Transposable elements

A transposable element (TE) is a DNA sequence that can change its position within the genome, sometimes creating mutations and altering the cell's genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes early in her career earned her a Nobel prize in 1983.

TEs make up a large fraction of the C-value of eukaryotic cells. They are generally considered "junk DNA". In Oxytricha, which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.

Classification
Transposable elements are only one of several types of mobile genetic elements. They are assigned to one of two classes according to their mechanism of transposition, which can be described as either "copy and paste" (for class I TEs) or "cut and paste" (for class II TEs).

Class I (retrotransposons): They copy themselves in two stages, first from DNA to RNA by transcription, then from RNA back to DNA by reverse transcription. The DNA copy is then inserted into the genome in a new position. Reverse transcription is catalyzed by a reverse transcriptase, which is often coded by the TE itself. Retrotransposons behave very similarly to retroviruses, such as HIV.

There are three main orders of retrotransposons (other orders are less abundant):
 * Those with long terminal repeats (LTRs): encode reverse transcriptase, similar to retroviruses;
 * LINEs: encode reverse transcriptase, lack LTRs, transcribed by RNA polymerase II;
 * SINEs: do not code for reverse transcriptase, transcribed by RNA polymerase III.

Retroviruses can be considered as TEs. Indeed, after entering a host cell and converting their RNA into DNA, retroviruses integrate this DNA into the DNA of the host cell. The integrated DNA form (provirus) of the retrovirus is viewed as a particularly specialized form of eukaryotic retrotransposon, which is able to encode RNA intermediates that usually can leave the host cells and infect other cells. The transposition cycle of retroviruses also has similarities to that of prokaryotic TEs. The similarities suggest a distant familial relationship between these two TEs types.

Class II (DNA transposons): By contrast, the cut-and-paste transposition mechanism of class II TEs does not involve an RNA intermediate. The transpositions are catalyzed by various types of transposase enzymes. Some transposases can bind non-specifically to any target site, while others bind to specific sequence targets. The transposase makes a staggered cut at the target site producing sticky ends, cuts out the DNA transposon and ligates it into the target site. A DNA polymerase fills in the resulting gaps from the sticky ends and DNA ligase closes the sugar-phosphate backbone. This results in target site duplication and the insertion sites of DNA transposons may be identified by short direct repeats (a staggered cut in the target DNA filled by DNA polymerase) followed by inverted repeats (which are important for the TE excision by transposase). The duplications at the target site can result in gene duplication, which plays an important role in evolution.

Not all DNA transposons transpose through a cut-and-paste mechanism. In some cases a replicative transposition is observed in which transposon replicates itself to a new target site (e.g. Helitron (biology)).

Cut-and-paste TEs may be duplicated if transposition takes place during S phase of the cell cycle when the "donor" site has already been replicated, but the "target" site has not.

Both classes of TEs may lose their ability to synthesise reverse transcriptase or transposase through mutation, yet continue to jump through the genome because other TEs are still producing the necessary enzymes. Hence, they can be classified as either "autonomous" or "non-autonomous". For instance for the class II TEs, the autonomous ones have an intact gene that encodes an active transposase enzyme; the TE does not need another source of transposase for its transposition. In contrast, non-autonomous elements encode defective polypeptides and accordingly require transposase from another source. When a TE is used as a genetic tool, the transposase is supplied by the investigator, often from an expression cassette within a plasmid.

Examples

 * The first TEs were discovered in maize (Zea mays), by Barbara McClintock in 1948, for which she was awarded a Nobel Prize in 1983. She noticed insertions, deletions, and translocations, caused by these elements. These changes in the genome could, for example, lead to a change in the color of corn kernels. About 85% of the genome of maize consists in TEs. The Ac/Ds system described by McClintock are class II TEs. Transposition of Ac in tobacco has been demonstrated by B. Baker (Plant Transposable Elements, pp 161–174, 1988, Plenum Publishing Corp., ed. Nelson).


 * One family of TEs in the fruit fly Drosophila melanogaster are called P elements. They seem to have first appeared in the species only in the middle of the twentieth century. Within 50 years, they have spread through every population of the species. Gerald M. Rubin and Allan C. Spradling pioneered technology to use artificial P elements to insert genes into Drosophila by injecting the embryo.


 * Transposons in bacteria usually carry an additional gene for function other than transposition---often for antibiotic resistance. In bacteria, transposons can jump from chromosomal DNA to plasmid DNA and back, allowing for the transfer and permanent addition of genes such as those encoding antibiotic resistance (multi-antibiotic resistant bacterial strains can be generated in this way). Bacterial transposons of this type belong to the Tn family. When the transposable elements lack additional genes, they are known as insertion sequences.


 * The most common form of transposable element in humans is the Alu sequence. It is approximately 300 bases long and can be found between 300,000 and a million times in the human genome.


 * Mariner-like elements are another prominent class of transposons found in multiple species including humans. The Mariner transposon was first discovered by Jacobson and Hartl in Drosophila. This Class II transposable element is known for its uncanny ability to be transmitted horizontally in many species. There are an estimated 14 thousand copies of Mariner in the human genome comprising 2.6 million base pairs. The first mariner-element transposons outside of animals were found in Trichomonas vaginalis.  These characteristics of the Mariner transposon have inspired the science fiction novel titled, "The Mariner Project".


 * Mu phage transposition is the best known example of replicative transposition. Its transposition mechanism is somewhat similar to a homologous recombination.


 * The five distinct yeast (Saccharomyces cerevisiae) retrotransposon families: Ty1, Ty2, Ty3, Ty4 and Ty5


 * A helitron is a TE found in eukaryotes that are thought to replicate by a rolling-circle mechanism.

In disease
TEs are mutagens. They can damage the genome of their host cell in different ways :
 * a transposon or a retroposon that inserts itself into a functional gene will most likely disable that gene;
 * after a DNA transposon leaves a gene, the resulting gap will probably not be repaired correctly;
 * multiple copies of the same sequence, such as Alu sequences can hinder precise chromosomal pairing during mitosis and meiosis, resulting in unequal crossovers, one of the main reasons for chromosome duplication.

Diseases that are often caused by TEs include hemophilia A and B, severe combined immunodeficiency, porphyria, predisposition to cancer, and Duchenne muscular dystrophy.

Additionally, many TEs contain promoters which drive transcription of their own transposase. These promoters can cause aberrant expression of linked genes, causing disease or mutant phenotypes.

Rate of transposition, induction and defense
One study estimated the rate of transposition of a particular retrotransposon, the Ty1 element in Saccharomyces cerevisiae. Using several assumptions, the rate of successful transposition event per single Ty1 element came out to be about once every few months to once every few years.

Cells defend against the proliferation of TEs in a number of ways. These include piRNAs and siRNAs which silence TEs after they have been transcribed.

Some TEs contain heat-shock like promoters and their rate of transposition increases if the cell is subjected to stress, thus increasing the mutation rate under these conditions, which might be beneficial to the cell.

Evolution
The evolution of TEs and their effect on genome evolution is currently a dynamic field of study.

TEs are found in many major branches of life. They may have originated in the last universal common ancestor, or arisen independently multiple times, or perhaps arisen once and then spread to other kingdoms by horizontal gene transfer. While some TEs may confer benefits on their hosts, most are regarded as selfish DNA parasites. In this way, they are similar to viruses. Various viruses and TEs also share features in their genome structures and biochemical abilities, leading to speculation that they share a common ancestor.

Since excessive TE activity can destroy a genome, many organisms have developed mechanisms to inhibit this activity. Bacteria may undergo high rates of gene deletion as part of a mechanism to remove TEs and viruses from their genomes while eukaryotic organisms use RNA interference (RNAi) to inhibit TE activity. Nevertheless, some TEs generated large families often associated with speciation events.

Evolution has been particularly harsh on DNA transposons. In vertebrate animal cells nearly all >100,000 DNA transposons per genome have genes that encode inactive transposase polypeptides. In humans, all of the Tc1-like transposons are inactive. As a result the first DNA transposon used as a tool for genetic purposes, the Sleeping Beauty transposon system, was a Tc1/mariner-like transposon that was resurrected from a long evolutionary sleep.

Interspersed Repeats within genomes are created by transposition events accumulating over evolutionary time. Because interspersed repeats block gene conversion, they protect novel gene sequences from being overwritten by similar gene sequences and thereby facilitate the development of new genes.

TEs may have been co-opted by the vertebrate immune system as a means of producing antibody diversity: The V(D)J recombination system operates by a mechanism similar to that of some TEs.

TEs contain many type of genes- including those conferring antibiotic resistance and ability to transpose to conjugative plasmid. Some TEs also contain integrons(genetic elements that can capture and express genes from other sources) that contain integrase enzyme which can integrate gene cassettes. There are over 40 antibiotic resistance genes identified on cassettes, also virulence genes.

Applications
The first TE was discovered in the plant maize (Zea mays, corn species), and is named dissociator (Ds). Likewise, the first TE to be molecularly isolated was from a plant (Snapdragon). Appropriately, TEs have been an especially useful tool in plant molecular biology. Researchers use them as a means of mutagenesis. In this context, a TE jumps into a gene and produces a mutation. The presence of such a TE provides a straightforward means of identifying the mutant allele, relative to chemical mutagenesis methods.

Sometimes the insertion of a TE into a gene can disrupt that gene's function in a reversible manner, in a process called insertional mutagenesis; transposase-mediated excision of the DNA transposon restores gene function. This produces plants in which neighboring cells have different genotypes. This feature allows researchers to distinguish between genes that must be present inside of a cell in order to function (cell-autonomous) and genes that produce observable effects in cells other than those where the gene is expressed.

TEs are also a widely used tool for mutagenesis of most experimentally tractable organisms. The Sleeping Beauty transposon system has been used extensively as an insertional tag for identifying cancer genes

The Tc1/mariner-class of TEs Sleeping Beauty transposon system, awarded as the Molecule of the Year 2009 is active in mammalian cells and are being investigated for use in human gene therapy.

De novo repeat identification
De novo repeat identification is an initial scan of sequence data that seeks to find the repetitive regions of the genome, and to classify these repeats. Many computer programs exist to perform de novo repeat identification, all operating under the same general principles. As short tandem repeats are generally 1-6 base pairs in length and are often consecutive, their identification is relatively simple. Dispersed repetitive elements, on the other hand, are more challenging to identify, due to the fact that they are longer and have often acquired mutations. However, it is important to identify these repeats as they are often found to be transposable elements (TEs).

De novo identification of transposons involves three steps: 1) find all repeats within the genome, 2) build a consensus of each family of sequences, and 3) classify these repeats (Makalowski et al. 2012). There are three groups of algorithms for the first step.  One group is referred to as the k-mer approach, where a k-mer is a sequence of length k.  In this approach, the genome is scanned for overrepresented k-mers; that is, k-mers that occur more often than is likely based on probability alone.  The length k is determined by the type of transposon being searched for.  The k-mer approach also allows mismatches, the number of which is determined by the analyst.  Some k-mer approach programs use the k-mer as a base, and extend both ends of each repeated k-mer until there is no more similarity between them, indicating the ends of the repeats.  Another group of algorithms employs a method called sequence self-comparison. Sequence self-comparison programs use databases such as AB-BLAST to conduct an initial sequence alignment. As these programs find groups of elements that partially overlap, they are useful for finding highly diverged transposons, or transposons with only a small region copied into other parts of the genome. Another group of algorithms follows the periodicity approach. These algorithms perform a Fourier transformation on the sequence data, identifying periodicities, regions that are repeated periodically, and are able to use peaks in the resultant spectrum to find candidate repetitive elements. This method works best for tandem repeats, but can be used for dispersed repeats as well. However, it is a slow process, making it an unlikely choice for genome scale analysis.

The second step of de novo repeat identification involves building a consensus of each family of sequences. A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus is the one that occurred most often in the sequences being compared to make the consensus. For example, in a family of 50 repeats where 42 have a T base pair in the same position, the consensus sequence would have a T at this position as well, as the base pair is representative of the family as a whole at that particular position, and is most likely the base pair found in the family’s ancestor at that position. Once a consensus sequence has been made for each family, it is then possible to move on to further analysis, such as TE classification and genome masking in order to quantify the overall TE content of the genome.