Transposable elements: not as quiet as a mouse

Abstract

In this issue of Genome Biology, Nellåker et al. show massive purging of deleterious transposable element variants, through negative selection, in 18 mouse strains.

Figure 1

History of transposable element variant (TEV) identification. (a) TEV detection using Southern blot, a technique based on genomic hybridization using transposable element (TE)-derived probes. This approach is usually limited by restriction enzyme site availability and provides only low sensitivity and specificity due to DNA hybridization. Only one single family of TE can be tested in each Southern blot. (b) TEV detection using PCR-based methods. By using PCR amplification of partial TE and flanking sequences, this approach dramatically improves both the sensitivity and specificity, and is suitable for detection of relatively high copy number TEs if sequencing is used. However, similar to Southern blot-based techniques, this approach is also limited by the availability of restriction enzyme sites. The analysis of PCR fragments can be done by gel electrophoresis or, as in [6], by sequencing. (c) TEV detection using genomic sequencing. Low-throughput sequencing involves cloning of bigger fragments (in the order of 1 kb) and has been used to map IAP and ETn TEVs [4]. High-throughput sequencing can efficiently produce high genomic coverage for a large number of strains [7]. Due to the much shorter average size of genomic DNA fragments (<100 bp), this approach requires more sophisticated computational algorithms for sequence mapping and TEV detection. In the figure, strains may represent individuals, populations or different species. RE, restriction enzyme; TE, transposable element; green arrows, RE sites.