13 December 2012
By Thomas Keane
Transposable elements (TEs) are mobile DNA segments that use the cellular machinery of the host for their replication, similar to the way in which viruses such as the flu replicate in our bodies. Transposable elements were first discovered in maize by Barbara McClintock in the early 20th century and have since been found in almost every organism. These DNA fragments have influenced the structure, shape and evolution of all mammalian genomes.
Scientists have repeatedly found that the size of a genome is proportional to the extent to which transposons have colonised a species genome. They are often referred to as genomic parasites and most are relics of ancient viral infections. In mammalian genomes such as human and mouse, TEs make up almost half of the genome sequence. The major TE families in the human and mouse genomes are LINEs and SINEs (long/short interspersed nuclear elements) along with various types of endogenous retroviruses (ERVs), ancient remnants of virus infections. TE activity can result in harmful mutations by disrupting the normal functioning of genes, leading to human diseases such as Haemophilia A.
For many years, researchers have tried to document TE differences among mouse strains but this process has been very slow and laborious. Our recent study, sequencing the genomes of 18 mice, has massively increased the catalogue of mouse TEVs by identifying 103,798 such variants of all the major TE classes (LINEs, SINEs and ERVs). Interestingly, we observed an uneven chromosome distribution of TEs across the strains with a notable depletion of all TE classes on the X chromosome. This suggests that the majority of TE insertions occur in the male germline.
When we analysed the TE catalogue along with the rest of the sequence variants in regions of the genome thought to be associated with quantitative traits in the mouse strains, we found that several of these traits (e.g. wound healing, home cage activity) were likely to be associated with the presence of a TE insertion. Although our catalogue is near to complete, much work remains to fully understand and interpret this vast collection.
Thomas Keane manages the Vertebrate Resequencing Informatics team at the Wellcome Trust Sanger Institute more...
Christoffer Nellåker, Thomas M Keane, Binnaz Yalcin et al (2012) 'The genomic landscape shaped by selection on transposable elements across 18 mouse strains'
Genome Biology 2012, 13:R45 doi:10.1186/gb-2012-13-6-r45