A comparative study on the regulatory region of the PERIOD1 gene among diurnal/nocturnal primates
© The Author(s). 2016
Received: 23 February 2016
Accepted: 14 September 2016
Published: 28 September 2016
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.
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.
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.
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.
The transition from nocturnal to diurnal habits must have been an epoch in primate evolution. It is widely accepted that mammals were originally nocturnal. Strepsirrhini is a suborder of primates that include most of the prosimians (lemurs, galagos, pottos, lorises, except for tarsiers), which are closer to ancestral types of primates. Because many strepsirrhines have nocturnal habits, it is plausible that a common ancestor of primates was also nocturnal. In contrast, another suborder, Haplorhini, which includes the tarsiers, the simians, and even Homo sapiens (humans), has diurnal habits except for the genus Aotus (owl monkeys) and the tarsiers. Thus, primates are thought to have shifted from nocturnal to diurnal habits in the evolutionary process .
Many phenotypic features that characterize the lineage leading to humans must have evolved as a sequel to diurnal behavior. Strepsirrhines and haplorhines generally have a dichromatic and a trichromatic vision, respectively. These are typical features because nocturnal species would not require acute color vision, which is of more use for diurnal species . The apes, close relatives of humans, commonly have uniform trichromatic vision  which is useful in individuals with diurnal habits.
The physiological mechanism determining whether nocturnal or diurnal habits are dominant is unclear. It is likely that the circadian phase has been changed between nocturnal and diurnal species. Almost all organisms have biological clocks that generate physiological rhythms of body temperature and metabolism at 24-h cycles, and regulate behavioral rhythms of sleepfulness and wakefulness, the circadian rhythm. In mammalians, transcriptional factors CLOCK and BMAL1 form dimers, and directly and indirectly activate transcription of the Per and Cry genes through the E-box sequence (CACGTG) that is the transcriptional factor binding (TFB) motif observed in regulatory regions, located on the upstream regions of genes in many cases. The activation is inhibited by accumulation of the PER and CRY proteins, the negative transcriptional feedback (NTF) loop. The NTF loop has a 24-h period and forms a circadian clock oscillator. By the oscillation of PER and CRY, the expression levels of the other clock and clock-related genes are controlled, and physiological and metabolic process are affected . Therefore, we should consider the possibility that mutations in clock/clock-related genes and/or in the regulatory region controlling their expression pattern might be the key of the dynamic transition of the circadian phase. But the genetic mechanisms generating the opposite circadian phase in the nocturnal/diurnal lineages of primates are unknown.
To find a clue to reveal the genetic mechanism of the transition from nocturnal to diurnal habits, we have focused on the PER1 gene because the transcriptional regulation of PER1 has been studied extensively . We sequence the ~4 kb upstream region including exon 1 of the PER1 gene, in which three E-boxes are included, for six primates (chimpanzee, marmoset, owl monkey, lemur, greater galago, and lesser galago), and compare those with the homologous region sequences for eight primates (human, chimpanzee, gorilla, orangutan, gibbon, macaque, tarsier, and bushbaby) from the international DNA database. We hypothesize that we would find a correlation between the upstream sequence data and that of the nocturnal/diurnal groups, if the expression regulation of PER1 affects the nocturnal/diurnal habits. If the upstream sequences of PER1 only show phylogenetic relationships, then it appears that the reversal of the daytime and nighttime in the diurnal/nocturnal primates is not related to the expression pattern of the PER1 gene. We investigated: (1) the number of substitutions in the E-boxes, (2) the topology of the phylogenetic tree, and (3) the guanine and cytosine (GC) contents, e.g., the proportion of GC in the ~4 kb upstream region. Our data demonstrate that the GC content of the region examined is significantly different from that in the nocturnal/diurnal grouping, whereas the substitutions of the E-boxes and the phylogenetic tree are not correlated with the grouping.
Materials and methods
Characteristics of used species and their nucleotide sequences
PCR and sequencing
Purposes of use
Sequences (5′ → 3′)
PCR & Sequencing
The PCR products were diluted 20-fold and used as templates in the direct sequencing reaction (following the commercial protocol) and were then analyzed in an ABI3130 DNA sequencer (Applied Biosystems, Tokyo, Japan). We determined the 3472–4028 bp nucleotide sequences for the PER1 promoter region by primer walking; and the primers used, #5–#20, are shown in Fig. 1a. The nucleotide sequence data determined in this study were deposited into the international DNA database DDBJ/EMBL/GenBank (accession nos. LC121024–LC121029).
Sequence alignments and data analysis
The GC contents and distribution of GC content variation of each sequence were calculated using GC function in the “SeqinR” R package : Window size and a step for the distribution of the GC contents were 500 and 25 bp, respectively. Ambiguous bases and alignment gaps contained in each window were excluded from the calculation. These statistical significances were assessed by Welch’s t test (p < 0.05). For the distribution of GC contents, p values were adjusted to 0.00044 after the Bonferroni corrections because of the multiple testing (Fig. 4).
Comparison of the PER1 regulatory regions
We determined ~4 kb sequences of the upstream region from the PER1 exon 2 that includes three E-boxes (Fig. 1a) for six species by PCR-direct sequencing through primer walking and compared with the orthologous sequences for the nine species listed in Table 1. As we predicted, the multiple alignment showed that the E-box sequences (CACGTG) of PER1 were well conserved in all the species (Fig. 1b). In the first E-box (E-box_1), a heterozygous site of G and C at the fourth position was detected in the greater galago (Per1GG). In the second E-box (E-box_2), substitutions from C to T at the first position and from C to A at the third position were found in the tarsier and the marmoset, respectively. No substitutions were observed in the third E-box (E-box_3). Thus, no sites distinguishable between the diurnal and nocturnal groups were found. The regions including the E-box motifs were very conservative in the primates examined in the present study.
Reconstruction of phylogenetic tree based on PER1 upstream sequences
We hypothesized that the branching pattern of the phylogenetic tree on the regulatory region could indicate that the nocturnal and the diurnal groups clustered separately if the habit-specific substitutions in the upstream region occurred and changed the expression patterns. The upper virtual tree represents the putative topology that reflects only the phylogenetic relationship of the species (Fig. 2a), while the lower virtual tree represents the clustering pattern that reflects the diurnal and the nocturnal habits (Fig. 2b).
To test which topology of the virtual trees is true, we constructed a phylogenetic tree based on the nucleotide sequences of the PER1 upstream obtained from the primates (Fig. 2c). Each branch showed high bootstrap values (92–100 %), indicating that statistically, the tree topology was highly reliable. The branching pattern did not show the diurnal/nocturnal grouping, but did show the phylogenetic grouping. Thus, overall sequences of the ~4 kb upstream region were likely to have evolved reflecting the phylogenetic relationship of the species.
Comparison of GC contents in PER1 upstream sequences
We obtained the nucleotide sequences of the upstream region of the PER1 gene for 13 species of primates and analyzed them using three different methods. First, we looked at the TFB motifs, E-boxes, in the regulatory region. Comparing the motif sequences between the primates, we found no differences between the diurnal and nocturnal species. Therefore, we suggest that the other TFB motifs might be related to the two habit styles, if the diurnal/nocturnal habits are regulated by the PER1 gene expression patterns. Secondly, we constructed a phylogenetic tree based on the upstream sequences and found no clustering patterns distinguishable between the diurnal and nocturnal species. Thus, the primary structure of the nucleotide sequences of the regulatory region gave no details about the factors changing expression patterns of PER1 and forming the diurnal/nocturnal habits.
There are GC-rich and GC-poor regions in vertebrate genomes, i.e., the “isochore structure” , and arguments that the GC content is associated with gene expression patterns [13, 14]. However, another study shows that correlations between the GC content and expression are very weak in the mammalian genome . Thus, the impact of the GC content on the gene expression pattern is quite controversial in overall genome analyses. However, a more recent study, using the genome sequence data of Gallus gallus (chicken) downloaded from the international DNA database, separately examined protein coding sequences, complete mRNA sequences, and upstream region sequences of genes, and found that the GC content of the upstream region is significantly and positively correlated with the expression level, expression breadth, and maximum expression level . In the present study, we found statistically significant differences between the diurnal and nocturnal groups in the mean GC contents of the upstream region of the PER1 gene. It is necessary to examine the upstream regions of other genes adjacent to the PER1 gene and the other genes located on chromosome 17 between diurnal and nocturnal primates or between Haplorhini and Strepsirrhini to confirm whether or not the difference is only observed in the PER1 gene. Nevertheless, this result gave rise to the speculation that the difference of the expression patterns owing to the GC contents affects the diurnal/nocturnal habits.
As an exception, the GC contents of the marmoset in the two cores were as low as the nocturnal group despite the diurnal habit. We think that there are two reasons. First, this inconsistency might be caused by the phylogenetic position of the marmoset. The clade of the new world monkeys includes both of the habits. In the clade of the marmoset, the upstream region of PER1 may not be related to the alteration from nocturnal to diurnal. Depending on the time that the primates had obtained the diurnal habit, if the marmoset’s diurnal habit occurred independently, and was different from those occurred in the old world monkeys and apes, the circadian rhythm could be regulated by the other regions. Second, in this study, we have a limit in sampling the species: the diurnal group contains more haplorhines than strepsirrhines, whereas the nocturnal group contains more strepsirrhines than haplorhines. The bias causes ambiguity in statistical tests. This is a fundamental issue: it is difficult to obtain the nocturnal Haplorhini species and the diurnal Strepsirrhini species, because the species distribution for the diurnal/nocturnal habits is already biased in nature. Nevertheless, it must be significant to test our hypothesis using additional diurnal strepsirrhines species in the near future.
We should note that the significant correlation Rao et al. (2013) showed was not based on the mammalian genome but rather based on the avian genome. Notwithstanding, that speculation suggests experimentally examining the expression level by transforming the upstream sequences of PER1 into cells and making a comparison between the diurnal and nocturnal primates. It must be interesting to test the owl monkey and the tarsiers because both of them are classified into Haplorhini but are nocturnal. Although we have applied the candidate gene approach focusing on the PER1 gene, there was a genome-wide study concerning transition from diurnal to nocturnal among haplorhines  that attempted to discover genes showing signals of positive selection between the diurnal and nocturnal species using the genomes of six primates. Our strategy, comparing the upstream region sequences, should also be taken into consideration in genome-wide analyses, including strepsirrhines in the near future, in addition to the functional analysis to determine whether or not the differences of the GC contents have some influence on the pattern of PER1 gene expression.
A statistically significant difference between the diurnal and nocturnal habits concerning the GC contents in the regulatory region of PER1 was found. Thus, this study successfully suggests a clue toward revealing the genetic mechanisms of the transition from the nocturnal to diurnal habits in primates.
We thank the Joint Usage/Research Center of the Primate Research Institute of Kyoto University and Dr. Hirohisa Hirai who directs the program for kindly providing the blood samples of primates. The authors thank Robert E. Brandt, Founder, CEO, and CME, of MedEd Japan, for editing and formatting the manuscript.
SK was supported by a Grant-in-Aid for Scientific Research (A) (19207018) from Japan Society for the Promotion of Science (JSPS), and by Grant-in-Aid for Scientific Research on Priority Areas "Comparative Genomics" (20017008) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT). HO was supported by a Grant-in-Aid for Challenging Exploratory Research (25650154) from the JSPS.
TK, YF, SK, and HO conceived and designed the experiments. YF conducted the experiments, and TK analyzed the data. TK and HO wrote the paper. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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