Recombination hot spots within the I region of the mouse H-2 complex map to the E beta and E alpha genes

Recombinant mouse strains with crossovers in the I region of the H-2 major histocompatibility complex were examined by restriction fragment analysis for the presence of polymorphic restriction sites within the E beta and E alpha genes. Nine recombinant mouse strains were shown to have crossed over within a 5 kb DNA segment that contains the large intron between the second and third exons of the E beta gene. These results are in accord with previous studies mapping a recombination hot spot within this gene. Seven recombinant mouse strains between the p and k haplotypes were shown to have crossed over in a 6 kb segment within the E alpha gene. These results show the existence of a recombination hot spot within the E alpha gene. Comparison of the H-2 haplotypes involved in these two recombination hot spots suggests that a specific DNA sequence in b, s, f, and q haplotypes may act to promote recombination in the E beta gene and a specific DNA sequence in the p haplotype may act to promote recombination in the E alpha gene.