Association of structural polymorphisms in the human period3 gene with delayed sleep phase syndrome

Abstract

Recent progress in biological clock research has facilitated genetic analysis of circadian rhythm sleep disorders, such as delayed sleep phase syndrome (DSPS) and non-24-h sleep-wake syndrome (N-24). We analyzed the human period3 (hPer3) gene, one of the human homologs of the Drosophila clock-gene period (Per), as a possible candidate for rhythm disorder susceptibility. All of the coding exons in the hPer3 gene were screened for polymorphisms by a PCR-based strategy using genomic DNA samples from sleep disorder patients and control subjects. We identified six sequence variations with amino acid changes, of which five were common and predicted four haplotypes of the hPer3 gene. One of the haplotypes was significantly associated with DSPS (Bonferroni's corrected P = 0.037; odds ratio = 7.79; 95% CI 1.59-38.3) in our study population. Our results suggest that structural polymorphisms in the hPer3 gene may be implicated in the pathogenesis of DSPS.

Fig. 1. (A) Schematic diagram of the hPer3 gene illustrating the locations of six polymorphisms with putative amino acid changes. Exons 1–21 are depicted as closed boxes and are numbered intermittently for clarity. Sizes of the introns and exons are not to scale. Polymorphisms with putative amino acid changes are shown above the gene. At the bottom are summarized the locations of the coding sequences for domains of hPER3. CLD, cytoplasmic localization domain. (B) Alignment of the amino acid sequences of vertebrate PER homologs. Only the region adjacent to the V647G polymorphism is shown. Amino acid residues that correspond to V647 in hPER3 are boxed. Arrows indicate the putative target residues of CK I ɛ (Toh et al., 2001). hPER1/2/3, human PER1/2/3; mPER1/2/3, mouse PER1/2/3; rPER2, rat PER2; qPER2/3, Japanese quail PER2/3; xPER2, Xenopus PER2; zPER3, zebrafish PER3.

Fig. 1. (A) Schematic diagram of the hPer3 gene illustrating the locations of six polymorphisms with putative amino acid changes. Exons 1–21 are depicted as closed boxes and are numbered intermittently for clarity. Sizes of the introns and exons are not to scale. Polymorphisms with putative amino acid changes are shown above the gene. At the bottom are summarized the locations of the coding sequences for domains of hPER3. CLD, cytoplasmic localization domain. (B) Alignment of the amino acid sequences of vertebrate PER homologs. Only the region adjacent to the V647G polymorphism is shown. Amino acid residues that correspond to V647 in hPER3 are boxed. Arrows indicate the putative target residues of CK I ɛ (Toh et al., 2001). hPER1/2/3, human PER1/2/3; mPER1/2/3, mouse PER1/2/3; rPER2, rat PER2; qPER2/3, Japanese quail PER2/3; xPER2, Xenopus PER2; zPER3, zebrafish PER3.

Fig. 2. Nucleotide and amino acid sequences of each allele in the polymorphic repeat region of the hPer3 gene. The 4-repeat and 5-repeat alleles are aligned for optimal homology. The dotted line indicates a gap in the sequence created for optimal alignment. The nucleotide and amino acid that are subject to 3110(T→C) [M1037T] polymorphism, which was exclusively observed on a 4-repeat allele, are boxed. The NcoI restriction site used in RFLP analysis is underlined.