The gene encoding the Ia antigen-associated invariant chain (Ii) is not linked to the H-2 complex

The invariant (Ii) chain of murine Ia antigens is associated with the intracellular but not the cell-surface forms of the A alpha:A beta and E alpha:E beta Ia complexes. Due to its unique subcellular localization, Ii has been postulated to play a part in the assembly or intracellular transport of the Ia alpha:beta complexes, which function in immune recognition. A more general role for Ii in the transport of other cell proteins has also been suggested. Because of the unusual subunit composition of Ia antigens and because the synthesis of alpha, beta and Ii chains is coordinately regulated, it was of interest to determine whether, like the alpha and beta chains, Ii is encoded by a gene in the I region of the H-2 histocompatibility complex. We report here the use of an Ii chain polymorphism present in Mus spretus to demonstrate that the gene for Ii is not linked to the H-2 complex. Thus, intracellular Ia antigens consist of the products of two linked genes and one unlinked gene.