Useful ‘junk’: Alu RNAs in the human transcriptome

Abstract.

Alu elements are the most abundant repetitive elements in the human genome; they have amplified by retrotransposition to reach the present number of more than one million copies. Alu elements can be transcribed in two different ways, by two independent polymerases. ‘Free Alu RNAs’ are transcribed by Pol III from their own promoter, while ‘embedded Alu RNAs’ are transcribed by Pol II as part of protein- and non-protein-coding RNAs. Recent studies have demonstrated that both free and embedded Alu RNAs play a major role in post transcriptional regulation of gene expression, for example by affecting protein translation, alternative splicing and mRNA stability. These discoveries illustrate how a part of the ‘junk DNA’ content of the human genome has been recruited to important functions in regulation of gene expression.