%0 Journal Article
%T Transposable Elements Are a Significant Contributor to Tandem Repeats in the Human Genome
%A Musaddeque Ahmed
%A Ping Liang
%J International Journal of Genomics
%D 2012
%I Hindawi Publishing Corporation
%R 10.1155/2012/947089
%X Sequence repeats are an important phenomenon in the human genome, playing important roles in genomic alteration often with phenotypic consequences. The two major types of repeat elements in the human genome are tandem repeats (TRs) including microsatellites, minisatellites, and satellites and transposable elements (TEs). So far, very little has been known about the relationship between these two types of repeats. In this study, we identified TRs that are derived from TEs either based on sequence similarity or overlapping genomic positions. We then analyzed the distribution of these TRs among TE families/subfamilies. Our study shows that at least 7,276£¿TRs or 23% of all minisatellites/satellites is derived from TEs, contributing ~0.32% of the human genome. TRs seem to be generated more likely from younger/more active TEs, and once initiated they are expanded with time via local duplication of the repeat units. The currently postulated mechanisms for origin of TRs can explain only 6% of all TE-derived TRs, indicating the presence of one or more yet to be identified mechanisms for the initiation of such repeats. Our result suggests that TEs are contributing to genome expansion and alteration not only by transposition but also by generating tandem repeats. 1. Introduction Over half of the human genome consists of repeat elements. The two types of repeat elements that are prevalent in human genome are tandem repeats (TRs) of sequences ranging from a single base to mega bases and interspersed repeats that mainly include transposable elements (TEs). The tandem repeats are classified in three major classes based on the size of the repeated sequence: microsatellites for short repeat units (usually <10£¿bp), minisatellites for head-to-tail tandem repeat of longer units (>10 and <100£¿bp), and satellites for even larger units (>100£¿bp). Among all types of tandem repeats, minisatellites and microsatellites have gained increasing attention over the past decade due to their contribution to intraspecies genetic diversity and use as genetic markers in population genetic studies. These repeat sequences are widespread in all eukaryotic genomes (reviewed in [1]) from yeast to mammals and often are highly polymorphic in populations of the same species. Consequently they are often used as a marker in numerous genotypic tests, for example, in forensic fingerprinting [2¨C5], in population genetics [6], and in monitoring of DNA damage induced by ionizing radiation [7]. Minisatellites lately have been of particular interest because their expansion has been implicated in alteration
%U http://www.hindawi.com/journals/ijg/2012/947089/