Genomic sequence allalysis of Fugu rubripes CFTR and flanking genes in a 60 kb region conserving synteny with 800 kb of human chromosome 7

To define control elements that regulate tissue-specific expression of the cystic fibrosis transmembrane regulator (CFTR), we have sequenced 60 kb of genomic DNA From the puffer fish Fugu rubripes (Fupu) that includes the CFT R gene. This region of the Fugu genome shows conservation of synteny with 8 00-kb sequence of the human genome encompassing the WNT2 CFTR, Z43555, and CBP90 genes. Additionally, the genomic structure of each gene is conserved. In a multiple sequence alignment of human, mouse, and Fugu, the putative W NT2 promoter sequence is shown to contain highly conserved elements that ma y be transcription Factor or other regulatory binding sites. We have found two putative ankyrin repeat-containing genes that Flank the CFTR gene. Over all sequence analysis suggests conservation of intron/exon boundaries betwe en Fugu and human CFTR and revealed extensive homology between functional p rotein domains. However, the immediate 5' regions of human and Fugu CFTR ar e highly divergent with few conserved sequences apart From those resembling diminished cAMP response elements (CRE) and CAAT box elements. Interesting ly, the polymorphic polyT tract located upstream of exon 9 is present in hu man and Fugu but absent in mouse. Similarly, an intron 1 and intron 9 eleme nt common to human and Fugu is absent in mouse. The euryhaline killifish CF TR coding sequence is highly homologous to the Fugu sequence, suggesting th at upregulation of CFTR in that species in response to salinity may be regu lated transcriptionally.