The Alu Family Has Many Widely Dispersed Members

KEY CONCEPT
- A major part of repetitive DNA in mammalian genomes consists of repeats of a single family organized like transposons and derived from RNA polymerase III transcripts.
 The most prominent SINE comprises a single family. Its short length and high degree of repetition make it comparable to simple sequence (satellite) DNA, except that the individual members of the family are dispersed around the genome instead of being confined to tandem clusters. Again, there is significant similarity between the members within a species compared with variation between species.
In the human genome, a large part of the moderately repetitive DNA exists as sequences of ~300 bp that are interspersed with nonrepetitive DNA. At least half of the renatured duplex material is cleaved by the restriction enzyme AluI at a single site located 170 bp along the sequence. The cleaved sequences all are members of a single family known as the Alu family, after the means of its identification. The human genome has about 1 million members (equivalent to 1 member per 3 kb of DNA). The individual Alu sequences are widely dispersed. A related sequence family is present in the mouse (where the approximately 350,000 members are called the B1 family), in the Chinese hamster (where it is called the Alu-equivalent family), and in other mammals.
The individual members of the Alu family are related rather than identical. The human family seems to have originated by means of a 130-bp tandem duplication, with an unrelated sequence of 31 bp inserted in the right half of the dimer. The two repeats are sometimes called the “left half” and the “right half” of the Alu sequence. The individual members of the Alu family have an average identity with the consensus sequence of 87%. The mouse B1 repeating unit is 130 bp long and corresponds to a monomer of the human unit. It has 70% to 80% homology with the human sequence.
The Alu sequence is related to 7SL RNA, a component of the signal-recognition particle involved in protein targeting to the endoplasmic reticulum, and Alu elements are likely derived from 7SL RNA transcripts. The 7SL RNA corresponds to the left half of an Alu sequence with an insertion in the middle. Thus, the ninety 5′ terminal bases of 7SL RNA are homologous to the left end of Alu, the central 160 bases of 7SL RNA have no homology to Alu, and the 3′ terminal bases of 7SL RNA are homologous to the right end of Alu. Like 7SL RNA genes, active Alu elements contain a functional internal RNA polymerase III promoter and are activel 
transcribed by this enzyme.
The members of the Alu family resemble transposons in being flanked by short direct repeats. They display, however, the curious feature that the lengths of the repeats are different for individual members of the family.
A variety of properties have been found for the Alu family, and its ubiquity has prompted many suggestions for its function. It is not yet possible, though, to discern its true role, if any (it may simply be a particularly successful selfish DNA). At least some members of the family can be transcribed into independent RNAs. In the Chinese hamster, some (though not all) members of the Aluequivalent family appear to be transcribed in vivo. Transcription
units of this sort are found in the vicinity of other transcription units. Members of the Alu family may be included within structural gene transcription units, as seen by their presence in long nuclear RNA.
The presence of multiple copies of the Alu sequence in a single nuclear molecule can generate secondary structure. In fact, the presence of Alu family members in the form of inverted repeats is responsible for most of the secondary structure found in mammalian nuclear RNA.