The chicken BF1 (classical MHC class I) gene shows evidence of selection for diversity in expression and in promoter and signal peptide regions.

The chicken MHC B contains two classical class I genes, BF1 and BF2, with the exception of two related haplotypes lacking BF1 due to insertion/rearrangement. In light of functional specialization of BF1 and BF2 molecules, we were interested in evaluating their relative expression at the mRNA level. We evaluated several MHC haplotypes for class I gene expression by RT-quantitative PCR. BF1 transcript levels were approximately two- to fivefold lower than BF2, with the exception of one haplotype in which BF1 expression was very low. To investigate molecular explanations for differences in BF locus or allele expression, we determined nucleotide sequences of Enhancer A and proximal promoter elements of nine different BF1 alleles, as well as their signal peptide sequences. Results showed that all BF1 alleles exhibit conservation of most of the identified promoter elements, but divergence from the Enhancer A sequence identified in the more highly expressed BF2 locus. Nonetheless, extensive BF1 allelic polymorphism was found in the promoter region and in the signal peptide, with two strongly separated allelic lineages identified for both. Patterns of promoter lineages, signal peptide lineages, and exon 2 mature protein coding sequences in individual BF1 alleles suggest that recombination among these elements has contributed to diversification of BF1 alleles. Finally, identification of a novel inactivating mutation in one BF1 allele suggests past selective pressure to eliminate BF1 function.