Employing Alu Elements to Detect Chromosomal Inversions

Abstract

Background and Objective Chromosomal inversion polymorphism events occur when a segment of DNA is flipped relative to its ancestral origin. They are frequent phenomena seen in the genomic evolution of related species and the initiation of cancer progression, and improved ability to detect such chromosomal inversion events would aid in evolutionary and oncological research. As balanced rearrangements, inversion polymorphisms remain difficult for traditional low-cost techniques to detect. Methods Here, the authors propose a novel methodology for detecting inversions by recording and analyzing the genetic loci of orthologous Alu sequences between any two given primate species. Alu insertion polymorphism events have long been used as a technique to identify evolutionary inversions, but their relative rarity limits identification of low- or medium-resolution inversions. However, the following methodology has largely eliminated this disadvantage by utilizing all Alu elements within the genome, and not exclusively insertion events. First, Alu elements from 31 subfamilies in the Chimpanzee (Pan troglodytes) and Gorilla (Gorilla gorilla) genomes (panTro4 and gorGor4, respectively) were extracted from the University of California Santa Cruz's Genome Table Browser (UCSC's GTB). For each Alu sequence in panTro4, Smith-Waterman string distances were calculated between that Alu sequence and every other Alu sequence in gorGor4 within its subfamily. This allowed the identification of orthologous, conserved Alu sequences between species, as well as each sequence pairings’ respective chromosome number and specific location. Orthologous chromosomes were then determined by the chromosomes containing the relatively highest number of orthologous sequences. Finally, inversions were mapped between those respective chromosomes and accompanied by graphical representations. Results Our methodology along with its produced graphical comparisons of primate species allowed for clear detection of patterns displaying inversions, which were then validated by previously published genomic differences between members of the primate Order. As a test case, the known inversion between chimpanzee and gorilla chromosome 7 was examined, which was both individually detected using 27 of the total 31 subfamilies and was definitively detected using the combination of all subfamilies (nearly 3,500 loci of ~300 base pairs each). For further validation, a list of all known inversions predicted from UCSC's GTB greater than 5 Mbp between the panTro4 and gorGor4 genomes was compiled. After comparison against each of these 10 predictions, 9 were detected with high confidence. Conclusion Such a high degree of accuracy with accepted findings demonstrates the validity of the novel Alu-based strategy in detecting inversion events within primate genomes. This methodology may have numerous practical applications in genomic comparisons of related species and identification of clinically relevant inversions. Further work must be done to confirm its efficacy in detecting such inversions among other species of the primate order and to resolve the minimum amount of computational comparison required in order to consistently and accurately identify inversion events.