Common polymorphism in a highly variable region upstream of the human lactase gene affects DNA-protein interactions

In most mammals lactase activity declines after weaning when lactose is no longer part of the diet, but in many humans lactase activity persists into adult life. The difference responsible for this phenotypic polymorphism has been shown to be cis-acting to the lactase gene. The causal sequence diffe rence has not been found so far, but a number of polymorphic sites have bee n found within and near to the lactase gene. We have shown previously that in Europeans there are two polymorphic sites in a small region between 974 bp and 852 bp upstream from the start of transcription, which are detectabl e by denaturing gradient gel electrophoresis (DGGE). In this study, analysi s of individuals from five other population groups by the same DGGE method reveals four new alleles resulting from three additional nucleotide changes within this very small region. Analysis of sequence in four primate specie s and comparison with the published pig sequence shows that the overall seq uence of this highly variable human region is conserved in pigs as well as primates, and that it lies within a 1kb region which has been shown to cont rol lactase downregulation in pigs. Electrophoretic mobility shift assay (E MSA) studies were carried out to determine whether common variation affecte d protein-DNA binding and several binding activities were found using this technique. A novel two base-pair deletion that is common in most population s tested, but is not present in Europeans, caused mo change in binding acti vity. However, a previously published C to T transition at -958 bp dramatic ally reduced binding activity, although the functional significance of this is not clear.