Evolution of a Hypervariable Region of the Low Density Lipoprotein Receptor (LDLR) Gene in Humans and other Hominoids

Alu repeats in primates have been shown to evolve at a neutral mutation rate, as anticipated for non-coding autosomal loci. However, we have identified Alu elements within the 3' untranslated region (UTR) of the low density lipoprotein receptor (LDLR) gene that exhibited highly accelerated rates of evolution. In humans, a 100- and 25-fold increase in average divergence, for an upstream Alu (Alu U) and a downstream Alu (Alu D) respectively, was estimated based on sequence analysis among eight individuals of diverse ethnic backgrounds. None of these individuals demonstrated identical sequences within a 950 base region consisting of these two Alu elements. The hypervariability of this genetic region in the nuclear genome yields a potentially powerful tool for human population studies, forensics and paternity. Additionally, the mutation rate of Alu U among non-human hominoids was also accelerated, although to a lesser extent of roughly 3-fold that of other Alu elements. Sequence analysis of various Hominoidea species demonstrated its utility as a phylogenetic tool. The mechanism for the hypervariability in mutation rates is unclear, but may be accelerated as a result of Alu-mediated gene conversion in the human lineage.