At least one class I gene in restriction fragment pattern-Y (Rfp-Y), the second MHC gene cluster in the chicken, is transcribed, polymorphic, and shows divergent specialization in antigen binding region

dMHC genes in the chicken are arranged into two genetically independent clu sters located on the same chromosome. These are the classical B system and restriction fragment pattern-Y (Rfp-Y), a second cluster of MHC genes ident ified recently through DNA hybridization. Because small numbers of MHC clas s I and class II genes are present in both B and Rfp-Y the two clusters mig ht be the result of duplication of an entire chromosomal segment. We subclo ned, sequenced, and analyzed the expression of two class I loci mapping to Rfp-Y to determine whether Rfp-Y should be considered either as a second, c lassical MHC or as a region containing specialized MHC-like genes, such as class Ib genes, The Rfp-Y genes are highly similar to each other (93%) and to classical class Ia genes (73% with chicken B class I; 49% with HLA-A). O ne locus is disrupted and unexpressed. The other, YFV, is widely transcribe d and polymorphic. Mature YFV protein associated with beta (2)m arrives on the surface of chicken B (RP9) lymphoma cells expressing YFV as an epitope- tagged transgene. Substitutions in the YFV Ag-binding region (ABR) occur at four of the eight highly conserved residues that are essential for binding of peptide-Ag in the class Ia molecules. Therefore, it is unlikely that Ag is bound in the YFV ABR in the manner typical of class Ia molecules. This ABR specialization indicates that even though YFV is polymorphic and widely transcribed, it is, in fact, a class Ib gene, and Rfp-Y is a region contai ning MHC genes of specialized function.