Editing Microsatellite (section)

==Biological effects of microsatellite mutations==
Many microsatellites are located in [[non-coding DNA]] and are biologically silent. Others are located in regulatory or even [[coding DNA]]&nbsp;– microsatellite mutations in such cases can lead to phenotypic changes and diseases. A genome-wide study estimates that microsatellite variation contributes 10–15% of heritable gene expression variation in humans.<ref name="Gymrek 22–29">{{cite journal | vauthors = Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard JK, Sharp AJ, Erlich Y | display-authors = 6 | title = Abundant contribution of short tandem repeats to gene expression variation in humans | journal = Nature Genetics | volume = 48 | issue = 1 | pages = 22–29 | date = January 2016 | pmid = 26642241 | pmc = 4909355 | doi = 10.1038/ng.3461 }}</ref><ref name="Biological effects"/>

===Effects on proteins===
In mammals, 20–40% of proteins contain repeating sequences of [[amino acid]]s encoded by short sequence repeats.<ref name="Marcotte 1998">{{cite journal | vauthors = Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D | title = A census of protein repeats | journal = Journal of Molecular Biology | volume = 293 | issue = 1 | pages = 151–60 | date = October 1999 | pmid = 10512723 | doi = 10.1006/jmbi.1999.3136 | s2cid = 11102561 }}</ref> Most of the short sequence repeats within protein-coding portions of the genome have a repeating unit of three nucleotides, since that length will not cause frame-shifts when mutating.<ref name="Sutherland 1995">{{cite journal | vauthors = Sutherland GR, Richards RI |author-link1=Grant Robert Sutherland | title = Simple tandem DNA repeats and human genetic disease | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 92 | issue = 9 | pages = 3636–41 | date = April 1995 | pmid = 7731957 | pmc = 42017 | doi = 10.1073/pnas.92.9.3636 | bibcode = 1995PNAS...92.3636S | doi-access = free }}</ref> Each trinucleotide repeating sequence is transcribed into a repeating series of the same amino acid. In yeasts, the most common repeated amino acids are glutamine, glutamic acid, asparagine, aspartic acid and serine.

Mutations in these repeating segments can affect the physical and chemical properties of proteins, with the potential for producing gradual and predictable changes in protein action.<ref name="Hancock 2005">{{cite journal | vauthors = Hancock JM, Simon M | title = Simple sequence repeats in proteins and their significance for network evolution | journal = Gene | volume = 345 | issue = 1 | pages = 113–8 | date = January 2005 | pmid = 15716087 | doi = 10.1016/j.gene.2004.11.023 }}</ref> For example, length changes in tandemly repeating regions in the [[Runx2]] gene lead to differences in facial length in domesticated dogs (''[[Canis familiaris]]''), with an association between longer sequence lengths and longer faces.<ref name="Fondon 2004">{{cite journal | vauthors = Fondon JW, Garner HR | title = Molecular origins of rapid and continuous morphological evolution | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 52 | pages = 18058–63 | date = December 2004 | pmid = 15596718 | pmc = 539791 | doi = 10.1073/pnas.0408118101 | bibcode = 2004PNAS..10118058F | doi-access = free }}</ref> This association also applies to a wider range of Carnivora species.<ref name="Sears 2007">{{cite journal | vauthors = Sears KE, Goswami A, Flynn JJ, Niswander LA | title = The correlated evolution of Runx2 tandem repeats, transcriptional activity, and facial length in carnivora | journal = Evolution & Development | volume = 9 | issue = 6 | pages = 555–65 | year = 2007 | pmid = 17976052 | doi = 10.1111/j.1525-142X.2007.00196.x | s2cid = 26718314 }}</ref> Length changes in polyalanine tracts within the [[HOXA13]] gene are linked to [[hand-foot-genital syndrome]], a developmental disorder in humans.<ref name="Utsch 2002">{{cite journal | vauthors = Utsch B, Becker K, Brock D, Lentze MJ, Bidlingmaier F, Ludwig M | title = A novel stable polyalanine [poly(A)] expansion in the HOXA13 gene associated with hand-foot-genital syndrome: proper function of poly(A)-harbouring transcription factors depends on a critical repeat length? | journal = Human Genetics | volume = 110 | issue = 5 | pages = 488–94 | date = May 2002 | pmid = 12073020 | doi = 10.1007/s00439-002-0712-8 | s2cid = 22181414 }}</ref> Length changes in other triplet repeats are linked to more than 40 neurological diseases in humans, notably [[trinucleotide repeat disorder]]s such as [[fragile X syndrome]] and [[Huntington's disease]].<ref name="Pearson 2005">{{cite journal | vauthors = Pearson CE, Nichol Edamura K, Cleary JD | title = Repeat instability: mechanisms of dynamic mutations | journal = Nature Reviews. Genetics | volume = 6 | issue = 10 | pages = 729–42 | date = October 2005 | pmid = 16205713 | doi = 10.1038/nrg1689 | s2cid = 26672703 }}</ref> Evolutionary changes from replication slippage also occur in simpler organisms. For example, microsatellite length changes are common within surface membrane proteins in yeast, providing rapid evolution in cell properties.<ref name="Bowen 2006">{{cite journal | vauthors = Bowen S, Wheals AE | title = Ser/Thr-rich domains are associated with genetic variation and morphogenesis in Saccharomyces cerevisiae | journal = Yeast | volume = 23 | issue = 8 | pages = 633–40 | date = June 2006 | pmid = 16823884 | doi = 10.1002/yea.1381 | s2cid = 25142061 | doi-access = free }}</ref> Specifically, length changes in the FLO1 gene control the level of adhesion to substrates.<ref name="Verstrepen 2005">{{cite journal | vauthors = Verstrepen KJ, Jansen A, Lewitter F, Fink GR | title = Intragenic tandem repeats generate functional variability | journal = Nature Genetics | volume = 37 | issue = 9 | pages = 986–90 | date = September 2005 | pmid = 16086015 | pmc = 1462868 | doi = 10.1038/ng1618 }}</ref> Short sequence repeats also provide rapid evolutionary change to surface proteins in pathenogenic bacteria; this may allow them to keep up with immunological changes in their hosts.<ref name="Moxon 1994">{{cite journal | vauthors = Moxon ER, Rainey PB, Nowak MA, Lenski RE | title = Adaptive evolution of highly mutable loci in pathogenic bacteria | journal = Current Biology | volume = 4 | issue = 1 | pages = 24–33 | date = January 1994 | pmid = 7922307 | doi = 10.1016/S0960-9822(00)00005-1 | bibcode = 1994CBio....4...24M | s2cid = 11203457 }}</ref> Length changes in short sequence repeats in a fungus (''[[Neurospora crassa]]'') control the duration of its [[circadian clock]] cycles.<ref name="Michael 2007">{{cite journal | vauthors = Michael TP, Park S, Kim TS, Booth J, Byer A, Sun Q, Chory J, Lee K | display-authors = 6 | title = Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock | journal = PLOS ONE | volume = 2 | issue = 8 | pages = e795 | date = August 2007 | pmid = 17726525 | pmc = 1949147 | doi = 10.1371/journal.pone.0000795 | bibcode = 2007PLoSO...2..795M | doi-access = free }}</ref>

===Effects on gene regulation===
Length changes of microsatellites within [[Promoter (genetics)|promoters]] and other [[Cis-regulatory element|cis-regulatory regions]] can change gene expression quickly, between generations. The human genome contains many (>16,000) short sequence repeats in regulatory regions, which provide 'tuning knobs' on the expression of many genes.<ref name="Gymrek 22–29"/><ref name="Rockman 2002">{{cite journal | vauthors = Rockman MV, Wray GA | title = Abundant raw material for cis-regulatory evolution in humans | journal = Molecular Biology and Evolution | volume = 19 | issue = 11 | pages = 1991–2004 | date = November 2002 | pmid = 12411608 | doi = 10.1093/oxfordjournals.molbev.a004023 | doi-access = free }}</ref>

Length changes in bacterial SSRs can affect [[Fimbria (bacteriology)|fimbriae]] formation in ''Haemophilus influenzae'', by altering promoter spacing.<ref name="Moxon 1994" /> Dinucleotide microsatellites are linked to abundant variation in cis-regulatory control regions in the human genome.<ref name="Rockman 2002" /> Microsatellites in control regions of the Vasopressin 1a receptor gene in voles influence their social behavior, and level of monogamy.<ref name="Hammock 2005">{{cite journal | vauthors = Hammock EA, Young LJ | title = Microsatellite instability generates diversity in brain and sociobehavioral traits | journal = Science | volume = 308 | issue = 5728 | pages = 1630–4 | date = June 2005 | pmid = 15947188 | doi = 10.1126/science.1111427 | bibcode = 2005Sci...308.1630H | s2cid = 18899853 }}</ref>

In [[Ewing sarcoma]] (a type of painful bone cancer in young humans), a point mutation has created an extended GGAA microsatellite which binds a transcription factor, which in turn activates the EGR2 gene which drives the cancer.<ref>{{cite journal | vauthors = Grünewald TG, Bernard V, Gilardi-Hebenstreit P, Raynal V, Surdez D, Aynaud MM, Mirabeau O, Cidre-Aranaz F, Tirode F, Zaidi S, Perot G, Jonker AH, Lucchesi C, Le Deley MC, Oberlin O, Marec-Bérard P, Véron AS, Reynaud S, Lapouble E, Boeva V, Rio Frio T, Alonso J, Bhatia S, Pierron G, Cancel-Tassin G, Cussenot O, Cox DG, Morton LM, Machiela MJ, Chanock SJ, Charnay P, Delattre O | display-authors = 6 | title = Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite | journal = Nature Genetics | volume = 47 | issue = 9 | pages = 1073–8 | date = September 2015 | pmid = 26214589 | pmc = 4591073 | doi = 10.1038/ng.3363 }}</ref> In addition, other GGAA microsatellites may influence the expression of genes that contribute to the clinical outcome of Ewing sarcoma patients.<ref>{{cite journal | vauthors = Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MM, Mirabeau O, Mazor G, Varon M, Hölting TL, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hartmann W, Dirksen U, Gymrek M, Anderson ND, Shlien A, Rotblat B, Kirchner T, Delattre O, Grünewald TG | display-authors = 6 | title = Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes | journal = Nature Communications | volume = 10 | issue = 1 | pages = 4128 | date = September 2019 | pmid = 31511524 | pmc = 6739408 | doi = 10.1038/s41467-019-12071-2 | bibcode = 2019NatCo..10.4128M }}</ref>

===Effects within introns===
Microsatellites within [[intron]]s also influence phenotype, through means that are not currently understood. For example, a GAA triplet expansion in the first intron of the X25 gene appears to interfere with transcription, and causes [[Friedreich's ataxia]].<ref name="Bidichandani 1998">{{cite journal | vauthors = Bidichandani SI, Ashizawa T, Patel PI | title = The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA structure | journal = American Journal of Human Genetics | volume = 62 | issue = 1 | pages = 111–21 | date = January 1998 | pmid = 9443873 | pmc = 1376805 | doi = 10.1086/301680 }}</ref> Tandem repeats in the first intron of the Asparagine synthetase gene are linked to acute lymphoblastic leukaemia.<ref name="Akagi 2008">{{cite journal | vauthors = Akagi T, Yin D, Kawamata N, Bartram CR, Hofmann WK, Song JH, Miller CW, den Boer ML, Koeffler HP | display-authors = 6 | title = Functional analysis of a novel DNA polymorphism of a tandem repeated sequence in the asparagine synthetase gene in acute lymphoblastic leukemia cells | journal = Leukemia Research | volume = 33 | issue = 7 | pages = 991–6 | date = July 2009 | pmid = 19054556 | pmc = 2731768 | doi = 10.1016/j.leukres.2008.10.022 }}</ref> A repeat polymorphism in the fourth intron of the NOS3 gene is linked to hypertension in a Tunisian population.<ref name="Jemaa 2008">{{cite journal | vauthors = Jemaa R, Ben Ali S, Kallel A, Feki M, Elasmi M, Taieb SH, Sanhaji H, Omar S, Kaabachi N | display-authors = 6 | title = Association of a 27-bp repeat polymorphism in intron 4 of endothelial constitutive nitric oxide synthase gene with hypertension in a Tunisian population | journal = Clinical Biochemistry | volume = 42 | issue = 9 | pages = 852–6 | date = June 2009 | pmid = 19111531 | doi = 10.1016/j.clinbiochem.2008.12.002 }}</ref> Reduced repeat lengths in the EGFR gene are linked with osteosarcomas.<ref name="Kersting 2008">{{cite journal | vauthors = Kersting C, Agelopoulos K, Schmidt H, Korsching E, August C, Gosheger G, Dirksen U, Juergens H, Winkelmann W, Brandt B, Bielack S, Buerger H, Gebert C | display-authors = 6 | title = Biological importance of a polymorphic CA sequence within intron 1 of the epidermal growth factor receptor gene (EGFR) in high grade central osteosarcomas | journal = Genes, Chromosomes & Cancer | volume = 47 | issue = 8 | pages = 657–64 | date = August 2008 | pmid = 18464244 | doi = 10.1002/gcc.20571 | s2cid = 19472307 | doi-access = free }}</ref>

An archaic form of splicing preserved in [[zebrafish]] is known to use microsatellite sequences within intronic mRNA for the removal of introns in the absence of U2AF2 and other splicing machinery. It is theorized that these sequences form highly stable [[Cloverleaf model of tRNA|cloverleaf]] configurations that bring the 3' and 5' intron splice sites into close proximity, effectively replacing the [[spliceosome]]. This method of RNA splicing is believed to have diverged from human evolution at the formation of [[tetrapod]]s and to represent an artifact of an [[RNA world]].<ref>{{cite journal | vauthors = Lin CL, Taggart AJ, Lim KH, Cygan KJ, Ferraris L, Creton R, Huang YT, Fairbrother WG | display-authors = 6 | title = RNA structure replaces the need for U2AF2 in splicing | journal = Genome Research | volume = 26 | issue = 1 | pages = 12–23 | date = January 2016 | pmid = 26566657 | pmc = 4691745 | doi = 10.1101/gr.181008.114 }}</ref>

===Effects within transposons===
Almost 50% of the human genome is contained in various types of transposable elements (also called transposons, or 'jumping genes'), and many of them contain repetitive DNA.<ref name="Sherer 2008">{{cite book | vauthors = Scherer S |date=2008 |title=A short guide to the human genome |location=New York |publisher=Cold Spring Harbor University Press}}</ref> It is probable that short sequence repeats in those locations are also involved in the regulation of gene expression.<ref name="Tomilin 2008">{{cite journal | vauthors = Tomilin NV | title = Regulation of mammalian gene expression by retroelements and non-coding tandem repeats | journal = BioEssays | volume = 30 | issue = 4 | pages = 338–48 | date = April 2008 | pmid = 18348251 | doi = 10.1002/bies.20741 | doi-access = free }}</ref>