Molecular cloning and characterization of the human CLOCK gene: Expressionin the suprachiasmatic nuclei

The Clock gene is an essential regulator of circadian rhythms. It encodes a member of the basic helix-loop-helix/PER-ARNT-SIM family of transcription factors known to play a central role in the control of diverse cellular eve nts. Previously we described the functional identification and molecular is olation of the Clock gene in the mouse, its interaction with the BMAL1 prot ein, and the role of this complex as a transcriptional activator in the cir cadian pacemaker. Here, we report the cloning, exon organization, chromosom al location, and mRNA expression of the human CLOCK gene. The coding sequen ce of human CLOCK extends for 2538 bp and is 89% identical to its mouse ort holog; its deduced amino acid sequence is 846 residues long and is 96% iden tical to mouse CLOCK. Radiation hybrid mapping localized human CLOCK to the long arm of human chromosome 4 (4q12). Direct sequencing of a genomic CLOC K clone indicated that the coding sequence of human CLOCK extends over 20 e xons and that its intron/exon organization is identical to that of the mous e ortholog, Northern blot analysis indicated widespread expression of two m ajor transcripts of 8 and 10 kb, and in situ hybridization of human brain t issue revealed elevated expression of CLOCK mRNA in the suprachiasmatic nuc lei, the locus of circadian control in mammals, and in the cerebellum. Comp arison of cDNA clones revealed two single nucleotide polymorphisms in nonco ding sequence flanking the CLOCK open reading frame. The central role of Cl ock in the organization of circadian rhythms suggests that it will be a use ful candidate gene for genetic analyses of disorders associated with dysfun ction of the circadian system. (C) 1999 Academic Press.