transposable element

Barbara McClintock discovered the first TEs in maize (Zea mays) at the Cold Spring Harbor Laboratory in New York. McClintock was experimenting with maize plants that had broken chromosomes.{{cite book | vauthors = McGrayne SB |title=Nobel Prize Women in Science: Their Lives, Struggles, and Momentous Discoveries |url=https://books.google.com/books?id=e7NaAAAAYAAJ |year=1998 |publisher=Carol Publishing |isbn=978-0-9702256-0-3 |edition=2nd |page=165}}

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 own anther. These kernels came from a long line of plants that had been self-pollinated, causing broken arms on the end of their ninth chromosomes. As the maize plants began to grow, McClintock noted unusual color patterns on the leaves. For example, one leaf had two albino patches of almost identical size, located side by side on the leaf. McClintock hypothesized that during cell division certain cells lost genetic material, while others gained what they had lost.{{harnvb|McGrayne|1998|p=166}} 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. 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.

McClintock also showed that gene mutations could be reversed.{{harnvb|McGrayne|1998|p=167}} She 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".{{cite journal | vauthors = McClintock B | title = Induction of Instability at Selected Loci in Maize | journal = Genetics | volume = 38 | issue = 6 | pages = 579–99 | date = November 1953 | doi = 10.1093/genetics/38.6.579 | pmid = 17247459 | pmc = 1209627 | url = http://www.genetics.org/cgi/pmidlookup?view=long&pmid=17247459 }}

At the 1951 Cold Spring Harbor Symposium where she first publicized her findings, her talk was met with silence.{{cite journal| title = Proceedings of the National Academy of Sciences Dec 2012, 109 (50) 20198-20199; DOI: 10.1073/pnas.1219372109| year = 2012| doi = 10.1073/pnas.1219372109| pmid = 23236127| last1 = Ravindran| first1 = S.| journal = Proceedings of the National Academy of Sciences of the United States of America| volume = 109| issue = 50| pages = 20198–20199| pmc = 3528533| doi-access = free}} Her work was largely dismissed and ignored until the late 1960s–1970s when, after TEs were found in bacteria, it was rediscovered.{{cite book | vauthors = Des Jardins J |title=The Madame Curie Complex: The Hidden History of Women in Science |url=https://books.google.com/books?id=HULGDNDSenYC&pg=PA246 |year=2010 |publisher=Feminist Press at CUNY |isbn=978-1-55861-655-4 |page=246}} She was awarded a Nobel Prize in Physiology or Medicine in 1983 for her discovery of TEs, more than thirty years after her initial research.{{cite book | veditors = Fedoroff N, Botstein D |title=The Dynamic Genome: Barbara McClintock's Ideas in the Century of Genetics |url=https://books.google.com/books?id=BF1xfIGd0b4C&pg=PA2 |date=1 January 1992 |publisher=Cold Spring Harbor Laboratory Press |isbn=978-0-87969-422-7 |page=2}}

Transposable elements 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).{{cite journal | vauthors = Kapitonov VV, Jurka J | s2cid = 1275744 | title = A universal classification of eukaryotic transposable elements implemented in Repbase | journal = Nature Reviews. Genetics | volume = 9 | issue = 5 | pages = 411–2; author reply 414 | date = May 2008 | pmid = 18421312 | doi = 10.1038/nrg2165-c1 | doi-access = free }}

{{Main|Retrotransposon}}

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 back into the genome at a new position. 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.

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 intact over the generations, preventing infertility.[https://wi.mit.edu/news/not-so-selfish-genetic-parasite-helps-preserve-fertility A not-so-selfish “genetic parasite” helps to preserve fertility]

Retrotransposons are commonly grouped into three main orders:

• Retrotransposons, with long terminal repeats (LTRs), which encode reverse transcriptase, similar to retroviruses
• Retroposons, long interspersed nuclear elements (LINEs, LINE-1s, or L1s), which encode reverse transcriptase but lack LTRs, and are transcribed by RNA polymerase II
• Short interspersed nuclear elements (SINEs) do not encode reverse transcriptase and are transcribed by RNA polymerase III

Retroviruses can also be considered TEs. For example, after the conversion of retroviral RNA into DNA inside a host cell, the newly produced retroviral DNA is integrated into the genome of the host cell. These integrated DNAs are termed proviruses. 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 the two.

{{Main|DNA transposon}}

[[File:DNA Transposon.png|thumb|upright=1.4|A. Structure of DNA transposons (Mariner type). Two inverted tandem repeats (TIR) flank the transposase gene. Two short tandem site duplications (TSD) are present on both sides of the insert.

B. Mechanism of transposition: Two transposases recognize and bind to TIR sequences, join and promote DNA double-strand cleavage. The DNA-transposase complex then inserts its DNA cargo at specific DNA motifs elsewhere in the genome, creating short TSDs upon integration.{{Cite thesis | vauthors = Walter M |year=2016 |title=Transposon regulation upon dynamic loss of DNA methylation |publisher=Université Pierre et Marie Curie|doi=10.13140/rg.2.2.18747.21286}}

]]

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 target sequences. 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).

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|date=September 2022}} Such duplications at the target site can result in gene duplication, which plays an important role in genomic evolution.{{cite book |veditors=Madigan M, Martinko J |title=Brock Biolog of Microorganisms |edition=11th |publisher=Prentice Hall |year=2006 |isbn=978-0-13-144329-7}}{{rp|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).

Class II TEs comprise less than 2% of the human genome, making the rest Class I.{{cite journal | vauthors = Kazazian HH, Moran JV | s2cid = 33460203 | title = The impact of L1 retrotransposons on the human genome | journal = Nature Genetics | volume = 19 | issue = 1 | pages = 19–24 | date = May 1998 | pmid = 9590283 | doi = 10.1038/ng0598-19 }}

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. Without Ac, Ds is not able to transpose.

Some researchers also identify a third class of transposable elements,{{cite book |last1=Capy P |title=Dynamics and evolution of transposable elements |date=1998 |publisher=Chapman & Hall |location=New York |isbn=978-3-540-61190-5}} which has been described as "a grab-bag consisting of transposons that don't clearly fit into the other two categories".{{cite web | vauthors = Baez J | title = Subcellular Life Forms.| url = https://math.ucr.edu/home/baez/subcellular.pdf | date = 2005 }} Examples of such TEs are the Foldback (FB) elements of Drosophila melanogaster, the TU elements of Strongylocentrotus purpuratus, and Miniature Inverted-repeat Transposable Elements.{{cite journal | vauthors = Boutanaev AM, Osbourn AE | title = Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 115 | issue = 28 | pages = E6650–E6658 | date = July 2018 | pmid = 29941591 | pmc = 6048515 | doi = 10.1073/pnas.1721318115 | bibcode = 2018PNAS..115E6650B | doi-access = free }}{{cite journal | vauthors = Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE | title = The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective | journal = Genome Biology | volume = 3 | issue = 12 | pages = RESEARCH0084 | date = 2002 | pmid = 12537573 | pmc = 151186 | doi = 10.1186/gb-2002-3-12-research0084 | doi-access = free }}

Transposons can damage the genome of their host cell in different ways:

• A transposon can insert into a functional gene and disable that gene.
• After a DNA transposon is excised, the resulting gap may not be repaired correctly.

• Many TEs contain promoters that drive transcription of their own genes. These promoters can cause aberrant expression of linked genes.

Diseases often caused by TEs include

• Hemophilia A and B
• LINE1 (L1) TEs that land on the human Factor VIII have been shown to cause haemophiliaKazazian HH, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE (March 1988). "Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man". Nature. 332 (6160): 164–6. Bibcode:1988Natur.332..164K. doi:10.1038/332164a0. PMID 2831458.
• Severe combined immunodeficiency
• Insertion of L1 into the APC gene causes colon cancer, confirming that TEs play an important role in disease development.Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, Kinzler KW, Vogelstein B, Nakamura Y (February 1992). "Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer". Cancer Research. 52 (3): 643–5. PMID 1310068.
• Porphyria
• Insertion of Alu element into the PBGD gene leads to interference with the coding region and leads to acute intermittent porphyria{{cite journal | vauthors = Mustajoki S, Ahola H, Mustajoki P, Kauppinen R | title = Insertion of Alu element responsible for acute intermittent porphyria | journal = Human Mutation | volume = 13 | issue = 6 | pages = 431–8 | date = June 1999 | pmid = 10408772 | doi = 10.1002/(sici)1098-1004(1999)13:6<431::aid-humu2>3.0.co;2-y | s2cid = 6218429 }} (AIP).
• Predisposition to cancer
• LINE1(L1) TE's and other retrotransposons have been linked to cancer because they cause genomic instability.
• Duchenne muscular dystrophy.Kazazian HH, Goodier JL (August 2002). "LINE drive. retrotransposition and genome instability". Cell. 110 (3): 277–80. doi:10.1016/S0092-8674(02)00868-1. PMID 12176313.Kapitonov VV, Pavlicek A, Jurka J (2006). Anthology of Human Repetitive DNA. Encyclopedia of Molecular Cell Biology and Molecular Medicine. doi:10.1002/3527600906.mcb.200300166. {{ISBN|978-3527600908}}.
• Caused by SVA transposable element insertion in the fukutin (FKTN) gene which renders the gene inactive.
• Alzheimer's Disease and other Tauopathies
• Transposable element dysregulation can cause neuronal death, leading to neurodegenerative disordersSun W, Samimi H, Gamez M, Zare H, Frost B (August 2018). "Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies". Nature Neuroscience. 21 (8): 1038–1048. doi:10.1038/s41593-018-0194-1. PMC 6095477. PMID 30038280.

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.{{cite journal | vauthors = Paquin CE, Williamson VM | s2cid = 39145808 | title = Temperature effects on the rate of ty transposition | journal = Science | volume = 226 | issue = 4670 | pages = 53–5 | date = October 1984 | pmid = 17815421 | doi = 10.1126/science.226.4670.53 | bibcode = 1984Sci...226...53P }} Some TEs contain heat-shock like promoters and their rate of transposition increases if the cell is subjected to stress,{{cite journal | vauthors = Strand DJ, McDonald JF | title = Copia is transcriptionally responsive to environmental stress | journal = Nucleic Acids Research | volume = 13 | issue = 12 | pages = 4401–10 | date = June 1985 | pmid = 2409535 | pmc = 321795 | doi = 10.1093/nar/13.12.4401 }} 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 include piRNAs and siRNAs,{{cite journal | vauthors = Chung WJ, Okamura K, Martin R, Lai EC | title = Endogenous RNA interference provides a somatic defense against Drosophila transposons | journal = Current Biology | volume = 18 | issue = 11 | pages = 795–802 | date = June 2008 | pmid = 18501606 | pmc = 2812477 | doi = 10.1016/j.cub.2008.05.006 | bibcode = 2008CBio...18..795C }} which silence 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 through epigenetic mechanisms like DNA 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.{{cite journal | vauthors = Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T | s2cid = 4429219 | title = Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis | journal = Nature | volume = 411 | issue = 6834 | pages = 212–4 | date = May 2001 | pmid = 11346800 | doi = 10.1038/35075612 | bibcode = 2001Natur.411..212M }}

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 an RNA 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 the miRNA that becomes the substrate for siRNA production. Inhibition of the RNAi silencing mechanism in this region showed an increase in LINE1 transcription.{{cite journal | vauthors = Yang N, Kazazian HH | s2cid = 32601334 | title = L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells | journal = Nature Structural & Molecular Biology | volume = 13 | issue = 9 | pages = 763–71 | date = September 2006 | pmid = 16936727 | doi = 10.1038/nsmb1141 }}

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 the last universal common ancestor, arose independently multiple times, or arose once and then spread to other kingdoms by horizontal gene transfer.{{cite journal | vauthors = Kidwell MG | s2cid = 33227644 | title = Horizontal transfer of P elements and other short inverted repeat transposons | journal = Genetica | volume = 86 | issue = 1–3 | pages = 275–86 | year = 1992 | pmid = 1334912 | doi = 10.1007/BF00133726 }}

Because excessive TE activity can damage exons, many organisms have acquired mechanisms to inhibit their 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 typically use RNA interference to inhibit TE activity. Nevertheless, some TEs generate large families often associated with speciation events.{{cite journal |last1=Ricci |first1=Marco |last2=Peona |first2=Valentina |last3=Guichard |first3=Etienne |last4=Taccioli |first4=Cristian |last5=Boattini |first5=Alessio |title=Transposable Elements Activity is Positively Related to Rate of Speciation in Mammals |journal=Journal of Molecular Evolution |date=31 May 2018 |volume=86 |issue=5 |pages=303–310 |doi=10.1007/s00239-018-9847-7 |pmid=29855654 |pmc=6028844 |bibcode=2018JMolE..86..303R }} Evolution often deactivates DNA transposons, leaving them as introns (inactive gene sequences). In vertebrate animal cells, nearly all 100,000+ DNA transposons per genome have genes that encode inactive transposase polypeptides.{{cite journal | vauthors = Plasterk RH, Izsvák Z, Ivics Z | title = Resident aliens: the Tc1/mariner superfamily of transposable elements | journal = Trends in Genetics | volume = 15 | issue = 8 | pages = 326–32 | date = August 1999 | pmid = 10431195 | doi = 10.1016/S0168-9525(99)01777-1 }} The first synthetic transposon designed for use in vertebrate (including human) cells, the Sleeping 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.{{cite journal | vauthors = Ivics Z, Hackett PB, Plasterk RH, Izsvák Z | s2cid = 17908472 | title = Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells | journal = Cell | volume = 91 | issue = 4 | pages = 501–10 | date = November 1997 | pmid = 9390559 | doi = 10.1016/S0092-8674(00)80436-5 | doi-access = free }} Human Tc1-like transposons are divided into Hsmar1 and Hsmar2 subfamilies. Although both types are inactive, one copy of Hsmar1 found in the SETMAR gene is under selection as it provides DNA-binding for the histone-modifying protein.{{cite journal | vauthors = Miskey C, Papp B, Mátés L, Sinzelle L, Keller H, Izsvák Z, Ivics Z | title = The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends | journal = Molecular and Cellular Biology | volume = 27 | issue = 12 | pages = 4589–600 | date = June 2007 | pmid = 17403897 | pmc = 1900042 | doi = 10.1128/MCB.02027-06 }} Many other human genes are similarly derived from transposons.{{cite web |title=Gene group: Transposable element derived genes |url=https://www.genenames.org/data/genegroup/#!/group/1416 |publisher=HUGO Gene Nomenclature Committee |access-date=4 March 2019}} Hsmar2 has been reconstructed multiple times from the fossil sequences.{{cite journal | vauthors = Gil E, Bosch A, Lampe D, Lizcano JM, Perales JC, Danos O, Chillon M | title = Functional characterization of the human mariner transposon Hsmar2 | journal = PLOS ONE| volume = 8 | issue = 9 | pages = e73227 | date = 11 September 2013 | pmid = 24039890 | pmc = 3770610 | doi = 10.1371/journal.pone.0073227 | bibcode = 2013PLoSO...873227G | doi-access = free }}

The frequency and location of TE integrations influence genomic structure and evolution and affect gene and protein regulatory networks during development and in differentiated cell types.{{Cite journal |last1=Ball |first1=Hope C. |last2=Ansari |first2=Mohammad Y. |last3=Ahmad |first3=Nashrah |last4=Novak |first4=Kimberly |last5=Haqqi |first5=Tariq M. |date=November 2021 |title=A retrotransposon gag-like-3 gene RTL3 and SOX-9 co-regulate the expression of COL2A1 in chondrocytes |journal=Connective Tissue Research |volume=62 |issue=6 |pages=615–628 |doi=10.1080/03008207.2020.1828380 |issn=1607-8438 |pmc=8404968 |pmid=33043724}} Large quantities of TEs within genomes may still present evolutionary advantages, however. 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 also 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 also serve to generate repeating sequences that can form dsRNA to act as a substrate for the action of ADAR in RNA editing.{{cite journal | vauthors = Jin Y, Zhang W, Li Q | title = Origins and evolution of ADAR-mediated RNA editing | journal = IUBMB Life| volume = 61 | issue = 6 | pages = 572–578 | date = June 2009 | doi = 10.1002/iub.207| pmid = 19472181 | doi-access = free }}

TEs can contain many types of genes, including those conferring antibiotic resistance and the ability to transpose to conjugative plasmids. Some TEs also contain integrons, genetic elements that can capture and express genes from other sources. These contain integrase, which can integrate gene cassettes. There are over 40 antibiotic resistance genes identified on cassettes, as well as virulence genes.

Transposons do not always excise their elements precisely, sometimes removing the adjacent base pairs; this phenomenon is called exon shuffling. Shuffling two unrelated exons can create a novel gene product or, more likely, an intron.{{cite journal | vauthors = Moran JV, DeBerardinis RJ, Kazazian HH | title = Exon shuffling by L1 retrotransposition | journal = Science | volume = 283 | issue = 5407 | pages = 1530–4 | date = March 1999 | pmid = 10066175 | doi = 10.1126/science.283.5407.1530 | bibcode = 1999Sci...283.1530M }}

Some non-autonomous DNA TEs found in plants can capture coding DNA from genes and shuffle them across the genome.{{cite journal | vauthors = Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR | title = Pack-MULE transposable elements mediate gene evolution in plants | journal = Nature | volume = 431 | issue = 7008 | pages = 569–573 | date = September 2004 | pmid = 15457261 | doi = 10.1038/nature02953 | bibcode = 2004Natur.431..569J | s2cid = 4363679 }} This process can duplicate genes in the genome (a phenomenon called transduplication), and can contribute to generate novel genes by exon shuffling.{{cite journal | vauthors = Catoni M, Jonesman T, Cerruti E, Paszkowski J | title = Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling | journal = Nucleic Acids Research | volume = 47 | issue = 3 | pages = 1311–1320 | date = February 2019 | pmid = 30476196 | pmc = 6379663 | doi = 10.1093/nar/gky1196 }}

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.{{cite journal | vauthors = Zhou W, Liang G, Molloy PL, Jones PA | title = DNA methylation enables transposable element-driven genome expansion | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 117 | issue = 32 | pages = 19359–19366 | date = August 2020 | pmid = 32719115 | pmc = 7431005 | doi = 10.1073/pnas.1921719117 | bibcode = 2020PNAS..11719359Z | doi-access = free }}

{{Main|Transposons as a genetic tool}}Transposable elements can be harnessed in laboratory and research settings to study genomes of organisms and even engineer genetic sequences. The use of transposable elements can be split into two categories: for genetic engineering and as a genetic tool.

• Insertional mutagenesis uses the features of a TE to insert a sequence. In most cases, this is used to remove a DNA sequence or cause a frameshift mutation.
• In some cases the insertion of a TE into a gene can disrupt that gene's function in a reversible manner where 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.

In addition to the qualities mentioned for Genetic engineering, a Genetic tool also:-

• Used for analysis of gene expression and protein functioning in signature-tagging mutagenesis.
• This analytical tool allows researchers the ability to determine phenotypic expression of gene sequences. Also, this analytic technique mutates the desired locus of interest so that the phenotypes of the original and the mutated gene can be compared.

• 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 Molecule of the Year in 2009, is active in mammalian cells and is being investigated for use in human gene therapy.
• TEs are used for the reconstruction of phylogenies by the means of presence/absence analyses. Transposons can act as biological mutagen in bacteria.
• Common organisms which the use of Transposons has been well developed are:
• Drosophila{{cite journal | vauthors = Tempel S, Rousseau C, Tahi F, Nicolas J | title = ModuleOrganizer: detecting modules in families of transposable elements | journal = BMC Bioinformatics | volume = 11 | pages = 474 | date = September 2010 | pmid = 20860790 | pmc = 2955051 | doi = 10.1186/1471-2105-11-474 | doi-access = free }}
• Arabidopsis thaliana
• Escherichia coli

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.{{cite journal |vauthors=Saha S, Bridges S, Magbanua ZV, Peterson DG |s2cid=26272439 |title=Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences |journal=Tropical Plant Biol. |volume=1 |pages=85–96 |year=2008 |issue=1 |doi=10.1007/s12042-007-9007-5 |bibcode=2008TroPB...1...85S }} 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).{{Cite book |vauthors=Makałowski W, Pande A, Gotea V, Makałowska I |title=Evolutionary Genomics |chapter=Transposable elements and their identification |volume=855 |pages=337–59 |year=2012 |pmid=22407715 |doi=10.1007/978-1-61779-582-4_12 |series=Methods in Molecular Biology |isbn=978-1-61779-581-7 }}

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 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.{{cite journal | vauthors = Saha S, Bridges S, Magbanua ZV, Peterson DG | title = Empirical comparison of ab initio repeat finding programs | journal = Nucleic Acids Research | volume = 36 | issue = 7 | pages = 2284–94 | date = April 2008 | pmid = 18287116 | pmc = 2367713 | doi = 10.1093/nar/gkn064 }} 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.

Transposable elements have been recognized as good candidates for stimulating gene adaptation, through their ability to regulate the expression levels of nearby genes.{{cite journal | vauthors = Mariño-Ramírez L, Lewis KC, Landsman D, Jordan IK | title = Transposable elements donate lineage-specific regulatory sequences to host genomes | journal = Cytogenetic and Genome Research | volume = 110 | issue = 1–4 | pages = 333–41 | year = 2005 | pmid = 16093685 | pmc = 1803082 | doi = 10.1159/000084965 }} 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", used D. 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 in D. melanogaster from temperate climates, leading the researchers to conclude that the selective pressures of the climate prompted genetic adaptation.{{cite journal | vauthors = González J, Lenkov K, Lipatov M, Macpherson JM, Petrov DA | title = High rate of recent transposable element-induced adaptation in Drosophila melanogaster | journal = PLOS Biology | volume = 6 | issue = 10 | pages = e251 | date = October 2008 | pmid = 18942889 | pmc = 2570423 | doi = 10.1371/journal.pbio.0060251 | doi-access = free }} 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 caused Drosophila 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.{{cite journal | vauthors = González J, Macpherson JM, Petrov DA | title = A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster | journal = Molecular Biology and Evolution | volume = 26 | issue = 9 | pages = 1949–61 | date = September 2009 | pmid = 19458110 | pmc = 2734154 | doi = 10.1093/molbev/msp107 }} 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.{{cite journal | vauthors = Sun W, Shen YH, Han MJ, Cao YF, Zhang Z | title = An adaptive transposable element insertion in the regulatory region of the EO gene in the domesticated silkworm, Bombyx mori | journal = Molecular Biology and Evolution | volume = 31 | issue = 12 | pages = 3302–13 | date = December 2014 | pmid = 25213334 | doi = 10.1093/molbev/msu261 | doi-access = free }}

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.

{{cmn|

• Decrease in DNA Methylation I (DDM1)
• Epigenetic regulation of transposable elements in the plant kingdom
• Evolution of sexual reproduction
• Horizontal gene transfer
• Intragenomic conflict
• PiggyBac transposon system
• Polinton
• Tn3 transposon
• Tn10
• Transpogene
• Transposon tagging

}}

• {{cite book | vauthors = Kidwell MG | year = 2005 | chapter = Transposable elements | title = The Evolution of the Genome | editor = T.R. Gregory | pages = 165–221 | publisher = Elsevier | location = San Diego | isbn = 978-0-123-01463-4 | title-link = The Evolution of the Genome }}
• {{cite book | veditors = Craig NL, Craigie R, Gellert M, and Lambowitz AM | year = 2002 | title = Mobile DNA II | publisher = ASM Press | location = Washington, DC | isbn = 978-1-555-81209-6 }}
• {{cite book | vauthors = Lewin B | year = 2000 | title = Genes VII | publisher = Oxford University Press | isbn = 978-0-198-79276-5 | url-access = registration | url = https://archive.org/details/genesvii00lewi }}

{{Reflist}}

• {{cite journal |title=An immune system so versatile it might kill you |journal=New Scientist |issue=2556 |date=21 June 2006 |url=https://www.newscientist.com/article/mg19025565.500}} – A possible connection between aberrant reinsertions and lymphoma.
• [http://www.girinst.org/ Repbase] – a database of transposable element sequences
• [http://www.dfam.org/ Dfam] - a database of transposable element families, multiple sequence alignments, and sequence models
• [http://www.repeatmasker.org/ RepeatMasker] – a computer program used by computational biologists to annotate transposons in DNA sequences
• [http://cshprotocols.cshlp.org/cgi/content/full/2009/8/pdb.prot5270 Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells]
• [https://www.youtube.com/watch?time_continue=53&v=eSD_tbjfSlA&feature=emb_logo Introduction to Transposons, 2018 YouTube video]

{{Repeated sequence}}

{{Genetic recombination}}

{{Self-replicating organic structures}}

{{Organisms et al.}}

{{Authority control}}

Category:Modification of genetic information

Category:Mobile genetic elements

Category:Molecular biology

Category:Non-coding DNA