Alu repeats and human genomic diversity

Abstract

During the past 65 million years, Alu elements have propagated to more than one million copies in primate genomes, which has resulted in the generation of a series of Alu subfamilies of different ages. Alu elements affect the genome in several ways, causing insertion mutations, recombination between elements, gene conversion and alterations in gene expression. Alu-insertion polymorphisms are a boon for the study of human population genetics and primate comparative genomics because they are neutral genetic markers of identical descent with known ancestral states.

Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus males

“…Our survey spanned 13 separate regions from the nonrecombining portion of the Y chromosome. We chose these regions on the basis of three criteria: (i) they fall within introns of single-copy genes 24 ; (ii) they contain at least one element from the Y family (including subfamilies) of Alu retrotransposons 12 ; and (iii) Alu insertions were fixed in our sample. We determined the family affiliation of Alu elements using RepeatMasker.…”

“…We assayed Y-chromosome variation using DNA sequences that encompass recently inserted Alu retrotransposons (e.g., the Y family of Alu elements and its subfamilies 12 ; Table 1), because these elements may have a higher mutation rate than other noncoding DNA as a result of their high density of CpG dinucleotides 13 . Focusing on these regions, we uncovered a much higher density of SNPs than reported in previous surveys.…”

Identification of repeat structure in large genomes using repeat probability clouds

“…Eukaryotic genomes contain many repetitive sequence, and understanding genome structure depends crucially on their identification [1][2][3]. The predominant repeat annotation approach, implemented in RepeatMasker [4], focuses on the identification of repeat element sequences based on their alignment with consensus sequences, and relies on a curated library of known repeat families provided by Repbase [5].…”

Useful ‘junk’: Alu RNAs in the human transcriptome

“…Very few Alu elements are able to retrotranspose; they emerged from a limited number of loci that are considered as master genes of Alu amplification. These master genes were active at different time periods during primate evolution, and Alu elements can therefore be classified into subfamilies of different ages, based on their primary sequence similarities (for a review see [5]). …”