Transposable elements (TEs) — commonly called ‘jumping genes’ — are stretches of DNA that move around the genome of a cell, and the genomes of many higher organisms are clut- tered with numerous copies of these enigmatic elements. They were discovered by Barbara McClintock in the 1950s (Box 1), but it has taken half a century to begin to understand how they act and the effects they can have. It is emerging that these elements have had a sig- nificant influence on the evolution of genomes, particularly by controlling gene activity. The elements contain in their sequence all the instructions needed to cut themselves out of their host DNA and splice themselves into another spot. But they are not always benign ‘junk’ DNA — they can insert into genes or gene regulatory elements, potentially disrupting the gene’s function, and they can trigger chromo- some rearrangements. So, even though most copies are selectively neutral and not in them- selves damaging, they have long been consid- ered as predominantly harmful to their hosts, as they can contribute to the appearance of muta- tions, some of which can result in disease. But TEs do not always have adverse effects, and their mutational activities contribute to the genetic diversity of the organism. Indeed, some TEs have been domesticated by their host genome, acting as genes or gene regulatory elements, and as a result constitute a source of genetic innovation for the organism 1,2 . Progress in understanding how these elements are regu- lated is bringing an appreciation of how an indi- vidual’s environment can affect the expression of their genetic complement to produce their own particular characteristics (phenotypes), such as physical appearance, behaviour, suscep- tibility to disease and even neuronal function. Diversity Transposable elements are scattered through- out the genomes of many plants and animals, and can form a large proportion of the genome size (Table 1). There are two main classes of TE: DNA transposons, which act through a DNA intermediate and multiply by using the host cell’s replication machinery, and retro- transposons, which act through an RNA inter- mediate. Retrotransposons are further sub- divided into those that have ‘long terminal repeats’ at their ends (LTR retrotransposons) and those that do not (non-LTR retrotrans- posons; Box 2). In addition, TEs with compos- ite structures are continually being discovered, illustrating the enormous flexibility of these elements. For example, DNA transposon-like elements called helitron rolling-circle elements were recently found to be responsible for copy- ing various gene segments into new locations in the maize genome, generating a huge diver- sity among individual maize plants 3 . When LTR retrotransposons are excised from the genome, they leave behind an LTR sequence. Some genomes, particularly those of plants, are full of these lone LTRs. Because they GENETICS Junk DNA as an evolutionary force Christian Biémont and Cristina Vieira Transposable elements were long dismissed as useless, but they are emerging as major players in evolution. Their interactions with the genome and the environment affect how genes are translated into physical traits. PIXFOLIO/ALAMY Transposable elements affect maize colour. 521 NEWS & VIEWS FEATURE Vol 443|5 October 2006 Nature Publishing Group ©2006