Functions and Utility of Alu Jumping Genes

Alu elements are a type of "jumping gene," or transposable element (TE), that exists only in primates. Like all TEs, they are discrete DNA sequences that move, or "jump," from one place on the genome to another, sometimes inserting copies of themselves directly into the middle of protein-coding genes. Although Alu elements have long been considered "junk" DNA, scientists are beginning to question whether these elements might serve important biological functions after all. While much remains to be discovered about the role of these prolific transposons, researchers now recognize that Alu elements are major players in human evolution, as well as useful tools for molecular genetic and forensic applications.

Alu elements are highly repetitive DNA sequences that can be classified as SINEs (short interspersed elements), which are themselves a type of "nonautonomous" retrotransposon. (Retrotransposons are TEs that move about the genome via an RNA intermediary.) An Alu element is transcribed into messenger RNA by RNA polymerase and then converted into a double-stranded DNA molecule by reverse transcriptase. The new double-stranded DNA molecule is then inserted into a new location in the genome. Because they are nonautonomous, like all SINEs, Alu elements don't have the genetic capacity to produce DNA copies of themselves or to integrate into new chromosomal locations. For those activities, they rely on another type of transposon, called L1. Most Alu elements are approximately 300 base pairs long, with considerable sequence variation.

Alu elements frequently duplicate when they jump, and scientists estimate that the human genome acquires one new Alu insert in approximately every 200 births. In other words, the number of Alu elements in the human population (and in other primate populations) tends to increase over time. Alu TEs are believed to have emerged in primates around 65 million years ago. Today, they are the most abundant type of human TE, making up an amazing 10% of the (diploid) human genome. Thus, in a mere 65 million years, these transposons have gone from zero to about 1 million copies per cell! Indeed, part of what makes Alu elements so important is that they are found in nearly every human (and other primate) gene. These elements are spread throughout the genome and occur at varying densities in different loci.

The fact that other nonprimate mammals function quite well without Alu elements confirms that these elements are not required for the basic function of cellular processes. Yet, because primate genomes have so many Alu elements, many biologists speculate that these TEs may have played an important role in our species' evolution, and that nature may have taken advantage of these elements in some way, such as by putting them to work in generating new proteins. This conflicts with the long-held belief that all transposable elements are just "junk," existing for no purpose other than self-replication.

Although they have yet to gather much data to support their arguments, scientists have hypothesized various roles for Alu elements, such as stimulation of protein translation, particularly under stressful cellular circumstances; this hypothesis is rooted in the fact that many Alu RNAs are expressed during times of stress. However, the hypothesis attracting the most attention of late is the one stating that Alu elements may have served an important evolutionary role by contributing to the formation of new genes or gene combinations, or perhaps by adding new functionality to already-existing genes through a process known as exonization (Sela et al., 2007). Exonization is the creation of a new exon from an Alu-containing (or any TE-containing) intron. (i.e., they are "spliced" out). The process of exonization is illustrated in Figure 1. First, the Alu TE is inserted into an intron of a gene. Initially, the Alu is spliced out of the mRNA as part of the intron. Over time (as many as several million years), however, mutations accumulate, leading to the formation of active splice sites on either end of the Alu element, and the Alu TE is thus eventually recognized as an exon, at least in some molecules of mRNA.

Scientists have reported thousands of Alu exonization events among primates. In humans, for example, Alu TEs are responsible for an estimated 62% of all new exons (Zhang & Chasin, 2006). This raises an important question: How could the insertion of so many new exons into vital genes not be detrimental? As Rotem Sorek of the Lawrence Berkeley National Laboratory in California, explains, "The answer lies in alternative splicing" (Sorek, 2007). With alternative splicing, some initial RNA transcripts that contain a new exon arising from Alu are spliced to include the new exon in the final mRNA, while other identical transcripts are spliced differently, thereby removing the Alu exon. As a result, some transcripts lack the new exon and produce the same "old" protein, while others produce entirely new proteins or protein variants. Some of these new proteins might be deleterious; others might be selectively neutral (neither harmful nor beneficial to the organism or cell); and some could very well be beneficial, thereby giving an organism (or a cell or gene) a selective edge while not eliminating the "old" protein altogether.

Scientists are only beginning to explore this possibility, and a few observations do seem to support the idea. For instance, not only do newly born exons undergo alternative splicing more frequently than old exons, but, according to Sorek (2007), almost all exonized Alu elements in the human genome are alternatively spliced. Therefore, even though the original transcript with the newly exonized Alu element is intact and could encode potentially deleterious RNA and protein products, alternative splicing leads to the production of multiple transcripts, multiple mRNAs, and, ultimately, multiple proteins. In fact, some scientists speculate that Alu elements have played a key role in the evolution of the primate brain, and that all of the protein possibilities afforded by Alu movement and exonization have contributed to the complexity of human neuronal circuitry and "higher-order" cognition (e.g., rational thought) (Mattick & Mehler, 2008).

On the other hand, scientists have associated some individual Alu insertions with human disease. The simple insertion of an Alu TE in the wrong place can often wreak molecular havoc. For example, in 1991, researchers discovered a case of neurofibromatosis caused by an Alu sequence inserted in an intron of the NF1 gene (Wallace et al., 1991). The presence of the Alu sequence caused a splicing error, which in turn caused one of the exons to be left out of the transcribed mRNA, thereby leading to a shift in the reading frame and production of an abnormal protein. Since then, researchers have reported a growing number of Alu-disease associations in disorders ranging from hemophilia to breast cancer. According to one estimate, about 0.4% of all human genetic disorders are caused by or associated with Alu TEs. In many cases, it is not clear whether the association is causal (i.e., whether the Alu insertion actually causes the disease), but the lack of any other noticeable mutation often leads researchers to suspect that it is.

Regardless of what they do to the genome (and the cell and organism) when they jump, Alu TEs have, at the very least, served science well. Today, molecular biologists use Alu TEs as research tools, evolutionary biologists use them to resolve questions about primate systematics and human history, and forensic investigators use then to home in on possible perpetrators of unsolved crimes.

Although biologists have been using Alu elements as a research tool for more than a quarter of a century, they are just beginning to collect and interpret data on the potential regulatory and developmental roles of Alu SINEs in humans and other primates. Originally considered "junk" genes, Alu TEs are now believed to be evolutionary contributors. Scientists speculate that the generation of new protein types, stimulation of protein translation, and creation of new gene combinations may all be affected by the presence of Alu elements. Additionally, because they are restricted to primates, Alu elements provide scientists with an interesting test case for general TE functioning and may lead to a better understanding of both the beneficial and deleterious effects of gene jumping within the genomes of numerous species.