Considerable haplotypic diversity in the RT1-CE class I gene region of the rat major histocompatibility complex

Abstract

The major histocompatibility complex (MHC) class I region extending between the Bat1 and Pou5f1 genes shows considerable genomic plasticity in mouse and rhesus macaque but not in human haplotypes. In the rat, this region is known as the RT1-CE region. The recently published rat MHC sequence gave rise to a complete set of class I gene sequences in a single MHC haplotype, namely the RT1(n) haplotype of the widely used BN inbred strain. To study the degree of genetic diversity, we compared the RT1-CE region-derived class I genes of the RT1(n) haplotype with class I sequences of other rat haplotypes. By using phylogenetic tree analyses, we obtained evidence for extensive "presence and absence" polymorphisms of single loci and even small subfamilies of class I genes in the rat. Alleles of RT1-CE region class I genes could also be identified, but the rate of allelic nucleotide substitutions appeared rather low, indicating that the diversity in the RT1-CE region is mainly based on genomic plasticity.

Two Structurally Related Rat Ly49 Receptors with Opposing Functions (Ly49 Stimulatory Receptor 5 and Ly49 Inhibitory Receptor 5) Recognize Nonclassical MHC Class Ib-Encoded Target Ligands

“…Although we have not yet been able to fine map the genes for the specific Ly49i5/Ly49s5 ligands within the nonclassical RT1-CE/N/M region, the lm1 data strongly suggest that some NK cell allogeneic ligands reside within the first RT1-CE cluster. It could be noted that the content of class I RT1-CE genes varies remarkably between different haplotypes (39), and it can hence prove difficult to generalize findings obtained in a single rat haplotype.…”

MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer

“…It is feasible that alleles may have been missed and that null alleles exist; however, the use of an alternative primer set and 5 0 RACE using a conserved reverse primer suggests that the difference in sequence variants identified per individual is owing to copy number variation, and not methodological artefacts. Variation in the number of Class I sequences in individuals within a species is not unique to Tasmanian devils and has been reported in cattle, rats, mice, Rhesus macaques and pigs (Amadou et al 1999;Otting et al 2005;Roos & Walter 2005;Birch et al 2006;TanakaMatsuda et al 2009). Copy number variation is thought to replace allelic polymorphism in some species such as the Rhesus macaque (Otting et al 2005) and RT1-CE region in the rat (Roos & Walter 2005).…”

“…Variation in the number of Class I sequences in individuals within a species is not unique to Tasmanian devils and has been reported in cattle, rats, mice, Rhesus macaques and pigs (Amadou et al 1999;Otting et al 2005;Roos & Walter 2005;Birch et al 2006;TanakaMatsuda et al 2009). Copy number variation is thought to replace allelic polymorphism in some species such as the Rhesus macaque (Otting et al 2005) and RT1-CE region in the rat (Roos & Walter 2005). In the devil, it appears that either entire loci are missing from some haplotypes (as the same sequences were amplified from both DNA and cDNA) or that alleles at recently duplicated loci have become fixed.…”

Pas de deux: Natural Killer Receptors and MHC Class I Ligands in Primates

“…MHC class I genes exhibit a high degree of turnover. Frequent duplications and deletions due to nonreciprocal recombinations shape the class I gene contents of most species [24] and even haplotypes of various species such as rhesus macaques [25,26], mice [27] and rats [28,29]. Yet, many of the amplified class I genes are only weakly expressed and are classified as non-classical class I (or class Ib) genes.…”