An upstream polymorphism associated with lactase persistence has increased enhancer activity

Intestinal lactase activity declines during childhood in some humans. This phenotypic polymorphism of lactase persistence or nonpersistence into adult life has been shown in a recent study to be 100% associated with a T/C nucleotide polymorphism at position -13910 and approximately 97% with an A/G nucleotide polymorphism at position -22018. The aim of this study was to investigate the role of these nucleotide polymorphisms for lactase-phlorizin hydrolase (LPH) gene expression.

The -13910 and -22018 regions were cloned from lactase-persistent and -nonpersistent individuals, and the regions were analyzed for gene regulatory activity of a luciferase reporter gene by transfection experiments using the intestinal cell line Caco-2. Electrophoretic mobility shift assays (EMSAs) were used to investigate protein/DNA interactions with the -13910 sequence.

We show that the -13910 region contains a strong enhancer. The -13910 regions from both lactase persistent (-13910T variant) and lactase nonpersistent (-13910C variant) have enhancer activity. However, the -13910T variant enhances the LPH promoter approximately 4 times more than the -13910C variant when analyzed in differentiated Caco-2 cells. A nuclear factor from both an intestinal and a nonintestinal extract binds strongly to the -13910T variant whereas the binding to the -13910C variant is much weaker.

The discovery of a functional difference between the 2 alleles at position -13910 supports the notion that the molecular difference between lactase persistence and nonpersistence is caused by the mutation at position -13910.