Transposable elements

Transposable elements
Transposable elements

By: Shehzad Ahmad Kang

A transposable element (TE,transposon or retrotransposon) is a  DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell’s genome size. Transposition often results in duplication of the TE. Barbara Mc Clintock’s discovery of these jumping genes.

A bacterial DNA transposon

TEs make up a large fraction of the C-value of eukaryotic cells. They are generally considered non-coding DNA, although it has been unambiguously shown that TEs are important in genome function and evolution.

Classification

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

Class I (retrotransposons):
Class I TEs are copied in two stages: first they are transcribed from DNA to RNA, and the RNA produced is then reverse transcribed to DNA. This copied DNA is then inserted at a new position into the genome. The reverse transcription step is catalyzed by a reverse transcriptase, which is often encoded by the TE itself. The characteristics of retrotransposons are similar toretroviruses, such as HIV.

Retrotransposons are commonly grouped into three main orders:
•    TEs with long terminal repeats (LTRs): encode reverse transcriptase, similar to retroviruses
•    LINEs: encode reverse transcriptase, lack LTRs, and are transcribed by RNA polymerase II
•    SINEs: do not encode reverse transcriptase and are transcribed by RNA polymerase III.

Retroviruses can also be considered TEs. For example, after entering a host cell and conversion of the retroviral RNA into DNA, the newly produced retroviral DNA is integrated into the genome of the host cell. These integrated DNAs represent a provirus of the retrovirus. The provirus is a specialized form of eukaryotic retrotransposon, which can produce RNA intermediates that may leave the host cell and infect other cells. The transposition cycle of retroviruses has similarities to that ofprokaryotic TEs, suggesting a distant relationship between these two TEs types.

Class II (DNA transposons):

The cut-and-paste transposition mechanism of class II TEs does not involve an RNA intermediate. The transpositions are catalyzed by several transposase enzymes. Some transposases non-specifically bind to any target site in DNA, whereas others bind to specific DNA sequence targets. The transposase makes a staggered cut at the target site resulting in single-strand 5′ or 3′ DNA overhangs (sticky ends). This step cuts out the DNA transposon, which is then ligated into a new target site; this process involves activity of a DNA polymerase that fills in gaps and of a DNA ligase that closes the sugar-phosphate backbone. This results in duplication of the target site. The insertion sites of DNA transposons may be identified by short direct repeats (created by the staggered cut in the target DNA and filling in by DNA polymerase) followed by a series of inverted repeats important for the TE excision by transposase. Cut-and-paste TEs may be duplicated if their transposition takes place during S phase of the cell cycle when a donor site has already been replicated, but a target site has not yet been replicated. Such duplications at the target site can result in gene duplication, which plays an important role in evolution.

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

Both classes of TEs may lose their ability to synthesise reverse transcriptase or transposase through mutation. However, such mutated TEs may continue to transpose through the genome if functional enzymes for the transposition are furnished by non-mutated TEs. Hence, transposition can be classified as either “autonomous” or “non-autonomous.” For instance, for class II TEs, autonomous ones have an intact gene that encodes an active transposase enzyme; transposition of the TE does not require transposase activity from another TE. In contrast, non-autonomous elements encode defective polypeptides and therefore require transposase from a functional TE. 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 toplasmid 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 thehuman 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 inDrosophila. 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, Ty4and Ty5

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

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 siRNAswhich 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.

Aplications

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.

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. 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 over represented 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.

References
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By: Shehzad Ahmad Kang, Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Corresponding author’s email; shehzadpbg@gmail.com

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