Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

Fabian Haß,Susanne Hummel,Oliver Piskurek

doi:10.3390/d9040048

Abstract

The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400–500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.

Highlights

Transposable elements (TEs) are widespread in prokaryotic and eukaryotic organisms [1].They affect the evolution of genomes [2,3] and alter gene expression [4,5,6]
With the integration of an internal Alu primer (IAP), together with two flanking Alu primer sets, the duplex approach can be used to reduce the amount of DNA needed
The amplification of internal bands excludes the possibility of false negative presence bands of the Alu element

Summary

Introduction

Transposable elements (TEs) are widespread in prokaryotic and eukaryotic organisms [1]. They affect the evolution of genomes [2,3] and alter gene expression [4,5,6]. Class II is the smaller group and consists of DNA transposons that move via a “cut and paste” mechanism [10]. Class I, or retroposons, move via a “copy and paste” mechanism [11]. Two major groups of retroposons in the human genome are the autonomous Long Interspersed Elements (LINEs) and the non-autonomous Short Interspersed

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