Human stearoyl-CoA desaturase: alternative transcripts generated from a single gene by usage of tandem polyadenylation sites

A critical step in the synthesis of unsaturated fatty acids is catalysed by stearoyl-CoA desaturase (Scd). To determine the regulation of human Scd, w e characterized the gene and its transcripts. Screening a human keratinocyt e cDNA library and analysis of 3'-RACE (rapid amplification of cDNA ends) p roducts from various tissues yielded a 5.2 kb cDNA encoding a 359 amino aci d protein with a calculated molecular mass of 41.5 kDa. Analysis of 3'-RACE products suggested that alternative usage of polyadenylation sites generat es two transcripts of 3.9 and 5.2 kb, a result consistent with Northern ana lysis. Southern analysis demonstrated the existance of two SCD loci in the human genome. Chromosomal mapping localized one locus to chromosome 10, and the second locus to chromosome 17. Characterization of genomic clones isol ated from chromosome-specific libraries revealed that only the locus on chr omosome 10 contained introns. Sequence analysis of the intron-less locus di splayed multiple nucleotide insertions and deletions, as well as in-frame s top codons. Reverse transcriptase-PCR analysis performed with primers speci fic to the intron-less locus failed to produce a PCR product from brain, li ver and skin RNA, indicating that the locus on chromosome 17 is most likely a transcriptionally inactive, fully processed pseudogene. These results su ggest strongly that there is one structural SCD gene in the human genome, a nd that it generates two transcripts by use of alternative polyadenyation s ites. Although the primary sequence and intron-exon structure of SCD is phy logenetically conserved, divergence between rodent and human is seen in the number of SCD genes and in the generation of alternative transcripts, sugg esting a species-specific component of SCD regulation and function.