The regulation of MHC class II gene expression controls T-cell activation and, hence, the immune response. Among the nuclear factors observed to bind to conserved DNA sequences in human leukocyte antigen (HLA) class II gene promoters, RFX is of special interest: Its binding is defective in congenital HLA class II deficiency, a disease of class II gene regulation. The cloning of an RFX cDNA has allowed us to show by transfection of a plasmid directing the synthesis of antisense RFX RNA that RFX is a class II gene regulatory factor. RFX is a novel 979-amino-acid DNA-binding protein that contains three structurally and functionally separate domains. The 91-amino-acid DNA-binding domain is distinct from other known DNA-binding motifs but may be distantly related to the helix-loop-helix motif. The most striking property of RFX is that it can bind stably to the class II X box as either a monomer or a homodimer and that the domain responsible for dimerization is distant from and functionally independent of the DNA-binding domain. This distinguishes RFX from other known dimeric DNA-binding proteins. It also implies that an RFX homodimer has two potential DNA-binding sites. We therefore speculate that RFX could form a DNA loop by cross-linking the two X-box sequences found far apart upstream of MHC class II genes.

RFX1 is a transactivator of human hepatitis B virus enhancer I. We show here that RFX1 belongs to a previously unidentified family of DNA-binding proteins ofwhich we have cloned three members, RFX1, RFX2, and RFX3, from humans and mice. Members of the RFX family constitute the nuclear complexes that have been referred to previously as enhancer factor C, EP, methylation-dependent DNA-binding protein, or rpL30a. RFX proteins share five strongly conserved regions which include the two domains required for DNA binding and dimerization. RFX1 is a transcription factor that was initially cloned by virtue of its affinity for the X-box motif (31, 32), a conserved cis-acting regulatory element present in the promoters of all major histocompatibility complex (MHC) class II genes from all species examined (for reviews, see references 3, 13, and 41). RFX1 was subsequently also found to bind with high affinity to inverted repeats known as enhanced factor C (EF-C) sites (also called EP or methylation-dependent DNAbinding protein [MDBP] sites), which are cis-acting regulatory elements present in the enhancers of several unrelated viruses, including hepatitis B virus (HBV), polyomavirus, and cytomegalovirus (CMV) (7,10,15,28,29,42,(50)(51)(52). Among these EF-C sites, the functional importance of the site in the HBV enhancer (EnhI) has been most clearly demonstrated (7,11,15,29,37,42 . Second, there is a C-terminal dimerization domain which does not display obvious sequence similarity to known dimerization motifs (32). Moreover, in contrast to the majority of dimeric DNAbinding proteins, the DNA-binding and dimerization domains of RFX1 are not closely linked in the protein and are functionally independent, such that RFX1 can bind in vitro as either a monomer or a dimer (32, 37). Finally, identity between RFX1 and EF-C (EP or MDBP) (37) has allowed us to document a unique feature not previously described for other cloned eukaryotic transcription factors. Namely, in addition to its classical site-specific DNA-binding activity, RFX1 (MDBP or EF-C) also shows a peculiar site-specific affinity for certain methylated sequences (10,22,37,45,50,52). These methylation-dependent RFX1 (MDBP or EF-C) binding sites are recognized specifically only when they contain 5-methylcytosine at CpG dinucleotides.Depending on the cell line examined, EF-C (EP or MDBP) sites are bound by one to three different nuclear complexes having identical target site specificity (10,29,37,50), and only one of these complexes represents an RFX1 homodimer (37). The rpL30(x and MHC class II X-box sites are also bound by several closely related complexes (17,24,35). This suggested the existence of a family of RFX proteins. Considering the novel features of RFX1, its crucial role in activating the enhancer of HBV, and its suspected role for transcription of the MHC class II and rpL30 genes, it was of interest to identify these additional RFX factors. We have now cloned and characterized two other highly conserved RFX genes, RFX2 and RFX3, from both humans and mice, the...

The regulation of major histocompatibility complex class II gene expression is directly involved in the control of normal and abnormal immune responses. In humans, HLA-DR, -DQ, and -DP class II heterodimers are encoded by a family of a-and fl-chain genes clustered in the major histocompatibility complex. Their expression is developmentally controlled and normally restricted to certain cell types. This control is mediated by cis-acting sequences in class II promoters and by trans-acting regulatory factors. Several nuclear proteins bind to class II promoter sequences. In a form of hereditary immunodeficiency characterized by a defect in a trans-acting regulatory factor controlling class II gene transcription, we have observed that one of these nuclear factors (RF-X) does not bind to its target sequence (the class H X box). A cDNA encoding RF-X was isolated by screening a phage expression library with an X-box binding-site probe. The recombinant protein has the binding specificity of RF-X, including a characteristic gradient of affinity for the X boxes of HLA-DR, -DP, and -DQ promoters. RF-X mRNA is present in the regulatory mutants, indicating a defect in the synthesis of a functional form of the RF-X protein.Class II major histocompatibility complex antigens are heterodimeric transmembrane glycoproteins. Their expression at the surface of antigen-presenting cells is essential for the recognition of foreign antigen by the T-cell receptor (1, 2). T-cell activation and antigen presentation depend not only on the structural specificity of the highly polymorphic class II molecules (1, 2), but also on the level of expression of class II antigens on individual cells (3). Regulation of expression of class II genes is therefore an important aspect of the control of the immune response.In humans, the genes encoding the a and f3 chains of the HLA-DP, HLA-DQ, and HLA-DR class II molecules are clustered in the D region of the major histocompatibility complex on chromosome 6 (4). These genes are subjected to tight and complex regulatory controls (4-7). Their expression is generally coordinated and restricted primarily to cells of the immune system such as B lymphocytes, activated T lymphocytes, macrophages, and dendritic cells. Within the B-cell lineage, class II expression is developmentally controlled. Finally, in certain class TI-negative cells, expression can be induced by stimulation with lymphokines such as interferon y or interleukin 4. Expression appears to be controlled primarily at the level of transcription.Progress has recently been made in the identification of cis-acting sequences in class II promoters (8-11) and of nuclear factors interacting with these sequences (8,(11)(12)(13)(14). We have identified five nuclear factors that bind to the promoter of the HLA-DR a-chain gene (ref. 14; M.K., W.R., C.H.S., and B.M., unpublished results). One ofthese factors, RF-X, binds to a sequence called the X box, which is present in all human and mouse class II promoters (15, 16). Interestingly, we have shown that RF-...

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