Codon usage bias and base composition in MHC genes in humans and common chimpanzees

Codon bias and base composition in major histocompatibility complex (MHC) s equences have been studied for both class I and II loci in Homo sapiens and Part troglodytes. There is low to moderate codon bias for the MHC of human s and chimpanzees. In the class I loci, the same level of moderate codon bi as is seen for HLA-B, HLA-C, Patr-A, Patr-B, and Patr-C, while at HLA-A the level of codon bias is lower. There is a correlation between codon usage b ias and G+C content in the A and B loci in humans and chimps, but not at th e C locus. To examine the effect of diversifying selection on codon bias, w e subdivided class I alleles into antigen recognition site (ARS) and non-AR S codons. ARS codons had lower bias than non-ARS codons. This may indicate that the constraint of codon bias on nucleotide substitution may be selecte d against in ARS codons. At the class II loci, there are distinct differenc es between alpha and beta chain genes with respect to codon usage, with the beta chain genes being much more biased. Species-specific differences in b ase composition were seen in exon 2 at the DRB1 locus, with lower GC conten t in chimpanzees. Considering the complex evolutionary history of MHC genes , the study of codon usage patterns provides us with a better understanding of both the evolutionary history of these genes and the evolution of synon ymous codon usage in genes under natural selection.