title: Does the rat have an H2-D orthologue next to Bat1?
abstract: Unlike all other mammalian species, which have only one class I region, rat and mouse possess a second class I region on the centromeric side of the MHC. The mouse has class Ia genes in both the centromeric H2-K and the telomeric H2-D region, whereas the rat has class Ia genes only in the centromeric RT1.A region. Bat1 is the last gene of the class III region in the mouse, and H2-D was mapped 10 kb telomeric of Bat1. To determine whether the rat possesses an H2-D orthologue, we sequenced a cosmid clone that contains rat Bat1 and an adjacent class I gene, RT1.46 (l). Homology searches suggest a transition in the rat sequence with a proximal stretch containing Nfkbil1, ATP6G, and Bat1, which is homologous to the mouse H2-D region, and a more-distal stretch, which contains the class I gene and has many similarities to mouse H2-Q region sequences. Downstream of Bat1 is a sequence stretch with great similarity to intron 3 of H2-D, which is not present in any of the rat class I genes but is found in mouse H2-K, D-, and - Q region genes. Numerous repetitive elements indicate that the region is prone to repeat-mediated rearrangements. A putative H2-D orthologue may have been present at this location and lost by genomic rearrangements, leaving the short intronic sequence behind. The class I gene RT1.46 (l) has an open reading frame, but it is unlike H2-D due to a unique 5'UTR shared with H2-Q1 and Q2, the absence of the B2 SINE repeat characteristic of H2-D/L, and the apparent lack of surface expression. We conclude that at least the LEW rat (RT1 (l)) does not possess an H2-D orthologue.
authors.affiliation: Howard Hughes Medical Institute, Center for Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA. doris@chop.swmed.edu
authors.forename: Doris
authors.initials: D
authors.lastname: Lambracht-Washington
authors.forename: Kirsten
authors.initials: K
authors.lastname: Fischer Lindahl
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003360:Cosmids / Q000235:genetics; D019143:Evolution, Molecular; D005805:Genes, MHC Class I; D006183:H-2 Antigens / Q000235:genetics*; D006649:Histocompatibility Antigens / Q000235:genetics; D007438:Introns; D008285:Major Histocompatibility Complex; D051379:Mice; D008969:Molecular Sequence Data; D010802:Phylogeny; D051381:Rats; D011917:Rats, Inbred Lew; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
chemical_list: D006183:H-2 Antigens; D006649:Histocompatibility Antigens; C038353:histocompatibility antigens RT, rat