transposon

transposon, class of genetic elements that can “jump” to different locations within a genome. Although these elements are frequently called “jumping genes,” they are always maintained in an integrated site in the genome. In addition, most transposons eventually become inactive and no longer move.

Transposons were first discovered in corn (maize) during the 1940s and ’50s by American scientist Barbara McClintock, whose work won her the Nobel Prize for Physiology or Medicine in 1983. Since McClintock’s discovery, three basic types of transposons have been identified. These include class II transposons, miniature inverted-repeat transposable elements (MITEs, or class III transposons), and retrotransposons (class I transposons).

Class II transposons

Class II elements are simply segments of DNA that move from one place to another via a “cut and paste” mechanism. Most, if not all, of these elements encode an enzyme called transposase, which acts to cleave the ends of the transposon, freeing it from its initial location in the genome. Transposase also cleaves target sites where the element is to be inserted. Once the transposon is ligated (bound) into its new position, gaps that are left in the DNA sequence are filled in through the synthesis of nucleotides. Class II transposons range in length from 1,000 to as many as 40,000 base pairs.

Miniature inverted-repeat transposable elements

MITEs are characterized by their short lengths, generally about 400 to 600 base pairs, and by a stretch of about 15 base pairs that occurs at each end of each element in an inverted fashion (as mirror sequences). The mechanism by which these elements move about genomes is not well understood. Thousands of MITEs have been identified in the genomes of Oryza sativa (cultivated rice), Caenorhabditis elegans (a type of nematode), and other organisms. Unlike some types of transposons, MITEs do not appear to encode proteins, and most insertions of these elements occur in euchromatin, the form of chromosomal material that contains the majority of active genes. As a result, a genetic regulatory function of MITEs has been proposed, and this has received support from evidence that some microRNAs (miRNAs), which play a role in RNA interference (a form of gene regulation), are derived from MITEs.

Retrotransposons

Retrotransposons represent a highly unique group of transposable elements and form large portions of the genomes of many eukaryotes (organisms with cells containing a clearly defined nucleus). Retrotransposons function by a “copy and paste” mechanism. Thus, they leave behind the original copy and generate a second copy that is inserted elsewhere in the genome. This process results in the insertion of repetitive sequences of DNA throughout the genome and is the mechanism responsible for the vast spread of transposable elements in many higher organisms.

The first step in retrotransposition occurs when the transposable DNA is copied into RNA. The RNA segment then jumps to another location in the genome. However, in order to be inserted into the genome at the new site, the RNA must be copied back into DNA by an enzyme called reverse transcriptase. There are several different types of retrotransposons, including long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). About 20 percent of the human genome is made up of LINEs.

Transposons and antibiotic resistance

The simplest kinds of transposons merely contain a copy of the transposase with no additional genes. They behave as parasitic elements and usually have no known associated function that is advantageous to the host. More often, transposable elements have additional genes associated with them—for example, antibiotic resistance factors. Antibiotic resistance typically occurs when an infecting bacterium acquires a plasmid that carries a gene encoding resistance to one or more antibiotics. Typically, these resistance genes are carried on transposable elements that have moved into plasmids and are easily transferred from one organism to another. Once a bacterium picks up such a gene, it enjoys a great selective advantage because it can grow in the presence of the antibiotic. Indiscriminate use of antibiotics actually promotes the buildup of these drug-resistant plasmids and strains.

Transposons and disease

The functions of transposons remain unclear. They have long been referred to as “junk” DNA because they appear to serve little or no purpose or as “selfish” DNA because they serve only to copy and amplify themselves within genomes. In rare cases, however, transposons are associated with genetic mutations or chromosomal rearrangements that cause disease in humans. Disease typically arises from the insertion of transposons into particular regions of genes that are involved in regulating gene activity. For example, insertions near promoter regions, which are short segments of DNA that are used to initiate gene transcription (the synthesis of RNA from DNA), can lead to overactivity of genes. In some cases this can give rise to cancer. In other cases the site where a class II element is cut out of the genome is not repaired correctly, resulting in mutations that interfere with gene regulation and thereby cause cell dysfunction. There are also several diseases, including hemophilia and Duchenne muscular dystrophy, that are associated with repetitive DNA arising from retrotransposons.