What Is Transposons
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).
Types of Transposons
Class I Transposons: Retrotransposons
Retrotransposons (also called Class I transposable elements) are mobile elements which move in the host genome by converting their transcribed RNA into DNA through the reverse transcription.
Thus, they differ from Class II transposable elements, or DNA transposons, in utilizing an RNA intermediate for the transposition and leaving the transposition donor site unchanged.
Retrotransposons are evolutionarily widespread genetic elements that replicate through reverse transcription of an RNA copy and integrate the product DNA into new sites in the host genome.
They comprise significant fractions of metazoan genomes. Because insertions can disrupt host genome function, retrotransposon activity is controlled at transcriptional and posttranscriptional levels.
Through reverse transcription, retrotransposons amplify themselves quickly to become abundant in eukaryotic genomes such as maize (49–78%) and humans (42%).
They are only present in eukaryotes but share features with retroviruses such as HIV, for example, discontinuous reverse transcriptase-mediated extrachromosomal recombination.
There are two main types of retrotransposons, long terminal repeats (LTRs) and non-long terminal repeats (non-LTRs). Retrotransposons are classified based on sequence and method of transposition. Most retrotransposons in the maize genome are LTR, whereas in humans they are mostly non-LTR.
Class II Transposons: DNA Transposons
Repeated DNA makes up a large fraction of a typical mammalian genome, and some repetitive elements are able to move within the genome (transposons and retrotransposons). DNA transposons move from one genomic location to another by a cut-and-paste mechanism.
They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome.
Indeed, they have been used for transgenesis and insertional mutagenesis in different organisms, since these elements are not generally dependent on host factors to mediate their mobility.
Thus, DNA transposons are useful tools to analyze the regulatory genome, study embryonic development, identify genes and pathways implicated in disease or pathogenesis of pathogens, and even contribute to gene therapy.
Class III Transposons: Miniature Inverted-Repeat Transposable Elements (MITEs)
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.
Autonomous and Non-Autonomous Transposons
Transposons can be autonomous and non-autonomous.
Autonomous transposons can move by themselves. The activator element (Ac) is an example of an autonomous transposon.
In contrast, non-autonomous transposons require the help of other transposons for their movement as they lack enzymes reverse transcriptase (for Class I) or transposase (for Class II). Dissociation elements (Ds) are an example of a non-autonomous.
Example of Transposons
Transposons Are Common approximately 90% of wheat DNA and 85% of corn DNA is made of transposons. Half of our own DNA most likely consists of transposons. Many transposons are actually copies of the same genes that repeat themselves.
Transposons in Maize
The first transposons were discovered in the 1940s by Barbara McClintock who worked with maize (Zea mays, called “corn” in the U.S.).
She found that they were responsible for a variety of types of gene mutations, usually insertions and deletions (indels) and translocations. Some of the mutations (c, bz) used as examples of how gene loci are mapped on the chromosome were caused by transposons.
In developing somatic tissues like corn kernels, a mutation (e.g., c) that alters color will be passed on to all the descendant cells. This produces the variegated pattern which is so prized in “Indian corn”.
It took about 40 years for other scientists to fully appreciate the significance of Barbara McClintock’s discoveries. She was finally awarded a Nobel Prize in 1983.
Transposons in Drosophila
P elements are Class II transposons found in Drosophila. They do little harm because expression of their transposase gene is usually repressed. However, when male flies with P elements mate with female flies lacking them, the transposase becomes active in the germline producing so many mutations that their offspring are sterile.
In nature this is no longer a problem. P elements seem to have first appeared in Drosophila melanogaster about 50 years ago. Since then, they have spread through every population of the species.
Today flies lacking P elements can only be found in old strains maintained in the laboratory. P elements have provided valuable tools for Drosophila geneticists.
Transgenic flies containing any desired gene can be produced by injecting the early embryo with an engineered P element containing that gene. Other transposons are being studied for their ability to create transgenic insects of agricultural and public health importance.
Transposons in Bacteria
Some transposons in bacteria carry in addition to the gene for transposase genes for one or more (usually more) proteins imparting resistance to antibiotics. When such a transposon is incorporated in a plasmid, it can leave the host cell and move to another.
This is the way that the alarming phenomenon of multidrug antibiotic resistance spreads so rapidly. Transposition in these cases occurs by a “copy and paste” mechanism.
This requires an additional enzyme a resolvase that is also encoded in the transposon itself. The original transposon remains at the original site while its copy is inserted at a new site.
Transposons Used in Laboratory
Although there are many different transposons, DNA transposons are most commonly used in the laboratory. Some common types of transposon systems used in research are described below:
Sleeping Beauty
Sleeping Beauty is a synthetic transposable element from inactivated Tc1/mariner transposons found in fish. Its preferred target site for integration is TA dinucleotides, leaving a CAG DNA footprint from its terminal sequences at the site of excision after cleavage by the transposase.
It has a cargo capacity of more than 100 kilobase pairs, although integration efficiency decreases with cargo size. Sleeping Beauty has almost a random integration profile in mammalian genomes. It is found in vertebrates and inserted in humans at rates similar to retroviral vectors.
piggyBac
piggyBac was identified in the cabbage looper moth. The target site of piggyBac is TTAA, and unlike other transposons, it does not leave behind a footprint after excision. It also moves DNA over 100 kilobase pairs in size and is active in vitro and in vivo in yeasts, plants, insects, and mammalian cells, including humans.
They are biased to integrate at transcription start sites, CpG islands, and DNase I hypersensitivity sites.
Tol2
It is the first active DNA transposon in the vertebrate (found in the Japanese medaka fish). The insertion of Tol2 into the fish’s tyrosinase gene caused albinism. The gene has a weak consensus sequence for its integration site compared to the other two transposons. Like piggyBac, these transposons also prefer integrating at transcription start sites, CpG islands, and DNase I hypersensitivity sites.
Applications of Transposons
As genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome. Indeed, they have been used for transgenesis and insertional mutagenesis in different organisms, since these elements are not generally dependent on host factors to mediate their mobility.
Mutagenesis Screenings
Transposons are potent tools for mutagenesis studies, where researchers deliberately induce mutations to study gene function.
By inserting transposons into specific locations in the genome, scientists can disrupt the normal operation of genes and observe the resulting phenotypic changes. This approach helps uncover the roles of different genes and their contributions to various biological processes.
Generating Transgenic Animals
Transposons play a pivotal role in the creation of transgenic animals. Scientists use transposons to deliver and integrate desired genes into the germline cells of animals, ensuring that the introduced genetic material is passed on to the next generations.
This application is particularly crucial for studying gene function, disease modeling, and the development of animals with desirable traits for agriculture.
Gene Transfer in Plant
Transposons are employed as powerful tools in plant genetic engineering. Researchers use transposons to transfer and express genes in plant genomes, enabling the development of genetically modified (GM) crops with improved traits such as resistance to pests, diseases, or environmental stress.
The ability of transposons to integrate efficiently into plant genomes facilitates the creation of stable and heritable genetic modifications.
RNA Guided Transposons Insertion
Advances in genetic engineering caused the development of RNA-guided transposon insertion systems, leveraging the principles of RNA interference (RNAi) and the precision of the CRISPR-Cas system.
This innovative approach allows researchers to guide transposons to specific genomic locations by designing complementary RNA sequences.
The combination of CRISPR technology and transposons enhances the precision and control over gene insertion, reducing off-target effects and providing a more sophisticated method for genome editing.
Understanding Genome Structure and Function
The study of transposons has deepened our understanding of genome structure and function. Transposons can influence the regulation of nearby genes by affecting chromatin structure and gene expression.
Investigating transposon dynamics provides valuable information about the intricate mechanisms that govern the organization and regulation of genetic material.
Forensic Applications
Transposons have been used in forensic genetics to analyze DNA samples. The unique patterns of transposon insertion in individual genomes can serve as genetic markers, aiding in the identification of individuals. This application has proven helpful in forensic investigations and paternity testing.
Enhancing Precision in Gene Editing
Using transposons with modern gene-editing technologies like CRISPR-Cas provides a versatile platform for precise gene editing. Transposons are engineered to carry specific DNA sequences that encode therapeutic genes.
By integrating these transposons at exact genomic locations using CRISPR technology, scientists can target and modify genes with unprecedented accuracy, opening up new possibilities for therapeutic interventions in human health.
Studying Gene Function and Regulation
Transposons aid in functional genomics studies by enabling the controlled disruption or modification of specific genes. This approach is invaluable for understanding the roles of individual genes and their contributions to various biological processes.
Researchers can uncover gene function and regulation mechanisms using transposons to manipulate gene expression.
Creating Disease Models
Transposons are instrumental in the generation of animal models for human diseases. By introducing transposons carrying disease-associated genes or mutations into the genomes of animals, scientists can mimic pathological conditions observed in humans.
These models are crucial for studying disease mechanisms, testing potential therapeutic interventions, and advancing our understanding of complex genetic disorders.
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.