Characterization of three splice variants and genomic organization of the mouse BMAL1 gene

The BMAL1 gene encodes a member of the basic helix-loop-helix/PER-ARNT-SIM (bHLH/PAS) family of transcription factors. it is a key regulator of circad ian rhythms. Using sequence information from human BMAL1 (hBMAL1) cDNAs pre viously reported by our laboratory, we have isolated and characterized cDNA s encoding three splice variants of the mouse BMAL1 (mBMAL1) gene. Of the t hree splice variants, mBMAL1b extends for 1878 bp in the coding sequence, w hich is 91% identical to that of hBMAL1b; its deduced amino acid sequence i s 626 residues long and is 98% identical to that of bBMAL1b, and sequence i dentities in the hHLH, PAS-A, and PAS-B regions are 98, 100, and 100%, resp ectively. mBMAL1b' arises from alternative; usage of exon 2, which results in a 7-amino-acid insertion and alternative splice acceptor usage at the in tron 9/exon 10 splice junction, which causes an alanine residue deletion. m BMAL1b' encodes 632 amino acids and contains the bHLH/PAS domains, mBMAL1g' is generated by alternative splice acceptor usage at the intron 6/exon 7 s plice junction, which results in a 28-bp deletion adjacent to the 5' end of the PAS domain. Since the 28-bp deletion shifts the reading frame, mBMAL1g ' is predicted to encode a product of only 222 amino acids that lacks the P AS domain. The tissue distributions of the three splice variants showed som e variation. The variations in the tissue distributions and predicted amino acid sequences suggest that the three splice variants may have different f unctions. Direct sequencing of the genomic mBMAL1 clones indicated that the coding sequence of mBMAL1 spans 32 kb and includes 17 exons. An unusual ex on/intron donor sequence was found in intron 14, which begins with GC at th e 5' end. Comparison with the bHLH/PAS family genes revealed that the intro n/exon splice pattern of mBMAL1 most closely matches that of the mAhr, whic h suggests that BMAL1 and Ahr belong to the same subclass and may be derive d from a common primordial gene. (C) 1999 Academic Press.