The slow/cardiac troponin C (cTnC) gene is expressed in three distinct striated muscle lineages: cardiac myocytes, embryonic fast skeletal myotubes, and adult slow skeletal myocytes. We have reported previously that cTnC gene expression in cardiac muscle is regulated by a cardiac-specific promoter/enhancer located in the 5' flanking region of the gene (bp -124 to +1). In this report, we demonstrate that the cTnC gene contains a second distinct and independent transcriptional enhancer which is located in the first intron. This second enhancer is skeletal myotube specific and is developmentally up-regulated during the differentiation of myoblasts to myotubes. This enhancer contains three functionally important nuclear protein binding sites: a CACCC box, a MEF-2 binding site, and a previously undescribed nuclear protein binding site, designated MEF-3, which is also present in a large number of skeletal muscle-specific transcriptional enhancers. Unlike most skeletal muscle-specific transcriptional regulatory elements, the cTnC enhancer does not contain a consensus binding site (CANNTG) The expression of many muscle-specific proteins is developmentally regulated at the level of transcription (7,34,39,66,85). Thus, one approach to understanding the molecular basis of mammalian myogenesis is to elucidate the transcriptional mechanisms that regulate the expression of muscle-specific genes. The identification and characterization of the basic helix-loop-helix (bHLH) family of muscle-determining transcription factors, including MyoD, myogenin, myf-5, and MRF4/herculin/myf-6, has added significantly to our understanding of skeletal myogenesis (1,3,10,17,49,61,80). Expression of each of these transcription factors appears to be sufficient to activate the skeletal muscle phenotype in many types of cultured cells (77), and hexanucleotide binding sites for these factors (CANNTG), termed E boxes, have been identified in most but not all skeletal muscle-specific transcriptional regulatory elements studied to date (reviewed in reference 71). bHLH proteins each contain a basic domain which is required for DNA binding and an HLH region which is involved in the formation of homo-and heterodimers (6,9,74). The basic domain of each myogenic bHLH family member contains conserved alanine and threonine residues that distinguish them from the nonmyogenic bHLH transcription factors (5, 9).