The functional organization of the rat brain creatine kinase (ckb) Initiation of transcription by RNA polymerase II is a major point at which regulation of gene expression occurs (15). The unique pattern of transcription characteristic of each gene is largely due to the interactions among all the various regulatory factors that bind the gene in its promoter and enhancer regions and to the further interaction of these factors with the transcriptional machinery. The transcriptional machinery is thus able to detect and integrate the regulatory information imposed on the gene.We have been studying transcriptional regulation of the creatine kinase genes. Creatine kinase (adenosine 5'-triphosphate-creatine phosphotransferase; EC 2.7.3.2) is an enzyme that catalyzes the reversible transfer of a phosphoryl group between ATP and creatine (for reviews, see references 35 and 59). Two cytosolic isoforms of creatine kinase, the brain (B) isoform and the muscle (M) isoform, which randomly associate to form three isozymes, MM, MB, and BB, have been described. Separate genes for the two cytosolic isoforms have been cloned from several species and appear to be the products of single-copy, unlinked genes (3,32,39,45,58). There is also a mitochondrial isoform that self-associates into octameric structures (47). A human mitochondrial gene has been isolated and characterized (25).The variety of modes of expression for the ck genes that must exist to accommodate the widely varying energy needs of cells make this gene family an interesting system in which to examine the molecular mechanisms involved in differential gene expression. The two cytosolic isoforms of creatine kinase, the muscle isoform and the brain isoform, have different tissue-specific patterns of expression (56). The muscle isoform is expressed predominantly in skeletal and cardiac muscle. The brain isoform, while being expressed at highest levels in brain, has a much broader range of expression than the muscle isoform has. Regulatory phenomena associated with brain isoform expression include up-regulation during differentiation of monocytes into macrophages * Corresponding author.(37), induction by peptide and steroid hormones (22 and references therein), high levels of expression in transformed cells (20), and stimulation by viral infection (11). Differential expression of the ckb gene in liver and brain (42) and up-regulation of the ckm gene during skeletal muscle differentiation (E. Arpaia and T. Smith, unpublished results; 32) have been shown to be regulated at least in part at the level of transcription.We previously reported evidence that a nonconsensus TTAA sequence at -28 bp appears to provide the principal TATA box function for the ckb promoter in vivo, even though there is a consensus TATAAATA sequence at -66 bp relative to the transcription start site (28). Under certain conditions in vitro, however, the upstream consensus TATA AATA sequence can function as a TATA box to mediate transcription from an upstream start site (28,42). In addition, we previously ...