Transposable elements are a significant contributor to tandem repeats in the human genome

Abstract

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.

Figure 1

Relative abundance of major families and subfamilies of TEs that generate TRs. Relative abundance is calculated by dividing the number of TE-derived minisatellites by the total number of members in that TE family. (a) Relative abundance of major families of TR-associated TEs. The actual number of TE-derived TRs is at the top of each bar. (b) Relative abundance of subfamilies of TR-associated Alus. The color-shaded boxes are average relative abundance for the group with blue for AluJ, green for AluS, and orange for AluY. It is evident that the average relative abundance increases from AluJ to AluS to AluY.

Figure 2

Box and Whiskers plot of the number of repeats for TRs derived from the three major classes of Alu. The average number of repeat units decreases from AluJ (2.42) to AluS (2.31) to AluY (2.30).

Figure 3

Regions of TE that are involved in generating TRs for Alus and LTR12. (a) Representation of a selected number of fragments of AluSz that have generated TRs. Selection was made randomly to demonstrate that the repeat can occur from any region of a TE. The height of each bar is proportional to the number of repeats. Green colored regions are duplicated in 2 loci, and red colored regions are duplicated in 3 loci; (b) The number of TRs spanning each nucleotide of AluS, AluJ, and AluY; (c) The number of TRs spanning each nucleotide of LTR12.