Transposable element

{{refimprove section|date=December 2025}}

{{refimprove section|date=December 2025}}

{{Self-contradictory|1=othersection|about=the number of types of transposable elements, stated in the lead and at section opening as two, then raised to three in a later section|date=December 2025}}

{{Self-contradictory|1=othersection|about=the number of types of transposable elements, stated in the lead and at section opening as two, then raised to three in a later section|date=December 2025}}

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).{{contradict-inline|date=December 2025}} {{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 }}

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 }}

=== Class I: Retrotransposons ===

=== Class I: Retrotransposons ===

{{Main|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]].

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. RNA conversion back into DNA is then facilitated through an enzyme called reverse transcriptase which is often encoded by the TE itself. This newly [[cDNA|copied DNA]] is then inserted back into the genome at a new position.{{Cite journal |last=Han |first=Jeffrey S. |date=2010-05-12 |title=Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions |url=https://doi.org/10.1186/1759-8753-1-15 |journal=Mobile DNA |language=en |volume=1 |issue=1 |pages=15 |doi=10.1186/1759-8753-1-15 |issn=1759-8753 |pmc=2881922 |pmid=20462415}} The characteristics of retrotransposons are similar to [[retrovirus]]es, such as [[HIV]] as HIV utilizes [[reverse transcriptase]] to make a double strand copy of its RNA genome which is then integrated into the host cells genome.{{Cite journal |last=Xavier Ruiz |first=Francesc |last2=Arnold |first2=Eddy |date=2020-04 |title=Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance |url=https://pmc.ncbi.nlm.nih.gov/articles/PMC7596924/ |journal=PMCID |volume=61 |pages=113–123 |doi=10.1016/j.sbi.2019.11.011 |issn=1879-033X |pmc=7596924 |pmid=31935541}}

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.{{cite web|url=https://wi.mit.edu/news/not-so-selfish-genetic-parasite-helps-preserve-fertility|title=A not-so-selfish "genetic parasite" helps to preserve fertility|vauthors=Friar G|date=30 May 2023|website=Whitehead Institute|access-date=14 September 2025}} The [[R2 RNA element|R2 retrotransposon]] of ''Drosophila'' 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.{{cite journal|vauthors=Nelson JO, Slicko A, Yamashito YM|title=The retrotransposon R2 maintains ''Drosophila'' ribosomal DNA repeats|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=120|issue=23|id=Art. No. e2221613120|doi=10.1073/pnas.2221613120|doi-access=free|pmid=37252996|pmc=10266012|year=2023 |article-number=e2221613120 |bibcode=2023PNAS..12021613N }}{{cite journal|vauthors=Yang J, Malik HS, Eickbush TH|title=Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=96|issue=14|year=1999|doi=10.1073/pnas.96.14.7847|doi-access=free|pmid=10393910|pmc=22150|pages=7847–7852 |bibcode=1999PNAS...96.7847Y }} The resulting chromatids, each with different quantities of rDNA, are tagged and differentially segregated during [[Asymmetric cell division|asymmetric division]] of progenitors into daughter stem cells, which receive the chromatids with more rDNA, and germ cell precursors.{{cite journal|vauthors=Watase GJ, Nelson JO, Yamashita YM|title=Nonrandom sister chromatid segregation mediates rDNA copy number maintenance in Drosophila|journal=Science Advances|year=2022|volume=8|issue=30|article-number=eabo4443 |doi=10.1126/sciadv.abo4443|id=Art. No. eabo4443|doi-access=free|pmid=35895823|pmc=9328678 |bibcode=2022SciA....8O4443W }}

Despite the potential negative effects of retrotransposons self insertion into necessary DNA sequences, which can result in important genes becoming unusable. They are essential in keeping different species' [[ribosomal DNA]] (rDNA) intact over the generations, preventing infertility.{{cite web|url=https://wi.mit.edu/news/not-so-selfish-genetic-parasite-helps-preserve-fertility|title=A not-so-selfish "genetic parasite" helps to preserve fertility|vauthors=Friar G|date=30 May 2023|website=Whitehead Institute|access-date=14 September 2025}} The [[R2 RNA element|R2 retrotransposon]] of ''Drosophila'' 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.{{cite journal|vauthors=Nelson JO, Slicko A, Yamashito YM|title=The retrotransposon R2 maintains ''Drosophila'' ribosomal DNA repeats|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=120|issue=23|id=Art. No. e2221613120|doi=10.1073/pnas.2221613120|doi-access=free|pmid=37252996|pmc=10266012|year=2023 |article-number=e2221613120 |bibcode=2023PNAS..12021613N }}{{cite journal|vauthors=Yang J, Malik HS, Eickbush TH|title=Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=96|issue=14|year=1999|doi=10.1073/pnas.96.14.7847|doi-access=free|pmid=10393910|pmc=22150|pages=7847–7852 |bibcode=1999PNAS...96.7847Y }} The resulting chromatids, each with different quantities of rDNA, are tagged and differentially segregated during [[Asymmetric cell division|asymmetric division]] of progenitors into daughter stem cells, which receive the chromatids with more rDNA, and germ cell precursors.{{cite journal|vauthors=Watase GJ, Nelson JO, Yamashita YM|title=Nonrandom sister chromatid segregation mediates rDNA copy number maintenance in Drosophila|journal=Science Advances|year=2022|volume=8|issue=30|article-number=eabo4443 |doi=10.1126/sciadv.abo4443|id=Art. No. eabo4443|doi-access=free|pmid=35895823|pmc=9328678 |bibcode=2022SciA....8O4443W }}

Currently retrotransposons are commonly grouped into two main categories:

As of this date,{{when|date=December 2025}} Retrotransposons are commonly grouped into three main categories:

* Retrotransposons, with [[long terminal repeat]]s (LTRs), which encode reverse transcriptase, similar to retroviruses;{{cn|date=December 2025}}

* Retrotransposons with [[long terminal repeat]]s (LTRs),that encode for reverse transcriptase similar to retroviruses;{{Cite journal |last=Havecker |first=Ericka R. |last2=Gao |first2=Xiang |last3=Voytas |first3=Daniel F. |date=2004-05-18 |title=The diversity of LTR retrotransposons |url=https://doi.org/10.1186/gb-2004-5-6-225 |journal=Genome Biology |language=en |volume=5 |issue=6 |pages=225 |doi=10.1186/gb-2004-5-6-225 |issn=1474-760X |pmc=463057 |pmid=15186483}}

* 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]];{{cn|date=December 2025}} and

* Retrotransposons with non long terminal repeats (Non-LTR), containing [[LINEs|long interspersed nuclear elements]] (LINEs, LINE-1s, or L1s) or [[Short interspersed nuclear element]]s (SINEs).

* [[Short interspersed nuclear element]]s (SINEs) that do not encode reverse transcriptase and are transcribed by [[RNA polymerase III]].{{cn|date=December 2025}}

Long interspersed nuclear clusters encode for reverse transcriptase and are transcribed by [[RNA polymerase II]]. Meanwhile SINEs do not encode for reverse transcriptase and are transcribed by [[RNA polymerase III]].

Retroviruses can also be considered TEs.{{says who|date=December 2025}} After 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, integrated DNA segments termed [[provirus]]es.{{cn|date=December 2025}} The provirus is a specialized form of [[eukaryotic]] retrotransposon,{{says who|date=December 2025}} which can produce RNA intermediates that may leave the host cell and infect other cells.{{cn|date=December 2025}} The transposition cycle of retroviruses has similarities to that of [[prokaryotic]] TEs,{{says who|date=December 2025}} suggesting a distant relationship between the two.{{speculation inline|date=December 2025}}{{cn|date=December 2025}}

=== Class II: DNA transposons ===

=== Class II: DNA transposons ===