Under the genomic radar: the stealth model of Alu amplification

Abstract

Alu elements are the most successful SINEs (Short INterspersed Elements) in primate genomes and have reached more than 1,000,000 copies in the human genome. The amplification of most Alu elements is thought to occur through a limited number of hyperactive "master" genes that produce a high number of copies during long evolutionary periods of time. However, the existence of long-lived, low-activity Alu lineages in the human genome suggests a more complex propagation mechanism. Using both computational and wet-bench approaches, we reconstructed the evolutionary history of the AluYb lineage, one of the most active Alu lineages in the human genome. We show that the major AluYb lineage expansion in humans is a species-specific event, as nonhuman primates possess only a handful of AluYb elements. However, the oldest existing AluYb element resided in an orthologous position in all hominoid primate genomes examined, demonstrating that the AluYb lineage originated 18-25 million years ago. Thus, the history of the AluYb lineage is characterized by approximately 20 million years of retrotranspositional quiescence preceding a major expansion in the human genome within the past few million years. We suggest that the evolutionary success of the Alu family may be driven at least in part by "stealth-driver" elements that maintain low retrotranspositional activity over extended periods of time and occasionally produce short-lived hyperactive copies responsible for the formation and remarkable expansion of Alu elements within the genome.

Figure 1.

Polymorphic AluYb8 elements in the common chimpanzee genome. Gel chromatographs of two loci are shown. The locus name is shown at right. The product sizes for filled and empty alleles (pre-integration size) are indicated at left. The DNA panel is composed of 12 unrelated common chimpanzee individuals and other primate species. The template used in each reaction is listed at top.

Figure 2.

Lineage-specific AluYb8 insertions. Four examples of gel chromatographs are shown. The locus designation is shown at right, while the product sizes for filled and empty alleles (pre-integration size) are indicated at left. The DNA template used in each reaction is listed at top. (A) Pygmy chimpanzee-specific AluYb8 insertion. (B) Common chimpanzee-specific AluYb8 insertion. (C) Chimpanzee lineage-specific AluYb8 insertion. (D) Gorilla-specific AluYb8 insertion.

Figure 3.

Sequence analysis of the Pan1 locus. (A) The gel chromatographs of PCR amplification results are shown. The template used in each lane is listed at the top of the gel. The product sizes for filled and empty sites (pre-integration size) are indicated at left. (B) Schematic diagrams for the possible evolutionary scenarios. Light-blue triangles denote the amplicons with an AluYb8 insertion; orange crosses denote the pre-integration products, and the yellow star denotes the recombination product in the common chimpanzee genome. Flanking sequences are shown as green boxes; target site direct repeats are shown in red and pink boxes. Alu elements are shown as arrows and the direction of arrow indicates the orientation (5′→3′), with the head of the arrow denoting the end of the Alu elements.

Figure 4.

Gene conversion of AluYb elements. Gel chromatographs of PCR products derived from a phylogenetic analysis of the Pan2 locus (A) and Pan3 locus (B) are shown at left. The DNA template used in each lane is shown at top. The product sizes for filled and empty alleles (pre-integration size) are indicated at left. The schematic diagrams depict the potential evolutionary scenarios on the right. Flanking sequences are shown as green boxes; target site direct repeats are shown in red boxes. Alu elements are shown as arrows, and the direction of the arrow indicates the orientation (5′→3′), with the head of the arrow denoting the end of the Alu elements.

Figure 5.

Median-joining network of the human-specific AluYb elements. The network of the AluYb lineage was reconstructed using the 36 non-Yb7/8/9 elements and the consensus sequences of the Yb7, Yb8, and Yb9 subfamilies as representatives of these three subfamilies. Black circles denote sequence types. Reconstructed nodes are identified as empty circles. The size of circles indicates the number of Alu loci with this sequence type, while arbitrary sizes were chosen for the Yb7/8/9 nodes to represent the relative sizes of the three subfamilies. Lines denote substitution steps, with a one-step distance being indicated in the bottom–right corner. Broken lines indicate that the length of the branch is not drawn to scale.

Figure 6.

Putative evolutionary scenario for the AluYb lineage. A schematic diagram of the hominid primates is shown with the approximate time scale shown on the bottom in million years. The blue lines indicate the expansion of the AluYb lineage, and the thickness of the lines represents its relative retrotransposition activity. The estimated copy number of AluYb elements in various primates is shown after their names. The blue triangle represents the estimated integration time period of AluYb founder gene, and the star represents the estimated integration time period of the oldest known AluYb8 element (Pan4).