Alu repeats and human genomic diversity

Abstract

Alu elements are a class of short interspersed elements (SINEs) that have expanded to a copy number of more than one million elements in primate genomes. The expansion of Alu elements is characterized by the dispersal, in a series of subfamilies, of elements of different evolutionary age that share common nucleotide substitutions. Alu elements have an impact on the genome in several ways, including insertion mutations, recombination between elements, gene conversion and gene expression. The human diseases caused by Alu insertions include neurofibromatosis, haemophilia, familial hypercholesterolaemia, breast cancer, insulin-resistant diabetes type II and Ewing sarcoma. Alu elements alter the distribution of methylation and, possibly, transcription of genes throughout the genome. The transcription of Alu elements changes in response to cellular stress and might be involved in maintaining or regulating the cellular stress response. Alu elements are a primary source for the origin of simple sequence repeats in primate genomes. Alu-insertion polymorphisms are a boon for the study of human population genetics and primate comparative genomics because they are neutral, identical-by-descent genetic markers with known ancestral states.