Promoter and intronic sequences of the human thiopurine S-methyltransferase (TPMT) gene isolated from a human PAC1 genomic library.

PURPOSE: To isolate and characterize the polymorphic human thiopurine S-methyltransferase (TPMT) gene.
METHODS: The human TPMT gene was isolated by PCR screening of a phage artificial chromosome (PAC) library, using exon- and intron-specific primers, then mapped and sequenced.
RESULTS: Two separate PAC1 clones were isolated that contained the same 25 kb gene with 9 exons encompassing the entire TPMT open reading frame. Structural characterization revealed distinct differences when compared to a TPMT gene previously isolated from a chromosome 6-specific human genomic library; the 5'-flanking region (putative promoter) contains 17 additional nucleotides located at position-77 upstream from the transcription start site, in addition to several nucleotide sequence differences, and intron 8 is only 1.6 kb, 5 kb shorter than previously reported. Southern and PCR analyses of genomic DNA from 18 unrelated individuals revealed only the TPMT gene structure corresponding to the PAC clones we isolated. Analysis of the TPMT promoter activity using the 5'-terminal region confirmed transcriptional activity in human HepG2 and CCRF-CEM cells. The 5'-flank is 71% GC rich and does not contain consensus sequences for TATA box or CCAAT elements. FISH analysis demonstrated the presence of the TPMT-homologous sequence on the short arm of chromosome 6 (sublocalized to 6p22).
CONCLUSIONS: These findings establish the genomic structure of the human TPMT gene, revealing differences in the promoter and intronic sequences compared to that previously reported and providing a basis for future studies to further elucidate its biological function and regulation.