Atransposable element (TE), alsotransposon, orjumping gene, is a type ofmobile genetic element, a nucleic acid sequence in DNA that can change its position within a genome.
The discovery of mobile genetic elements earnedBarbara McClintock a Nobel Prize in 1983.[1]
TEs are very common in nature, especially inplants andanimals. About 50% of themaize genome, for instance, is made up by TEs.[2]
There are at least[further explanation needed] two classes of TEs: Class I TEs orretrotransposons generally function viareverse transcription, while Class II TEs orDNA transposons encode the proteintransposase, which they require for insertion and excision, and some of these TEs also encode other proteins.[3]
Barbara McClintock discovered the first TEs inmaize (Zea mays) at theCold Spring Harbor Laboratory in New York. McClintock was experimenting with maize plants that had broken chromosomes.[4]
In the winter of 1944–1945, McClintock planted corn kernels that were self-pollinated, meaning that the silk (style) of the flower received pollen from its ownanther.[4] These kernels came from a long line of plants that had been self-pollinated, causing broken arms on the end of their ninth chromosomes.[4] As the maize plants began to grow, McClintock noted unusual color patterns on the leaves.[4] For example, one leaf had two albino patches of almost identical size, located side by side on the leaf.[4] McClintock hypothesized that during cell division certain cells lost genetic material, while others gained what they had lost.[5] However, when comparing the chromosomes of the current generation of plants with the parent generation, she found certain parts of the chromosome had switched position.[5] This refuted 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.[5]
McClintock also showed that gene mutations could be reversed.[6] She presented her report on her findings in 1951, and published an article on her discoveries inGenetics in November 1953 entitled "Induction of Instability at Selected Loci in Maize".[7]
At the 1951 Cold Spring Harbor Symposium where she first publicized her findings, her talk was met with silence.[8] Her work was largely dismissed and ignored until the late 1960s–1970s when, after TEs were found in bacteria, it was rediscovered.[9] She was awarded aNobel Prize in Physiology or Medicine in 1983 for her discovery of TEs, more than thirty years after her initial research.[10]
Transposable elements represent one of several types ofmobile genetic elements. TEs are assigned to one of two classes according to their mechanism of transposition, which can be described as eithercopy and paste (Class I TEs) orcut and paste (Class II TEs).[11]
Class I TEs are copied in two stages: first, they aretranscribed from DNA toRNA, and the RNA produced is thenreverse transcribed to DNA. Thiscopied DNA is then inserted back into the genome at a new position. The reverse transcription step is catalyzed by areverse transcriptase, which is often encoded by the TE itself. The characteristics of retrotransposons are similar toretroviruses, such asHIV.
Despite the potential negative effects of retrotransposons, like inserting itself into the middle of a necessary DNA sequence, which can render important genes unusable, they are still essential to keep a species'ribosomal DNA (rDNA) intact over the generations, preventing infertility.[12] TheR2 retrotransposon ofDrosophila creates double-stranded breaks by endonuclease activity during its process of replication within its target rDNA, allowing for homologous recombination between sister chromatids to repair the breaks.[13][14] The resulting chromatids, each with different quantities of rDNA, are tagged and differentially segregated duringasymmetric division of progenitors into daughter stem cells, which receive the chromatids with more rDNA, and germ cell precursors.[15]
Retrotransposons are commonly grouped into three main orders:
Retroviruses can also be considered TEs. For example, after the conversion of retroviral RNA into DNA inside ahost cell, the newly produced retroviral DNA is integrated into thegenome of the host cell. These integrated DNAs are termedproviruses. The provirus is a specialized form ofeukaryotic 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 the two.
The cut-and-paste transposition mechanism of class II TEs does not involve an RNA intermediate. The transpositions are catalyzed by severaltransposase enzymes. Some transposases non-specifically bind to any target site in DNA, whereas others bind to specific target sequences. The transposase makes a staggered cut at the target site producingsticky ends, cuts out the DNA transposon and ligates it into the target site. ADNA polymerase fills in the resulting gaps from the sticky ends andDNA 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 byinverted repeats (which are important for the TEexcision bytransposase).
Cut-and-paste TEs may be duplicated if their transposition takes place duringS phase of thecell 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 ingene duplication, which plays an important role in genomicevolution.[17]: 284
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).
Class II TEs comprise less than 2% of the human genome, making the rest Class I.[18]
Transposition can be classified as either "autonomous" or "non-autonomous" in both Class I and Class II TEs. Autonomous TEs can move by themselves, whereas non-autonomous TEs require the presence of another TE to move. This is often because dependent TEs lack transposase (for Class II) or reverse transcriptase (for Class I).
Activator element (Ac) is an example of an autonomous TE, and dissociation elements (Ds) is an example of a non-autonomous TE. WithoutAc,Ds is not able to transpose.
Some researchers also identify a third class of transposable elements,[19] which has been described as "a grab-bag consisting of transposons that don't clearly fit into the other two categories".[20] Examples of such TEs are the Foldback (FB) elements ofDrosophila melanogaster, the TU elements ofStrongylocentrotus purpuratus, andMiniature Inverted-repeat Transposable Elements.[21][22]
Transposable elements can be all over a genome, as in the case of maize, in which TEs make up 50% of the genome.[2] In yeast (which has 5 classes of retrotransposons, Ty1-Ty5), over 90% of the Ty1 through T4 elements are located within 750 bp upstream of genes transcribed byRNA polymerase III, particularlytRNA genes. The Ty5 elements are all located at thetelomeres or regions with telomericchromatin.[2]
Transposons can damage the genome of their host cell in different ways:
Diseases often caused by TEs include
One study estimated the rate of transposition of a particular retrotransposon, theTy1 element inSaccharomyces 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.[29] Some TEs containheat-shock like promoters and their rate of transposition increases if the cell is subjected to stress,[30] thus increasing the mutation rate under these conditions, which might be beneficial to the cell.
Cells defend against the proliferation of TEs in a number of ways. These includepiRNAs andsiRNAs,[31] whichsilence TEs after they have been transcribed.
If organisms are mostly composed of TEs, one might assume that disease caused by misplaced TEs is very common, but in most cases TEs are silenced throughepigenetic mechanisms likeDNA methylation, chromatin remodeling and piRNA, such that little to no phenotypic effects nor movements of TEs occur as in some wild-type plant TEs. Certain mutated plants have been found to have defects in methylation-related enzymes (methyl transferase) which cause the transcription of TEs, thus affecting the phenotype.[3][32]
One hypothesis suggests that only approximately 100 LINE1 related sequences are active, despite their sequences making up 17% of the human genome. In human cells, silencing of LINE1 sequences is triggered by anRNA interference (RNAi) mechanism. Surprisingly, the RNAi sequences are derived from the 5′ untranslated region (UTR) of the LINE1, a long terminal which repeats itself. Supposedly, the 5′ LINE1 UTR that codes for the sense promoter for LINE1 transcription also encodes the antisense promoter for themiRNA that becomes the substrate for siRNA production. Inhibition of the RNAi silencing mechanism in this region showed an increase in LINE1 transcription.[3][33]
TEs are found in almost all life forms, and the scientific community is still exploring their evolution and their effect on genome evolution. It is unclear whether TEs originated in thelast universal common ancestor, arose independently multiple times, or arose once and then spread to other kingdoms byhorizontal gene transfer.[34]
Because excessive TE activity can damageexons, many organisms have acquired mechanisms to inhibit their activity. Bacteria may undergo high rates ofgene deletion as part of a mechanism to remove TEs and viruses from their genomes, whileeukaryotic organisms typically useRNA interference to inhibit TE activity. Nevertheless, some TEs generate large families often associated withspeciation events.[35] Evolution often deactivates DNA transposons, leaving them asintrons (inactive gene sequences). In vertebrate animal cells, nearly all 100,000+ DNA transposons per genome have genes that encode inactive transposase polypeptides.[36]
Sleeping Beauty/Tc1/mariner. The first synthetic transposon designed for use in vertebrate (including human) cells, theSleeping Beauty transposon system, is a Tc1/mariner-like transposon. Its dead ("fossil") versions are spread widely in the salmonid genome and a functional version was engineered by comparing those versions.[37] Human Tc1-like transposons are divided into Hsmar1 and Hsmar2 subfamilies. Although both types are inactive, one copy of Hsmar1 found in theSETMAR gene is under selection as it provides DNA-binding for the histone-modifying protein.[38] Many other human genes are similarly derived from transposons.[39] Hsmar2 has been reconstructed multiple times from the fossil sequences.[40]
Selective advantages. TEs may affect gene regulatory networks and thus have evolutionary advantages.[41]Interspersed repeats are created by transposition; since they can inhibitgene conversion, they protect novel gene sequences from being overwritten by similar gene sequences and thereby facilitate the development of new genes. TEs may also have been co-opted by thevertebrate immune system as a means of producing antibody diversity. TheV(D)J recombination system operates by a mechanism similar to that of some TEs. TEs also serve to generate repeating sequences that can formdsRNA to act as a substrate for the action ofADAR in RNA editing.[42]
TEs can contain many types of genes, including those conferring antibiotic resistance and the ability to transpose to conjugative plasmids. Some TEs also containintegrons, genetic elements that can capture and express genes from other sources. These containintegrase, which can integrategene cassettes. There are over 40 antibiotic resistance genes identified on cassettes, as well as virulence genes.[citation needed]
Novel genes and exon shuffling. Transposons do not always excise their elements precisely, sometimes removing the adjacent base pairs; this can lead to merged exons in a process calledexon shuffling. Shuffling two unrelated exons can create a novel gene product or, more likely, an intron.[43]
Some non-autonomous DNA TEs found in plants can capture coding DNA from genes and shuffle them across the genome.[44] This process can duplicate genes in the genome (a phenomenon called transduplication), and can contribute to generate novel genes by exon shuffling.[45]
There is a hypothesis that states that TEs might provide a ready source of DNA that could be co-opted by the cell to help regulate gene expression. Research showed that many diverse modes of TEs co-evolution along with some transcription factors targeting TE-associated genomic elements and chromatin are evolving from TE sequences. Most of the time, these particular modes do not follow the simple model of TEs and regulating host gene expression.[46]
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 performde novo repeat identification, all operating under the same general principles.[47] As short tandem repeats are generally 1–6 base pairs in length and are often consecutive, their identification is relatively simple.[48] 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).[47]
De novo identification of transposons involves three steps: 1) find all repeats within the genome, 2) build aconsensus 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 thek-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.[47] Another group of algorithms employs a method called sequence self-comparison. Sequence self-comparison programs use databases such asAB-BLAST to conduct an initialsequence 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.[49] Another group of algorithms follows the periodicity approach. These algorithms perform aFourier 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.[47]
The second step ofde novo repeat identification involves building a consensus of each family of sequences. Aconsensus 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.[47] 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.
Transposable elements have been recognized as good candidates for stimulating gene adaptation, through their ability to regulate the expression levels of nearby genes.[50] Combined with their "mobility", transposable elements can be relocated adjacent to their targeted genes, and control the expression levels of the gene, dependent upon the circumstances.
The study conducted in 2008, "High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster", usedD. melanogaster that had recently migrated from Africa to other parts of the world, as a basis for studying adaptations caused by transposable elements. Although most of the TEs were located on introns, the experiment showed a significant difference in gene expressions between the population in Africa and other parts of the world. The four TEs that caused the selective sweep were more prevalent inD. melanogaster from temperate climates, leading the researchers to conclude that the selective pressures of the climate prompted genetic adaptation.[51] From this experiment, it has been confirmed that adaptive TEs are prevalent in nature, by enabling organisms to adapt gene expression as a result of new selective pressures.
However, not all effects of adaptive TEs are beneficial to the population. In the research conducted in 2009, "A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster", a TE, inserted between Jheh 2 and Jheh 3, revealed a downgrade in the expression level of both of the genes. Downregulation of such genes has causedDrosophila to exhibit extended developmental time and reduced egg to adult viability. Although this adaptation was observed in high frequency in all non-African populations, it was not fixed in any of them.[52] This is not hard to believe, since it is logical for a population to favor higher egg to adult viability, therefore trying to purge the trait caused by this specific TE adaptation.
At the same time, there have been several reports showing the advantageous adaptation caused by TEs. In the research done with silkworms, "An Adaptive Transposable Element insertion in the Regulatory Region of the EO Gene in the Domesticated Silkworm", a TE insertion was observed in the cis-regulatory region of the EO gene, which regulates molting hormone 20E, and enhanced expression was recorded. While populations without the TE insert are often unable to effectively regulate hormone 20E under starvation conditions, those with the insert had a more stable development, which resulted in higher developmental uniformity.[53]
These three experiments all demonstrated different ways in which TE insertions can be advantageous or disadvantageous, through means of regulating the expression level of adjacent genes. The field of adaptive TE research is still under development and more findings can be expected in the future.
Recent studies have confirmed that TEs can contribute to the generation of transcription factors. However, how this process of contribution can have an impact on the participation of genome control networks. TEs are more common in many regions of the DNA and it makes up 45% of total human DNA. Also, TEs contributed to 16% of transcription factor binding sites. A larger number of motifs are also found in non-TE-derived DNA, and the number is larger than TE-derived DNA. All these factors correlate to the direct participation of TEs in many ways of gene control networks.[46]
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