Editing Repeated sequence (DNA) (section)

=== Interspersed repeats ===
[[Interspersed repeat]]s are identical or similar DNA sequences which are found in different locations throughout the genome.<ref>{{Cite web |title=Interspersed repetitive sequences - Latest research and news {{!}} Nature |url=https://www.nature.com/subjects/interspersed-repetitive-sequences |access-date=2022-09-30 |website=www.nature.com}}</ref> Interspersed repeats are distinguished from tandem repeats in that the repeated sequences are not directly adjacent to each other but instead may be scattered among different chromosomes or far apart on the same chromosome. Most interspersed repeats are [[transposable element]]s (TEs), mobile sequences which can be "cut and pasted" or "copied and pasted" into different places in the genome.<ref name=Wicker07>{{cite journal | vauthors = Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH | display-authors = 6 | title = A unified classification system for eukaryotic transposable elements | journal = Nature Reviews. Genetics | volume = 8 | issue = 12 | pages = 973–982 | date = December 2007 | pmid = 17984973 | doi = 10.1038/nrg2165 | s2cid = 32132898 }}</ref> TEs were originally called "jumping genes" for their ability to move, yet this term is somewhat misleading as not all TEs are discrete genes.<ref name=Nicolau21>{{cite journal | vauthors = Nicolau M, Picault N, Moissiard G | title = The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation | journal = Cells | volume = 10 | issue = 11 | pages = 2952 | date = October 2021 | pmid = 34831175 | pmc = 8616336 | doi = 10.3390/cells10112952 | doi-access = free }}</ref>

Transposable elements that are transcribed into RNA, reverse-transcribed into DNA, then reintegrated into the genome are called [[retrotransposon]]s.<ref name=Wicker07 /> Just as tandem repeats are further subcategorized based on the length of the repeating sequence, there are many different types of retrotransposons. Long interspersed nuclear elements ([[Long interspersed nuclear element|LINEs]]) are typically 3–7 kilobases in length.<ref name=Kramerov11>{{cite journal | vauthors = Kramerov DA, Vassetzky NS | title = SINEs | journal = Wiley Interdisciplinary Reviews. RNA | volume = 2 | issue = 6 | pages = 772–786 | date = 2011 | pmid = 21976282 | doi = 10.1002/wrna.91 | s2cid = 222199613 }}</ref> Short interspersed nuclear elements ([[Short interspersed nuclear element|SINEs]]) are typically 100-300 base pairs and no longer than 600 base pairs.<ref name=Kramerov11 /> Long-terminal repeat retrotransposons (LTRs) are a third major class of retrotransposons and are characterized by highly repetitive sequences as the ends of the repeat.<ref name=Wicker07 /> When a transposable element does not proceed through RNA as an intermediate, it is called a [[DNA transposon]].<ref name=Wicker07 /> Other classification systems refer to retrotransposons as "Class I" and DNA transposons as "Class II" transposable elements.<ref name=Nicolau21 />

Transposable elements are estimated to constitute 45% of the human genome.<ref>{{cite journal | vauthors = Lee HE, Ayarpadikannan S, Kim HS | title = Role of transposable elements in genomic rearrangement, evolution, gene regulation and epigenetics in primates | journal = Genes & Genetic Systems | volume = 90 | issue = 5 | pages = 245–257 | date = 2015 | pmid = 26781081 | doi = 10.1266/ggs.15-00016 | doi-access = free }}</ref> Since uncontrolled propagation of TEs could wreak havoc on the genome, many regulatory mechanisms have evolved to silence their spread, including DNA methylation, histone modifications, non-coding RNAs (ncRNAs) including small interfering RNA (siRNA), chromatin remodelers, histone variants, and other epigenetic factors.<ref name=Nicolau21 /> However, TEs play a wide variety of important biological functions. When TEs are introduced into a new host, such as from a virus, they increase genetic diversity.<ref name=Nicolau21 /> In some cases, host organisms find new functions for the proteins which arise from expressing TEs in an evolutionary process called TE exaptation.<ref name=Nicolau21 /> Recent research also suggests that TEs serve to maintain higher-order chromatin structure and 3D genome organization.<ref>{{cite journal | vauthors = Mangiavacchi A, Liu P, Della Valle F, Orlando V | title = New insights into the functional role of retrotransposon dynamics in mammalian somatic cells | journal = Cellular and Molecular Life Sciences | volume = 78 | issue = 13 | pages = 5245–56 | date = July 2021 | pmid = 33990851 | pmc = 8257530 | doi = 10.1007/s00018-021-03851-5 }}</ref> Furthermore, TEs contribute to regulating the expression of other genes by serving as distal [[Enhancer (genetics)|enhancers]] and transcription factor binding sites.<ref>{{cite journal | vauthors = Ichiyanagi K | title = Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs | journal = Genes & Genetic Systems | volume = 88 | issue = 1 | pages = 19–29 | date = 2013 | pmid = 23676707 | doi = 10.1266/ggs.88.19 | doi-access = free }}</ref>

The prevalence of interspersed elements in the genome has garnered attention for more research on their origins and functions. Some specific interspersed elements have been characterized, such as the Alu repeat and LINE1.