Previous studies have demonstrated that a 3.0-kilobase, rat whey acidic protein (WAP) transgene containing 949 base pairs (bp) 5'- and 70 bp 3'-flanking DNA is expressed specifically in the mammary gland of transgenic mice in a copy number-dependent, position-independent manner (1). In order to localize the critical regulatory elements important for tissue-specific, high level WAP gene expression, DNase I hypersensitivity mapping studies of WAP transgenes were performed in nuclei isolated from mammary gland and liver. Two regions of DNase I hypersensitivity located at approximately -150 and -800 by from the site of transcription initiation, respectively, were detected only in nuclei isolated from the lactating mammary gland. Within the distal hypersensitive region several binding sites for members of the CTF/NFI family of transcription factors were identified using in vitro DNase I and dimethyl sulfate interference footprinting and electrophoretic mobility shift assays. Genomic footprinting established that such protein-DNA interactions occur preferentially in the lactating mammary gland. The analysis of several 5' deletion constructs identified the region between -853 and -729 bp as essential for WAP transgene expression. These results suggest that the distal DNase I hypersensitive region contains binding sites for CTF/NFI and plays a critical role in the regulation of WAP gene expression in transgenic mice.