Allelic differences in bovine kappa-CN gene which may regulate gene expression

The most common kappa casein (kappa-CN) variants, kappa-CN A acid kappa-CN B, are synthesised differentially in the lactating mammary gland of heteroz ygous animals (kappa-CN AB). In this study we evaluated several approaches for quantification of allele specific mRNA transcripts. The most consistent results were obtained using allele specific RT-PCR and capillary electroph oresis. On average, 13.4% more allele B specific than A specific transcript s were found. DNA sequencing of the proximal promoter region in several hom ozygous animals (kappa-CN AA, BE, EE) did not reveal any allele specific po lymorphisms. Using the EMSA and DNase I footprinting we confirmed functiona l binding sites for three transcription factors (AP-2, NF1 and MGF) within the kappa-CN proximal promoter region. Sequence analysis of the 3'-UTR of t he kappa-CN gene revealed seven allele specific sites. Two of these allelic differences were close to previously identified 3'-end regulatory sequence s. In addition allele specific differences in length between mRNAs of both variants were found. The two later findings suggest a possible post transla tional control determining content differences of kappa-CN in milk.