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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^{1 ,2}

Marielle Afanassieff^3,*,, Ronald M. Goto^*, Jennifer Ha^*, Mark A. Sherman, Lingwen Zhong^*, Charles Auffray, Françoise Coudert, Rima Zoorob and Marcia M. Miller^4,*

^* Department of Molecular Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010; Institut National de la Recherche Agronomique, Station de Pathologie Aviaire et Parasitologie, Nouzilly, France; Department of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010; and Centre National de la Recherche Scientifique, Unité Propre de Recherche 420, Génétique Moléculaire et Biologie du Développement, Villejuif, France

MHC genes in the chicken are arranged into two genetically independent clusters located on the same chromosome. These are the classical B system and restriction fragment pattern-Y (Rfp-Y), a second cluster of MHC genes identified recently through DNA hybridization. Because small numbers of MHC class I and class II genes are present in both B and Rfp-Y, the two clusters might be the result of duplication of an entire chromosomal segment. We subcloned, 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, classical 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). One locus is disrupted and unexpressed. The other, YFV, is widely transcribed and polymorphic. Mature YFV protein associated with ₂m 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 containing MHC genes of specialized function.

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