Neuronal nitric-oxide synthase (nNOS) is subject to alternative splicing. In mice with targeted deletions of exon 2 (nNOS ⌬͞⌬ ), two alternatively spliced forms, nNOS and ␥, which lack exon 2, have been described. We have compared localizations of native nNOS␣ and nNOS and ␥ by in situ hybridization and immunohistochemistry in wild-type and nNOS ⌬͞⌬ mice. To assess nNOS catalytic activity in intact animals we localized citrulline, which is formed stoichiometrically with NO, by immunohistochemistry. nNOS is prominent in several brain regions of wild-type animals and shows 2-to 3-fold up-regulation in the cortex and striatum of nNOS ⌬͞⌬ animals. The persistence of much nNOS mRNA and protein, and distinct citrulline immunoreactivity (cit-IR) in the ventral cochlear nuclei and some cit-IR in the striatum and lateral tegmental nuclei, indicate that nNOS is a major functional form of the enzyme in these regions. Thus, nNOS, and possibly other uncharacterized splice forms, appear to be important physiological sources of NO in discrete brain regions and may account for the relatively modest level of impairment in nNOS ⌬͞⌬ animals.Nitric oxide (NO), formed by neuronal nitric-oxide synthase (nNOS) (1), has major signaling functions in the central and peripheral nervous system (2, 3). Alternative splicing of the nNOS gene is prominent with more than 10 differently spliced nNOS transcripts reported (4-10). The principal, exon 2-containing, form of nNOS (nNOS␣) accounts for the great majority of catalytic activity in the brain, as mice with targeted deletions of exon 2 (nNOS ⌬͞⌬ ) display an Ϸ95% reduction in NOS catalytic activity (11). Though NO has been implicated in development (12) and synaptic plasticity (13), these mice appear grossly normal, lack obvious histopathological abnormalities in the central nervous system, and reproduce effectively (11), suggesting that the residual NOS activity might protect the nNOS ⌬͞⌬ mutant mice from serious pathology. Two alternatively spliced forms of nNOS,  and ␥, that lack exon 2 and thus persist in the nNOS ⌬͞⌬ mice, have a regional distribution that parallels the pattern of the residual activity (4).The human nNOS gene contains 29 exons of which all but exon 1 are translated to generate nNOS␣, a 150-kDa protein (1, 8). nNOS and ␥, as described in mice, are generated by alternative splicing that skips exon 2 and employs different first exons, 1a and 1b, respectively (4) (Fig. 1). Translation of nNOS is initiated at a CTG-initiation codon within exon 1a generating a 136-kDa NOS protein with six unique N-terminal amino acids. Translation of nNOS␥ is initiated at an ATGinitiation codon within exon 5 generating a truncated, 125-kDa form of nNOS␣. Both nNOS and nNOS␥ lack the PSD-95͞ discs large͞ZO-1 homology domain (PDZ) domain that is localized within exon 2. This domain, also referred to as DHR or GLGF, mediates association of nNOS␣ with postsynaptic density protein 95 ref. 4). PSD-95 appears to anchor nNOS␣ to neuronal membranes in the vicinity of the Nmethyl-D-as...