PERIOD1 Gene Among Diurnal/Nocturnal Primates

Takafumi Katsumura et al. J Physiol Anthropol. .
Free PMC article

Abstract

Background: The circadian clock is set up around a 24-h period in humans who are awake in the daytime and sleep in the nighttime, accompanied with physiological and metabolic rhythms. Most haplorhine primates, including humans, are diurnal, while most "primitive" strepsirrhine primates are nocturnal, suggesting primates have evolved from nocturnal to diurnal habits. The mechanisms of physiological changes causing the habits and of genetic changes causing the physiological changes are, however, unknown. To reveal these mechanisms, we focus on the nucleotide sequences of the regulatory region of the PERIOD1 (PER1) gene that is known as one of the key elements of the circadian clock in mammalians.

Methods: We determined nucleotide sequences of the regulatory region of PER1 concerning the gene expression for six primates and compared those with those of eight primates from the international DNA database. Based on the sequence data, we constructed a phylogenetic tree including both the diurnal/nocturnal species and investigated the guanine and cytosine (GC) content in the regulatory region.

Results: The motif sequences regulating gene expression were evolutionary conservative in the primates examined. The phylogenetic tree simply showed phylogenetic relationship among the species and no branching pattern distinguishable between the diurnal and nocturnal groups. We found two cores showing a statistically significant difference between the diurnal and the nocturnal habits related to the GC contents of the regulatory region of PER1.

Conclusion: Our results suggest the possibility that the two cores in the upstream region of PER1 are related to the regulation of gene expression leading to behavioral differences between diurnal and nocturnal primates.

Keywords: Circadian clock; Diurnal; GC content; Nocturnal; PERIOD1.

Figures

Fig. 1
Fig. 1
Sequence determined regulatory region a with the primer positions used for primer walking and b with three E-boxes of PER1. Green and red arrows upon the structure model of PER1 upstream indicate the forward and reverse primers, respectively, and the gray lines and the numbers represent the lengths of the expected PCR product estimated by the human genome sequence. The numbers closest to the arrows are consistent with the primer IDs in Table 2
Fig. 2
Fig. 2
Hypothetical and actual gene trees using the upstream nucleotide sequences of PER1. Left a upper and b lower trees represent the putative topology that reflects only the phylogenetic relationship of the species and the clustering pattern that reflects the diurnal and the nocturnal habits, respectively. c Right gene tree is a maximum likelihood tree reconstructed based on 15 nucleotide sequences of the PER1 upstream
Fig. 3
Fig. 3
Comparisons with a GC contents of haplorhines and strepsirrhines and b nocturnal. Boxplot represents five-number summary statistics for each group, with lower and upper error bars indicating minimum and maximum observations excluding outliers, the tops and bottoms of boxes represent the third and the first quartiles, respectively, and the middle bar represents the median. Colored dots indicate the GC contents of the examined individual. Significant differences were identified using Welch’s t test
Fig. 4
Fig. 4
Distributions of GC contents across the upstream region of PER1. A double-headed arrow indicates the GC-rich region of diurnal primates compared to nocturnal ones. Semi-transparent color at each point represents the 95 % confidence interval of the mean

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