出典(authority):フリー百科事典『ウィキペディア(Wikipedia)』「2013/08/26 11:42:30」(JST)
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 McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.[1]
TEs make up a large fraction of the C-value of eukaryotic cells. They are generally considered non-coding DNA. In Oxytricha, which has a unique genetic system, they play a critical role in development.[2] They are also very useful to researchers as a means to alter DNA inside a living organism.
Barbara McClintock discovered the first TEs in maize, Zea mays, at the Cold Spring Harbor Laboratory. McClintock was experimenting with maize plants that had broken chromosomes.[3] In the winter of 1944-1945 McClintock planted corn kernels that were self-pollinated, meaning that the flowers were pollinated by the silk of their own plant.[3] These kernels came from a long line of plants that had been self-pollinated, causing broken arms on the end of their ninth chromosome.[3] As the maize plants began to grow, McClintock noted unusual color patterns on the leaves.[3] For example, one leaf had two albino patches of almost identical size, located side by side on the leaf.[3] McClintock hypothesized that during cell division certain cells lost genetic material, while others gained what they had lost.[4] However, when comparing the chromosomes of the current generation of plants and their parent generation, she found certain parts of the chromosomes had switched positions on the chromosome.[4] She disproved the popular genetic theory of the time that genes were fixed in their position on a chromosome. McClintock found that genes could not only move, but they could also be turned on or off due to certain environmental conditions or during different stages of cell development.[4] McClintock also showed that gene mutations could be reversed.[5] McClintock presented her report on her findings in 1951, and published an article on her discoveries in Genetics in November 1953 entitled, ″Induction of Instability at Selected Loci in Maize.″[6] Her work would be largely dismissed and ignored until the late 1960s-1970s when it would be rediscovered after TEs were found in bacteria.[7] She was awarded a Nobel Prize in Medicine or Physiology in 1983 for her discovery of TEs, more than thirty years after her research and initial discovery.[8]
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).[9]
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.[citation needed] The reverse transcription step is catalyzed by a reverse transcriptase, which is often encoded by the TE itself. The characteristics of retrotransposons are similar to retroviruses, such as HIV.[citation needed]
Retrotransposons are commonly grouped into three main orders:
Retroviruses can also be considered TEs.[citation needed] 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 of prokaryotic TEs, suggesting a distant relationship between these two TEs types.[citation needed]
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.[citation needed] 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.[citation needed] Such duplications at the target site can result in gene duplication, which plays an important role in evolution.[10]:284
Not all DNA transposons transpose through the cut-and-paste mechanism. In some cases, a replicative 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.[citation needed] When a TE is used as a genetic tool, the transposase is supplied by the investigator, often from an expression cassette within a plasmid.[11]
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TEs are mutagens. They can damage the genome of their host cell in different ways:[22]
Diseases that are often caused by TEs include hemophilia A and B, severe combined immunodeficiency, porphyria, predisposition to cancer, and Duchenne muscular dystrophy.[23][24]
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.
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.[25]
Cells defend against the proliferation of TEs in a number of ways. These include piRNAs and siRNAs[26] 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,[27] thus increasing the mutation rate under these conditions, which might be beneficial to the cell.
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.[28] 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.[29] 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.[30]
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.
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 [31]
The Tc1/mariner-class of TEs Sleeping Beauty transposon system, awarded as the Molecule of the Year 2009[32] is active in mammalian cells and are being investigated for use in human gene therapy.[33][34][35]
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.[36] 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).[37]
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.[37] 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.[38] 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.[37]
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.[37] 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.
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リンク元 | 「transpositional」「転位性」「translocational」「translocationally」 |
拡張検索 | 「transposable element」「DNA transposable element」 |
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