Computer-aided analysis of potential transcription-factor binding sites in the rabbit β-casein gene promoter

Computer analysis of putative cis- and trans-regulatory sequences in the promoter region of the rabbit β-casein gene is described. Nucleotide sequences up to 2096 bp upstream of the initiation site were compared to known consensus sequences of both ubiquitous and specific transcription factor motifs as well as to those described as characteristic for milk protein genes. Our analysis demonstrated that 5 independent motifs described for milk protein gene promoters exist. Four of them — ‘Groenen structure’, ‘Yu-Lee’ 1 and 6 sequence and ‘Oka box A’ — were found in the β-casein gene promoter; surprisingly, no typical milk box was found. More than one hundred and fifty putative binding motifs were found, representing 56 various consensus sequences. These sequences are located both inside and outside structures typical of milk protein gene promoters and include sequences homologous to mammary gland specific, hormone specific and ubiquitous transcription factors. Our analysis suggests that milk protein gene promoters can bind many transcription factors and assure complex regulation by hormonal and tissue specific factors.