Alu elements: an intrinsic source of human genome instability

Abstract

Alu elements are ∼300bp sequences that have amplified via an RNA intermediate leading to the accumulation of over 1 million copies in the human genome. Although a few of the copies are active, Alu germline activity is the highest of all human retrotransposons and does significantly contribute to genetic disease and population diversity. There are two basic mechanisms by which Alu elements contribute to disease: through insertional mutagenesis and as a large source of repetitive sequences that contribute to nonallelic homologous recombination (NAHR) that cause genetic deletions and duplications.

Figure 1. Alu retrotransposition cycle

Alu RNA is transcribed by RNA polymerase III in the nucleus and associates with several proteins to form an RNP (see Inset 1). Inset 1: The Alu RNA binds two of the signal recognition proteins, SRP9 and SRP14 (green circles), and the polyA binding protein (PABP, blue circles). Other proteins are thought to bind the complex, but are yet to be identified (pink circle marked with a “?”). Because the Alu RNA does not code for proteins, to undergo retrotransposition Alu highjacks L1 ORF2p. The L1 ORF2p is obtained from the active L1 elements in the genome. These L1 elements will generate an mRNA that will go to the cytoplasm for translation (see Inset 2). Inset 2: During translation of the L1 mRNA, it is thought that Alu RNPs associated with ribosomes will recruit the needed L1 protein(s), such as ORF2p. The role of SRP9 and SRP14 has been previously suggested to be the targeting of Alu to ribosomes. The proximity of the Alu RNP to the translating L1 RNA likely favors the recruitment of the L1 ORF2p needed for Alu retrotransposition. However, it is unknown if there is a direct association between the L1 ORF2p and the Alu RNP (indicated by the “?”) or how these components reach the nucleus for insertion. Once in the nucleus, the Alu RNA undergoes the insertion process (see Inset 3). Inset 3: The Alu retrotransposition insertion mechanism is based on a model developed for the R2Bm element. The model proposes a target primed reverse transcription (TPRT) where the 3′ A-rich region of the Alu RNA base pairs with a T-rich region of the cleaved genomic DNA to provide the priming site for reverse transcription by the L1 ORF2p. This eliminates the unique 3′ tail of the Alu RNA (yellow line portion) from the reverse transcription and only inserts the Alu portion. Alu insertions are usually stably maintained in the genome, as there is no known specific mechanism for their removal. Due to the random nature of Alu insertion many inserts are found within genes and both mature and primary mRNA can contain multiple Alu sequences (see Inset 4). Inset 4: Many primary mRNA of genes contain Alu sequences (shown as red arrows) and a significant portion of mRNAs contain one or more Alu elements (located in either orientation) in their 3′ UTR. These Alus located within genes have been implicated in a number of regulatory mechanisms for gene expression.