The human gene encoding the Ia-associated y (or invariant) chain was isolated by screening a genomic library in phage X with cDNA probes. The frequency of positive clones in the library, the overlapping restriction maps of the cloned fragments, and the patterns of genomic hybridization suggested that the y-chain gene exists as a single copy per haploid genome. The gene consists of 8 exons, spanning approximately 12 kilobases of DNA. All exon sequences were in an open reading frame, contained appropriate splice junction sequences, and encompassed the entire sequence of full-length V-chain mRNA, suggesting that the gene we isolated is most likely functional. Furthermore, "CAAT"-type and "TATA"-type promoter sequences were found at the expected positions upstream from the proposed cap site. The organization of the V-chain gene has none of the distinctive features of the immunoglobulin superfamily of genes, of which la a and (3 chains are members. Therefore, the evolutionary origins, and perhaps the functions, of the la y chains are distinct from those of the other two Ia subunits a and (3. Despite the unrelatedness of these genes, consensus sequences found approximately 150 base pairs upstream from all the Ta a-and E8-chain genes sequenced to date were also found in analogous positions in the V-chain gene, suggesting a possible role in the coregulation of expression of these genes.Ia molecules are polymorphic cell surface glycoproteins expressed primarily by antigen-presenting cells and B lymphocytes (reviewed in ref. 1). They are of key importance in the immune system, since they restrict recognition of foreign antigen to T-helper lymphocytes sharing the appropriate Ta phenotypes. Ia molecules are formed by three noncovalently bound transmembrane glycoproteins, the highly polymorphic a and 8 chains, encoded by the major histocompatibility complex (MHC) class II genes, and the nonpolymorphic y (or invariant) chain (reviewed in ref. 2). At the cell surface, they comprise only a-(3 dimers, as y chains dissociate from Ia oligomers during Golgi processing (3,4). The expression of a, ,3, and y chains is strictly coregulated during development, most likely at the level of gene transcription (5, 6), as indicated by their virtually identical tissue distribution (7,8) and their parallel induction by y-interferon (5). An understanding of the regulatory mechanisms of Ta expression is of great interest, since expression of Ia molecules by immune cells is a key requirement for recognition of foreign antigens by T lymphocytes (9), and since Ia expression by nonimmune cells has been involved in the pathogenesis of autoimmune diseases (10). The cloning of a-and (-chain genes (reviewed in ref. 11) has provided necessary tools for studying the molecular basis for Ia function and expression. Thus, the detailed structure of several a and (8 chains from many haplotypes has been deduced from their respective genes, and the organization of the MHC class II gene family in mouse and man is almost entirely known. Expression ofthese ...