Abstract
Alu elements belong to the primate-specific SINE family of retrotransposons and constitute almost 11% of the human genome. Alus are transcribed by RNA polymerase (Pol) III and are inserted back into the genome with the help of autonomous LINE retroelements. Since Alu elements are preferentially located near to or within gene-rich regions, they can affect gene expression by distinct mechanisms of action at both DNA and RNA levels. In this review we focus on recent advances of how Alu elements are pervasively involved in gene regulation. We discuss the impacts of Alu DNA sequences that are in close proximity to genes, Pol-III-transcribed free Alu RNAs, and Pol-II-transcribed Alu RNAs that are embedded within coding or noncoding RNA transcripts. The recent elucidation of Alu functions reveals previously underestimated roles of these selfish or junk DNA sequences in the human genome.
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