The 5' flanking region of the brain Ca2+/ calmodulin-dependent protein kinase II a-subunit gene was identified and characterized. A total of 430 bases was sequenced upstream from the translation initiation codon, and the site of transcription initiation was located at -149 or -147 bases as determined by primer extension and S1 nuclease protection analysis, respectively. TATA and CAAT boxes were absent from their standard positions; however, the 5' flanking region was rich in G+C and contained a GGGCG and a TATATAA sequence 76 and 160 bases upstream from the transcription initiation site, respectively. Moreover, the sequence CAACGG was found 85 and 146 bases upstream from this site, indicating presumptive binding sites for the Myb protein. Gel-mobility shift assays revealed that a 120-base-pair fragment, which included the G+C-rich, TATA, and CAACGG sequences bound nuclear proteins specifically. DNA-protein complexes with similar gel mobilities were obtained with nuclear extracts from rat forebrain or cerebellum and from neonatal or adult brains. Extracts from rat liver, kidney, and spleen generated specific DNA-protein complexes with different electrophoretic mobilities, suggesting the occurrence of different nuclear proteins that bind to 5' regulatory elements of the Ca2+/calmodulin-dependent kinase II asubunit gene.Neuronal multifunctional Ca2+/calmodulin-dependent protein kinase II (CaM kinase II) represents a major Ca2+-operated molecular switch subject to regulation by Ca2+/ calmodulin and by autophosphorylation (1, 2). This abundant enzyme is located within different subcellular compartments including cytosol, cytoskeleton, nuclei, presynaptic terminals, and postsynaptic densities (3-13) and may regulate important neuronal functions such as neurotransmitter release and long-term potentiation (14-17).Soluble CaM kinase II was initially purified from brain as a 10-to 12-subunit oligomer with an apparent Mr of -600,000, composed primarily of two related a and P subunits. The a-to-,8 ratio varies from 3 or 4:1 in forebrain to 1:4 in cerebellum (3-5, 18). A third relatively minor subunit, p', has also been identified (3). a and 8 subunits are encoded by distinct genes (19-21), whereas ,3' is generated by alternative splicing of the 8-gene transcript (22).Enzyme levels and subunit composition were dependent on the stage of neuronal development; the levels increased dramatically between the second and fourth postnatal weeks in rat brain (23)(24)(25)(26)(27). The use of cDNA probes revealed that the a and 8 subunits of CaM kinase II are encoded by 5-to 5.4-kilobase (kb) and 3.9-to 4.8-kb mRNA species, respectively (19-21), and that the level of the 5-kb mRNA species increased 10-fold during the first 3 postnatal weeks in rat forebrain; a further 2.5-fold increase occurred by the end of 90 days (19).CaM Kinase II isoenzymes from skeletal muscle (28), liver (29, 30), lung (31), and heart (32) have also been isolated, and the wide distribution of CaM kinase II immunoreactive proteins was demonstrated (33, 34)...