title: Genomic organization of the rat Clock gene and sequence analysis in inbred rat strains.
abstract: While mutations in genes that function in the core molecular clock may disrupt circadian periodicity, their relevance to diurnal variation in metabolic, cardiovascular, and respiratory function is unknown. The circadian Clock gene product is an essential regulator of central and peripheral circadian rhythms in mammals. We have elucidated the complete exon-intron organization of the Clock gene in rat and have carried out an extensive search for single nucleotide polymorphisms (SNPs) in a panel of 12 inbred rat strains that exhibit diversity in studies of central and peripheral organ function and disease. The rat Clock gene consists of 23 exons spanning approximately 75 kb. Comparative sequence analysis identified 33 novel SNPs, including 32 that distinguish the Brown Norway (BN) rat from the other strains studied. Most notable were two novel mutations in the BN sequence at exon 8, Ile131Val and Ile132Val, occurring in a segment of the highly conserved PAS-A domain of the protein. These results afford the opportunity to assess the impact of genetic variation in Clock on central and peripheral functions subject to the core molecular clock and to test the importance of Clock variants in explaining diversity among rat strains in the expression of phenotypes, such as blood pressure, subject to circadian oscillation.
authors.affiliation: The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK.
authors.forename: Peng Y
authors.initials: PY
authors.lastname: Woon
authors.forename: Anne M
authors.initials: AM
authors.lastname: Curtis
authors.forename: Pamela J
authors.initials: PJ
authors.lastname: Kaisaki
authors.forename: Karène
authors.initials: K
authors.lastname: Argoud
authors.forename: Karin J
authors.initials: KJ
authors.lastname: Wallace
authors.forename: Marie-Thérèse
authors.initials: MT
authors.lastname: Bihoreau
authors.forename: Garret A
authors.initials: GA
authors.lastname: FitzGerald
authors.forename: Dominique
authors.initials: D
authors.lastname: Gauguier
mesh_terms: D020121:5' Untranslated Regions; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D056926:CLOCK Proteins; D004247:DNA / Q000235:genetics; D005091:Exons; D023281:Genomics; D006801:Humans; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D051381:Rats; D011919:Rats, Inbred Strains; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D015534:Trans-Activators / Q000737:chemistry / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D015534:Trans-Activators; D004247:DNA; D056926:CLOCK Proteins; C538943:CLOCK protein, human; C538945:Clock protein, rat