24. Other mobile DNA in mammalian genomes

Alu elements

In primate genomes, a major SINE, the Alu element, maintains a prominent position. In the human genome, there are some 1.1 million Alus, accounting for about 11% of the genome mass. Alu elements evolved from 7SL RNA of the signal recognition particle. Alus are dimers of roughly 140 non-identical nucleotide monomers that are separated by an A-rich region. The left monomer contains an internal RNA polymerase III promoter composed of short A and B boxes. At the 3' end is a poly A tail, similar to that seen in the L1 and SVA elements. Alus acquired their name because these elements contain an Alu restriction endonuclease site.

Alus started to amplify in genomes about 65 million years ago and reached a peak of amplification about 40 million years ago. Because of their fairly recent amplification, Alus are not present in non-primate mammalian genomes, although there is an element with sequence similarity to Alu, B1, in the mouse genome. Alu elements have been classified into subfamilies based on their sequence variation that can also be used to age them in genomes. The great majority of Alus, the J and S subfamilies, are generally very old and inactive, while about 200,000 of the 1.1 million Alus in the human genome belong to the Y subfamily and its younger subtypes. The most active Alu subtype is AluYa5, which, although present in only about 3,000 copies per geno....Deininger and Batzer, 1999in trans