Genomic organization and differential expression of channel catfish MHC class I genes

Two clones, designated Icpu-UA/3 and Icpu-UA/26, were isolated from a genom ic library prepared from a single homozygous gynogenetic channel catfish. S equence analysis showed that each clone encoded a gene product containing f eatures conserved among MHC class I molecules. The genomic organization of both clones indicated that each domain, with the exception of the cytoplasm ic, was encoded by a separate exon. Moreover, like mammals, catfish cytopla smic regions were encoded by three exons rather than two as previously desc ribed for other teleost MHC class I genes. Analysis of nucleotide sequences upstream of catfish class I genes revealed the presence of several regulat ory motifs similar to those seen in mammalian class I genes. These included a TATA box, Enhancer B, Site alpha, ISRE, and GAS elements. To determine t he functional significance of these elements, EMSAs and tissue expression a ssays were performed. EMSAs demonstrated that an Enhancer B element within Icpu-UA/26, and an imperfect Enhancer B element and/or a GC-rich region wit hin Icpu-UA/3 were responsible for formation of specific DNA/protein comple xes. Expression studies detected Icpu-UA/26 transcripts in all tissues test ed, whereas Icpu-UA/3 encoded messages were seen in a limited number of tis sues. These results define the intron/exon organization of catfish MHC clas s I genes, suggest that Icpu-UA/3 encodes a nonclassical gene, and provide the first functional evidence that upstream sequences, similar to those see n in mammalian class I genes, play important roles in regulating teleost MH C gene expression. (C) 2001 Elsevier Science Ltd. All rights reserved.