Proteins containing the basic-helix-loop-helix (B-HLH) domain have been shown to be important in regulating cellular differentiation. We have isolated a cDNA for a human B-HLH factor, denoted HEB, that shares nearly complete identity in the B-HLH domain with the immunoglobulin enhancer binding proteins encoded by the E2A and ITF2 genes (E proteins). Functional characterization of the protein expressed from this cDNA indicates that HEB is a third member of the E-protein class of B-HLH factors. HEB mRNA was found to be expressed in several tissues and cell types, including skeletal muscle, thymus, and a B-cell line. HEB, ITF2, and the E12 product of the E2A gene all bound to a similar spectrum of E-box sequences as homo-oligomers. All three factors also formed hetero-oligomers with myogenin, and the DNA-binding specificity and binding off-rates (dissociation rates) were modulated after hetero-oligomerization. Both homoand hetero-oligomers of these proteins were able to distinguish between very closely related E-box sequences. In addition, HEB was shown to form hetero-oligomers with the E12 and ITF2 proteins. Finally, HEB was able to activate gene expression. These data demonstrate that HEB shares characteristics with other E proteins and show that HEB can interact with members of both the myogenic regulatory class and the E-protein class of B-HLH factors. HEB is therefore likely to play an important role in regulating lineage-specific gene expression.The regulation of cell type specification in mammals is accomplished in part by interactions between sequencespecific DNA-binding proteins. One class of proteins that has been implicated in controlling these decisions binds to specific DNA sequences via a basic (B) region that lies adjacent to amino acids that are predicted to form a helixloop-helix (HLH) structure. This class of B-HLH proteins includes the myogenic regulatory factors MyoD, myogenin, myf5, and MRF4/herculin/myf6 (3,4,13,14,26,30,32,41,43). These myogenic factors can form heterodimers with a second group of B-HLH proteins, recently termed the E proteins (23), which include the E2A gene products E12 and E47 and the ITF2 protein (7,23,25,28). The heterodimers formed by these factors play a central role in regulating muscle cell differentiation, apparently via their functions as transcription factors (5,8,18,23).The HLH domain has been shown to mediate dimerization. It is required for homo-oligomerization of the E proteins and for hetero-oligomerization of the E proteins with myogenic activation factors (6, 12, 40). The B region of each of these proteins is found immediately N terminal to the HLH domain and is responsible for DNA binding (6,12,40). The identified binding sites for B-HLH proteins share a consensus sequence, NNCANNTGNN, termed an E box. E-box sequences are found to bind to tissue-specific factors or to be important for the activity of enhancers and promoters of various tissue-specific genes, such as immunoglobulin genes (21, 24), muscle-specific genes (7,17,19,22,25,31,33,34,37,42), and pan...