We demonstrated that MIF-1, identified initially as a binding activity that associated with the intron I element of the c-myc gene, consists of two polypeptides, the myc intron-binding peptide (MIBP1) and the major histocompatibility class II promoter-binding protein, RFX1. Using a polyclonal antiserum directed against either oligonucleotide affinity-purified MIBP1 or a peptide derived from RFX1, we showed that MIBP1 and RFX1 are distinct molecules that associate in vivo and are both present in DNA-protein complexes at the c-myc (MIF-1) and major histocompatibility complex class II (RFX1) binding sites. We have also found that MIBP1 and RFX1 bind to a regulatory site (termed EP) required for enhancer activity of hepatitis B virus. In addition, we have identified MIF-1-like sequences within regulatory regions of several other viral genes and have shown that MIBP1 binds to these sites in cytomegalovirus, Epstein-Barr virus, and polyomavirus. We have also demonstrated that the MIF-1 and EP elements can function as silencers in the hepatocarcinoma HepG2 and the cervical carcinoma HeLa cell lines. These findings indicate that MIBP1 and EP/RFX1 can associate in vivo and may regulate the expression of several distinct cellular and viral genes.The product of the c-myc oncogene has been implicated in diverse cellular processes, including cell proliferation, differentiation, and tumorigenesis. The observation that c-Myc can heterodimerize with other cellular proteins to transactivate gene expression in vitro has suggested that c-Myc may function to modulate genes involved in cell growth and differentiation pathways (3,4,14). The regulation of the c-myc gene involves a complex interplay of cis-and trans-acting elements, and several nuclear proteins that interact with regulatory sequences found in the 5Ј upstream and exon I untranslated regions of the c-myc gene have been identified (16,31). In addition, a 20-bp region of intron I was defined as a binding site for a phosphoprotein, initially designated MIF-1, and it was demonstrated that binding to this site was abolished by a point mutation present in the corresponding region of a translocated Burkitt's lymphoma c-myc gene (34,35). Adjacent binding sites in c-myc intron I were also identified and designated MIF-2 and MIF-3 (33), and somatic mutations found in Burkitt's lymphoma samples were shown to be frequently clustered within discrete domains that define these recognition sequences (33). These findings suggested that the mutations clustering in this region of the c-myc gene in Burkitt's lymphoma may be targeting specific regulatory elements for c-myc regulation, although direct evidence for this is lacking.It was recently demonstrated that the RFX1 protein, which binds to the X box of the major histocompatibility complex (MHC) class II genes, the methylated DNA-binding protein (MDBP), and the EP protein, which binds to the enhancer of hepatitis B virus (HBV), all represent the same DNA binding activity (29,36). The X-box sequence has been shown to play a role in regula...