Editing Genome (section)

===== Retrotransposons =====
[[Retrotransposon]]s<ref>{{Cite web|title=Transposon {{!}} genetics|url=https://www.britannica.com/science/transposon|access-date=2020-12-05|website=Encyclopedia Britannica}}</ref> are found mostly in eukaryotes but not found in prokaryotes. Retrotransposons form a large portion of the genomes of many eukaryotes. A retrotransposon is a transposable element that transposes through an [[RNA]] intermediate. Retrotransposons<ref>{{Cite book|last=Sanders|first=Mark Frederick|title=Genetic Analysis: an integrated approach third edition|publisher=Pearson, always learning, and mastering|year=2019|isbn=9780134605173|location=New York|pages=425}}</ref> are composed of [[DNA]], but are transcribed into RNA for transposition, then the RNA transcript is copied back to DNA formation with the help of a specific enzyme called reverse transcriptase. A retrotransposon that carries reverse transcriptase in its sequence can trigger its own transposition but retrotransposons that lack a reverse transcriptase must use reverse transcriptase synthesized by another retrotransposon. [[Retrotransposon]]s can be transcribed into RNA, which are then duplicated at another site into the genome.<ref>{{cite journal |vauthors = Deininger PL, Moran JV, Batzer MA, Kazazian HH |title = Mobile elements and mammalian genome evolution |journal = Current Opinion in Genetics & Development |volume = 13 |issue = 6 |pages = 651–58 |date = December 2003 |pmid = 14638329 |doi = 10.1016/j.gde.2003.10.013 }}</ref> Retrotransposons can be divided into [[long terminal repeat]]s (LTRs) and non-long terminal repeats (Non-LTRs).<ref name="Kazazian 1626–1632"/>

'''Long terminal repeats (LTRs)''' are derived from ancient retroviral infections, so they encode proteins related to retroviral proteins including gag (structural proteins of the virus), pol (reverse transcriptase and integrase), pro (protease), and in some cases env (envelope) genes.<ref name="Wessler 17600–17601"/> These genes are flanked by long repeats at both 5' and 3' ends. It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size.<ref>{{cite journal |vauthors = Kidwell MG, Lisch DR |title = Transposable elements and host genome evolution |journal = Trends in Ecology & Evolution |volume = 15 |issue = 3 |pages = 95–99 |date = March 2000 |pmid = 10675923 |doi = 10.1016/S0169-5347(99)01817-0 |bibcode = 2000TEcoE..15...95K }}</ref>

'''Non-long terminal repeats (Non-LTRs)''' are classified as [[long interspersed nuclear element]]s (LINEs), [[short interspersed nuclear element]]s (SINEs), and Penelope-like elements (PLEs). In ''Dictyostelium discoideum'', there is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes.<ref>{{cite journal |vauthors = Richard GF, Kerrest A, Dujon B |title = Comparative genomics and molecular dynamics of DNA repeats in eukaryotes |journal = Microbiology and Molecular Biology Reviews |volume = 72 |issue = 4 |pages = 686–727 |date = December 2008 |pmid = 19052325 |pmc = 2593564 |doi = 10.1128/MMBR.00011-08 }}</ref>

Long interspersed elements (LINEs) encode genes for reverse transcriptase and endonuclease, making them autonomous transposable elements. The human genome has around 500,000 LINEs, taking around 17% of the genome.<ref>{{cite journal |vauthors = Cordaux R, Batzer MA |title = The impact of retrotransposons on human genome evolution |journal = Nature Reviews. Genetics |volume = 10 |issue = 10 |pages = 691–703 |date = October 2009 |pmid = 19763152 |pmc = 2884099 |doi = 10.1038/nrg2640 }}</ref>

Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous, so they rely on the proteins encoded by LINEs for transposition.<ref>{{cite journal |vauthors = Han JS, Boeke JD |title = LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? |journal = BioEssays |volume = 27 |issue = 8 |pages = 775–84 |date = August 2005 |pmid = 16015595 |doi = 10.1002/bies.20257 |s2cid = 26424042 }}</ref> The [[Alu element]] is the most common SINE found in primates. It is about 350 base pairs and occupies about 11% of the human genome with around 1,500,000 copies.<ref name="Kazazian 1626–1632"/>