Editing Genome (section)

== Eukaryotic genomes ==
{{See also|Eukaryotic chromosome fine structure}}
[[File:Human karyotype with bands and sub-bands.png|thumb|In a typical human cell, the genome is contained in 22 pairs of [[autosome]]s, two [[sex chromosomes]] (the female and male variants shown at bottom right), as well as the [[human mitochondrial genetics|mitochondrial genome]] (shown to scale as "MT" at bottom left). {{further|Karyotype}}]]
Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from [[Jack jumper ant]]s and an [[Diploscapter pachys|asexual nemotode]],<ref>{{cite web|title=Scientists sequence asexual tiny worm whose lineage stretches back 18 million years|url=https://www.sciencedaily.com/releases/2017/09/170921141303.htm|website=ScienceDaily|access-date=7 November 2017}}</ref> which each have only one pair, to a [[Ophioglossum|fern species]] that has 720 pairs.<ref>{{cite journal|last1=Khandelwal|first1=Sharda |name-list-style = vanc |title=Chromosome evolution in the genus Ophioglossum L.|journal=Botanical Journal of the Linnean Society|date=March 1990|volume=102|issue=3|pages=205–17|doi=10.1111/j.1095-8339.1990.tb01876.x }}</ref> It is surprising the amount of DNA that eukaryotic genomes contain compared to other genomes. The amount is even more than what is necessary for DNA protein-coding and noncoding genes because eukaryotic genomes show as much as 64,000-fold variation in their sizes.<ref name=":0a" /> However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs).

A typical human cell has two copies of each of 22 [[autosome]]s, one inherited from each parent, plus two [[sex chromosome]]s, making it diploid. [[Gamete]]s, such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to the chromosomes in the nucleus, organelles such as the [[chloroplasts]] and [[mitochondria]] have their own DNA. Mitochondria are sometimes said to have their own genome often referred to as the "[[mitochondrial genome]]". The DNA found within the chloroplast may be referred to as the "[[plastome]]". Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome.

Unlike prokaryotes where exon-intron organization of protein coding genes exists but is rather exceptional, eukaryotes generally have these features in their genes and their genomes contain variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA.<ref name="Lewin 2004">{{cite book |last = Lewin |first = Benjamin |name-list-style = vanc |title=Genes VIII|date=2004|publisher=Pearson/Prentice Hall|location=Upper Saddle River, NJ|isbn=978-0-13-143981-8|edition=8th}}</ref>

=== DNA sequencing ===
High-throughput technology makes sequencing to assemble new genomes accessible to everyone. Sequence polymorphisms are typically discovered by comparing resequenced isolates to a reference, whereas analyses of coverage depth and mapping topology can provide details regarding structural variations such as chromosomal translocations and segmental duplications.

=== Coding sequences ===
DNA sequences that carry the instructions to make proteins are referred to as coding sequences. The proportion of the genome occupied by coding sequences varies widely. A larger genome does not necessarily contain more genes, and the proportion of non-repetitive DNA decreases along with increasing genome size in complex eukaryotes.<ref name="Lewin 2004"/>

=== Noncoding sequences ===
{{Main|Non-coding DNA}}
{{See also|Intergenic region}}

Noncoding sequences include [[intron]]s, sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences make up 98% of the human genome. There are two categories of repetitive DNA in the genome: [[tandem repeats]] and interspersed repeats.<ref>{{cite book|editor-last=Stojanovic|editor-first=Nikola|name-list-style = vanc |title=Computational genomics : current methods|date=2007|publisher=Horizon Bioscience|location=Wymondham|isbn=978-1-904933-30-4}}</ref>

==== Tandem repeats ====
Short, non-coding sequences that are repeated head-to-tail are called [[tandem repeats]]. Microsatellites consisting of 2–5 basepair repeats, while minisatellite repeats are 30–35 bp. Tandem repeats make up about 4% of the human genome and 9% of the fruit fly genome.<ref name="Padeken">{{cite journal |vauthors = Padeken J, Zeller P, Gasser SM |title = Repeat DNA in genome organization and stability |journal = Current Opinion in Genetics & Development |volume = 31 |pages = 12–19 |date = April 2015 |pmid = 25917896 |doi = 10.1016/j.gde.2015.03.009 }}</ref> Tandem repeats can be functional. For example, [[telomere]]s are composed of the tandem repeat TTAGGG in mammals, and they play an important role in protecting the ends of the chromosome.

In other cases, expansions in the number of tandem repeats in exons or introns can cause [[Trinucleotide repeat disorder|disease]].<ref name="Usdin">{{cite journal |vauthors = Usdin K |title = The biological effects of simple tandem repeats: lessons from the repeat expansion diseases |journal = Genome Research |volume = 18 |issue = 7 |pages = 1011–19 |date = July 2008 |pmid = 18593815 |pmc = 3960014 |doi = 10.1101/gr.070409.107 }}</ref> For example, the human gene huntingtin (Htt) typically contains 6–29 tandem repeats of the nucleotides CAG (encoding a polyglutamine tract). An expansion to over 36 repeats results in [[Huntington's disease]], a neurodegenerative disease. Twenty human disorders are known to result from similar tandem repeat expansions in various genes. The mechanism by which proteins with expanded polygulatamine tracts cause death of neurons is not fully understood. One possibility is that the proteins fail to fold properly and avoid degradation, instead accumulating in aggregates that also sequester important transcription factors, thereby altering gene expression.<ref name="Usdin"/>

Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion.<ref>{{cite journal |vauthors = Li YC, Korol AB, Fahima T, Beiles A, Nevo E |title = Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review |journal = Molecular Ecology |volume = 11 |issue = 12 |pages = 2453–65 |date = December 2002 |pmid = 12453231 |doi = 10.1046/j.1365-294X.2002.01643.x |s2cid = 23606208 |doi-access = free |bibcode = 2002MolEc..11.2453L }}</ref>

==== Transposable elements ====
Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome.<ref name="Padeken" /><ref name="constraints and plasticity in genome and molecular" /><ref name="Wessler 17600–17601">{{cite journal |vauthors = Wessler SR |title = Transposable elements and the evolution of eukaryotic genomes |journal = Proceedings of the National Academy of Sciences of the United States of America |volume = 103 |issue = 47 |pages = 17600–01 |date = November 2006 |pmid = 17101965 |doi = 10.1073/pnas.0607612103 |bibcode = 2006PNAS..10317600W |pmc = 1693792 |doi-access = free }}</ref> TEs are categorized as either as a mechanism that replicates by copy-and-paste or as a mechanism that can be excised from the genome and inserted at a new location. In the human genome, there are three important classes of TEs that make up more than 45% of the human DNA; these classes are The long interspersed nuclear elements (LINEs), The interspersed nuclear elements (SINEs), and endogenous retroviruses. These elements have a big potential to modify the genetic control in a host organism.<ref name=":0a">{{Cite journal|last1=Zhou|first1=Wanding|last2=Liang|first2=Gangning|last3=Molloy|first3=Peter L.|last4=Jones|first4=Peter A.|date=11 August 2020|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|doi=10.1073/pnas.1921719117|issn=1091-6490|pmc=7431005|pmid=32719115|bibcode=2020PNAS..11719359Z |doi-access=free }}</ref>

The movement of TEs is a driving force of genome evolution in eukaryotes because their insertion can disrupt gene functions, homologous recombination between TEs can produce duplications, and TE can shuffle exons and regulatory sequences to new locations.<ref name="Kazazian 1626–1632">{{cite journal |vauthors = Kazazian HH |s2cid = 1956932 |title = Mobile elements: drivers of genome evolution |journal = Science |volume = 303 |issue = 5664 |pages = 1626–32 |date = March 2004 |pmid = 15016989 |doi = 10.1126/science.1089670 |bibcode = 2004Sci...303.1626K }}</ref>

===== 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"/>

===== DNA transposons =====
[[DNA transposon]]s encode a transposase enzyme between inverted terminal repeats. When expressed, the transposase recognizes the terminal inverted repeats that flank the transposon and catalyzes its excision and reinsertion in a new site.<ref name="Padeken" /> This cut-and-paste mechanism typically reinserts transposons near their original location (within 100&nbsp;kb).<ref name="Kazazian 1626–1632"/> DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm [[Caenorhabditis elegans|''C. elegans'']].<ref name="Kazazian 1626–1632"/>