Genomic organization and chromosomal assignment of the human beta1, 4-N-acetylgalactosaminyltransferase gene. Identification of multiple transcription units.

The beta1,4-N-acetylgalactosaminyltransferase (beta1,4GalNAc-T) (EC) gene is expressed in normal brain tissues and in various malignant transformed cells, such as malignant melanoma, neuroblastoma, and adult T cell leukemia. To analyze the regulatory mechanisms of gene expression, we determined the genomic organization of the beta1, 4GalNAc-T gene. The gene consists of at least 11 exons and spans >8 kilobase pairs. The coding region is located in exons 2-11. To determine the transcription initiation sites, 5'-rapid amplification of cDNA ends analysis and ribonuclease protection assays were performed using RNA obtained from the human melanoma cell line SK-MEL-31. Consequently, we defined three transcription initiation sites and the alternative usage of three exons. Exons 1a and 1b partially overlap; the latter is part (3'-side) of the former and corresponds to the 5'-noncoding region of the cDNA clone previously isolated. The third transcript, exon 1c, corresponds to nucleotides -520 to -412 (position +1 = A of ATG of beta1,4GalNAc-T cDNA), which are considered to be in intron 1 based on the cloned cDNA sequence. Ribonuclease protection assays revealed the corresponding protection bands in samples of the gene-expressing cell lines. 5'-Flanking regions of individual initiation sites showed promoter activity when analyzed by chloramphenicol acetyltransferase assay in SK-MEL-31 cells. The multiple transcription initiation sites and their promoters/enhancers identified here might be differentially involved in the cell type-specific expression of the beta1,4GalNAc-T gene. This gene was assigned to human chromosome 12q13.3 by means of fluorescence in situ hybridization.