Editing Transposable element (section)

== Classification ==

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).<ref>{{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 }}</ref>

=== Retrotransposon ===
{{Main|Retrotransposon}}
Class I TEs are copied in two stages: first, they are [[Transcription (genetics)|transcribed]] from DNA to [[RNA]], and the RNA produced is then [[reverse transcription|reverse transcribed]] to DNA. This [[cDNA|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 [[retrovirus]]es, 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.<ref>[https://wi.mit.edu/news/not-so-selfish-genetic-parasite-helps-preserve-fertility A not-so-selfish “genetic parasite” helps to preserve fertility]</ref>

Retrotransposons are commonly grouped into three main orders:
* Retrotransposons, with [[long terminal repeat]]s (LTRs), which encode reverse transcriptase, similar to retroviruses
* Retroposons, [[LINEs|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 element]]s (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 (biology)|host]] cell, the newly produced retroviral DNA is integrated into the [[genome]] of the host cell. These integrated DNAs are termed ''[[provirus]]es''. 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.

=== DNA transposons ===
{{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.<br />
'''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.<ref>{{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}}</ref>
]]

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 repeat]]s (which are important for the TE [[DNA repair|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]].<ref name="Brock">{{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}}</ref>{{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 (biology)|helitron]]).

Class II TEs comprise less than 2% of the human genome, making the rest Class I.<ref name="The impact of L1 retrotransposons o">{{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 }}</ref>

=== Autonomous and non-autonomous ===
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.

=== Class III ===
Some researchers also identify a third class of transposable elements,<ref>{{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}}</ref> which has been described as "a grab-bag consisting of transposons that don't clearly fit into the other two categories".<ref>{{cite web | vauthors = Baez J | title = Subcellular Life Forms.| url = https://math.ucr.edu/home/baez/subcellular.pdf | date = 2005 }}</ref> Examples of such TEs are the Foldback (FB) elements of ''Drosophila melanogaster'', the TU elements of ''[[Strongylocentrotus purpuratus]]'', and [[Miniature Inverted-repeat Transposable Elements]].<ref>{{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 }}</ref><ref>{{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 }}</ref>