To examine the mechanisms involved in tissue-specific expression of the preproenkephalin (PPE) gene, we first studied the DNA methylation pattern of the rat PPE promoter in adult rat tissues. We found that two MspI sites (CCGG) in the 5'-flanking region of the PPE gene are partially methylated in all tissues examined, regardless of whether the PPE gene is expressed or not. In contrast, sites within a CG island surrounding the major transcription start sites were found to be completely unmethylated in all tissues. These data indicate that the lack of PPE gene expression in tissues such as the adult liver cannot be totally explained by complete methylation of CCGG sites in the PPE 5' promoter and do not support the hypothesis that differential methylation of sites in the PPE promoter dominates PPE gene expression in the adult rat. We also examined the chromatin structure of the PPE gene in different tissues using the DNase hypersensitivity assay. Two major DNase-hypersensitive sites were detected at -1800 and -200 bases upstream of exon 1. The -200 site was present in nuclei isolated from tissues which express the PPE gene (caudate-putamen, adrenal gland, and ventromedial hypothalamus) and absent from tissues which do not (liver and kidney), indicating a correlation between this hypersensitive site and PPE gene expression. We also detected minor hypersensitive sites in downstream regions (intron A and exon 2) and obtained evidence that sites within intron A are sexually dimorphic and influenced by estrogen treatment, suggesting that intron A of the PPE gene may be important for estrogen regulation of hypothalamic PPE gene expression.