Editing Microsatellite

{{Short description|Repeating sequences of 2–13 base pairs of DNA}}
{{About|the DNA sequence|small orbiting spacecraft|Microsatellite (spaceflight)}}

A '''microsatellite''' is a tract of repetitive [[DNA]] in which certain [[Sequence motif|DNA motifs]] (ranging in length from one to six or more [[base pairs]]) are repeated, typically 5–50 times.<ref name="Richard 2008"/><ref>{{cite journal | vauthors = Tóth G, Gáspári Z, Jurka J | title = Microsatellites in different eukaryotic genomes: survey and analysis | journal = Genome Research | volume = 10 | issue = 7 | pages = 967–981 | date = July 2000 | pmid = 10899146 | pmc = 310925 | doi = 10.1101/gr.10.7.967 }}</ref> Microsatellites occur at thousands of locations within an organism's [[genome]]. They have a higher [[mutation]] rate than other areas of DNA<ref name="Brinkmann-1998"/> leading to high [[genetic diversity]]. Microsatellites are often referred to as '''short tandem repeats''' ('''STRs''') by [[forensic genetics|forensic geneticists]] and in [[genetic genealogy]], or as '''simple sequence repeats''' ('''SSRs''') by plant geneticists.<ref>{{MeshName|Short+Tandem+Repeat}}</ref>

Microsatellites and their longer cousins, the [[minisatellite]]s, together are classified as [[variable number tandem repeat|VNTR]] (variable number of [[tandem repeat]]s) DNA. The name [[Satellite DNA|"satellite" DNA]] refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA.<ref name="Kit1">{{cite journal | vauthors = Kit S | title = Equilibrium sedimentation in density gradients of DNA preparations from animal tissues | journal = Journal of Molecular Biology | volume = 3 | issue = 6 | pages = 711–6 | date = December 1961 | pmid = 14456492 | doi = 10.1016/S0022-2836(61)80075-2 }}</ref>

They are widely used for [[DNA profiling]] in [[Loss of heterozygosity#Detection|cancer diagnosis]], in [[kinship]] analysis (especially [[DNA paternity testing|paternity testing]]) and in forensic identification. They are also used in [[genetic linkage]] analysis to locate a gene or a mutation responsible for a given trait or disease. Microsatellites are also used in [[population genetics]] to measure levels of relatedness between subspecies, groups and individuals.

==History==
Although the first microsatellite was characterised in 1984 at the [[University of Leicester]] by Weller, [[Alec Jeffreys|Jeffreys]] and colleagues as a polymorphic GGAT repeat in the human [[myoglobin]] gene, the term "microsatellite" was introduced later, in 1989, by Litt and Luty.<ref name="Richard 2008"/> The name [[Satellite DNA|"satellite" DNA]] refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA.<ref name="Kit1"/> The increasing availability of DNA amplification by PCR at the beginning of the 1990s triggered a large number of studies using the amplification of microsatellites as genetic markers for forensic medicine, for paternity testing, and for positional cloning to find the gene underlying a trait or disease. Prominent early applications include the identifications by microsatellite genotyping of the eight-year-old skeletal remains of a British murder victim ([[Erika Hagelberg|Hagelberg]] et al. 1991), and of the Auschwitz concentration camp doctor [[Josef Mengele]] who escaped to South America following World War II ([[Alec Jeffreys|Jeffreys]] et al. 1992).<ref name="Richard 2008"/>

==Structures, locations, and functions==
A microsatellite is a tract of tandemly repeated (i.e. adjacent) DNA motifs that range in length from one to six or up to ten nucleotides (the exact definition and delineation to the longer minisatellites varies from author to author),<ref name="Richard 2008"/><ref name="Gulcher2012"/> and are typically repeated 5–50 times. For example, the sequence TATATATATA is a dinucleotide microsatellite, and GTCGTCGTCGTCGTC is a trinucleotide microsatellite (with A being [[Adenine]], G [[Guanine]], C [[Cytosine]], and T [[Thymine]]). Repeat units of four and five nucleotides are referred to as tetra- and pentanucleotide motifs, respectively. Most [[eukaryote]]s have microsatellites, with the notable exception of some yeast species. Microsatellites are distributed throughout the genome.<ref name="King 1997">{{cite journal | vauthors = King DG, Soller M, Kashi Y |year=1997 |title=Evolutionary tuning knobs  | journal=Endeavour |volume=21 |issue=1 |pages=36–40 |doi=10.1016/S0160-9327(97)01005-3}}</ref><ref name="Richard 2008">{{cite journal | author1 = Richard GF | author2 = Kerrest A | author3 = Dujon B | author-link3 = Bernard Dujon| 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><ref>{{Cite journal| vauthors = Chistiakov DA, Hellemans B, Volckaert FA |date=2006-05-31|title=Microsatellites and their genomic distribution, evolution, function and applications: A review with special reference to fish genetics | journal=Aquaculture|volume=255|issue=1–4|pages=1–29|doi=10.1016/j.aquaculture.2005.11.031|bibcode=2006Aquac.255....1C }}</ref> The human genome for example contains 50,000–100,000 dinucleotide microsatellites, and lesser numbers of tri-, tetra- and pentanucleotide microsatellites.<ref name="Turnpenny 2005">{{cite book | vauthors = Turnpenny P, Ellard S |date=2005 |title=Emery's Elements of Medical Genetics |url=https://archive.org/details/emeryselementsof0000turn_12ed |url-access=registration |edition=12th |location=London |publisher=Elsevier|isbn=9780443100451 }}</ref> Many are located in non-coding parts of the human genome and therefore do not produce proteins, but they can also be located in regulatory regions and [[coding region]]s.

Microsatellites in non-coding regions may not have any specific function, and therefore might not be [[Natural selection|selected]] against; this allows them to accumulate mutations unhindered over the generations and gives rise to variability that can be used for DNA fingerprinting and identification purposes. Other microsatellites are located in regulatory flanking or [[intronic]] regions of genes, or directly in [[codon]]s of genes&nbsp;– microsatellite mutations in such cases can lead to phenotypic changes and diseases, notably in [[Trinucleotide repeat disorder|triplet expansion diseases]] such as [[fragile X syndrome]] and [[Huntington's disease]].<ref name="Pearson 2005"/>

[[Telomeres]] are linear sequences of DNA that sit at the very ends of chromosomes and protect the integrity of genomic material (not unlike an [[aglet]] on the end of a shoelace) during successive rounds of cell division due to the "end replication problem".<ref name="Gulcher2012" /> In white blood cells, the gradual shortening of telomeric DNA has been shown to inversely correlate with [[ageing]] in several sample types.<ref>{{cite journal | vauthors = Goldman EA, Eick GN, Compton D, Kowal P, Snodgrass JJ, Eisenberg DT, Sterner KN | title = Evaluating minimally invasive sample collection methods for telomere length measurement | journal = American Journal of Human Biology | volume = 30 | issue = 1 | pages = e23062 | date = January 2018 | pmid = 28949426 | pmc = 5785450 | doi = 10.1002/ajhb.23062 }}</ref> Telomeres consist of repetitive DNA, with the hexanucleotide repeat motif TTAGGG in vertebrates.{{Citation needed|date=June 2022}} They are thus classified as [[minisatellite]]s. Similarly, insects have shorter repeat motifs in their telomeres that could arguably be considered microsatellites.{{Citation needed|date=June 2022}}

==Mutation mechanisms and mutation rates==
[[File:STR-Slippage Dr.Peter Forster.jpg|thumb|DNA strand slippage during replication of an STR locus. Boxes symbolize repetitive DNA units. Arrows indicate the direction in which a new DNA strand (white boxes) is being replicated from the template strand (black boxes). Three situations during DNA replication are depicted. (a) Replication of the STR locus has proceeded without a mutation. (b) Replication of the STR locus has led to a gain of one unit owing to a loop in the new strand; the aberrant loop is stabilized by flanking units complementary to the opposite strand. (c) Replication of the STR locus has led to a loss of one unit owing to a loop in the template strand. (Forster et al. 2015)]]
Unlike [[point mutations]], which affect only a single nucleotide, microsatellite mutations lead to the gain or loss of an entire repeat unit, and sometimes two or more repeats simultaneously. Thus, the [[mutation rate]] at microsatellite [[Locus (genetics)|loci]] is expected to differ from other mutation rates, such as base substitution rates.<ref>{{cite journal |author1 = Jeffreys AJ|author-link1 =Alec Jeffreys|author2 =  Wilson V|author3 =  Thein SL|author-link3 =
Swee Lay Thein| title = Hypervariable 'minisatellite' regions in human DNA | journal = Nature | volume = 314 | issue = 6006 | pages = 67–73 | date = 1985 | pmid = 3856104 | doi = 10.1038/314067a0 | s2cid = 4356170 | bibcode = 1985Natur.314...67J }}</ref><ref name="Andreasson">{{cite journal | vauthors = Andreassen R, Egeland T, Olaisen B | title = Mutation rate in the hypervariable VNTR g3 (D7S22) is affected by allele length and a flanking DNA sequence polymorphism near the repeat array | journal = American Journal of Human Genetics | volume = 59 | issue = 2 | pages = 360–367 | date = August 1996 | pmid = 8755922 | pmc = 1914730 }}</ref> The mutation rate at microsatellite loci depends on the repeat motif sequence, the number of repeated motif units and the purity of the canonical repeated sequence.<ref name="Molecular basis of genetic instabil">{{cite journal | vauthors = Wells RD | title = Molecular basis of genetic instability of triplet repeats | journal = The Journal of Biological Chemistry | volume = 271 | issue = 6 | pages = 2875–2878 | date = February 1996 | pmid = 8621672 | doi = 10.1074/jbc.271.6.2875 | doi-access = free }}</ref>  A variety of mechanisms for mutation of microsatellite loci have been reviewed,<ref name="Molecular basis of genetic instabil"/><ref>{{cite journal | vauthors = Hancock JM, Santibáñez-Koref MF | title = Trinucleotide expansion diseases in the context of micro- and minisatellite evolution, Hammersmith Hospital, April 1-3, 1998 | journal = The EMBO Journal | volume = 17 | issue = 19 | pages = 5521–5524 | date = October 1998 | pmid = 9755151 | pmc = 1170879 | doi = 10.1093/emboj/17.19.5521 }}</ref>  and their resulting polymorphic nature has been quantified.<ref name="Biological effects">{{cite journal | vauthors = Wren JD, Forgacs E, Fondon JW, Pertsemlidis A, Cheng SY, Gallardo T, Williams RS, Shohet RV, Minna JD, Garner HR | display-authors = 6 | title = Repeat polymorphisms within gene regions: phenotypic and evolutionary implications | journal = American Journal of Human Genetics | volume = 67 | issue = 2 | pages = 345–356 | date = August 2000 | pmid = 10889045 | pmc = 1287183 | doi = 10.1086/303013 }}</ref> The actual cause of mutations in microsatellites is debated.

One proposed cause of such length changes is replication slippage, caused by mismatches between DNA strands while being replicated during [[meiosis]].<ref name="Tautz 1994">{{cite journal | vauthors = Tautz D | title = Simple sequences | journal = Current Opinion in Genetics & Development | volume = 4 | issue = 6 | pages = 832–7 | date = December 1994 | pmid = 7888752 | doi = 10.1016/0959-437X(94)90067-1 }}</ref> [[DNA polymerase]], the enzyme responsible for reading DNA during replication, can slip while moving along the template strand and continue at the wrong nucleotide. DNA polymerase slippage is more likely to occur when a repetitive sequence (such as CGCGCG) is replicated. Because microsatellites consist of such repetitive sequences, DNA polymerase may make errors at a higher rate in these sequence regions. Several studies have found evidence that slippage is the cause of microsatellite mutations.<ref name="Klintschar 2004">{{cite journal | vauthors = Klintschar M, Dauber EM, Ricci U, Cerri N, Immel UD, Kleiber M, Mayr WR | title = Haplotype studies support slippage as the mechanism of germline mutations in short tandem repeats | journal = Electrophoresis | volume = 25 | issue = 20 | pages = 3344–8 | date = October 2004 | pmid = 15490457 | doi = 10.1002/elps.200406069 | s2cid = 22298567 }}</ref><ref name="Forster 2015">{{cite journal | vauthors = Forster P, Hohoff C, Dunkelmann B, Schürenkamp M, Pfeiffer H, Neuhuber F, Brinkmann B | title = Elevated germline mutation rate in teenage fathers | journal = Proceedings. Biological Sciences | volume = 282 | issue = 1803 | pages = 20142898 | date = March 2015 | pmid = 25694621 | pmc = 4345458 | doi = 10.1098/rspb.2014.2898 }}</ref> Typically, slippage in each microsatellite occurs about once per 1,000 generations.<ref name="Weber 1993">{{cite journal | vauthors = Weber JL, Wong C | title = Mutation of human short tandem repeats | journal = Human Molecular Genetics | volume = 2 | issue = 8 | pages = 1123–8 | date = August 1993 | pmid = 8401493 | doi = 10.1093/hmg/2.8.1123 | doi-access = free }}</ref> Thus, slippage changes in repetitive DNA are three orders of magnitude more common than [[point mutation]]s in other parts of the genome.<ref name="Jarne 1996">{{cite journal | vauthors = Jarne P, Lagoda PJ | title = Microsatellites, from molecules to populations and back | journal = Trends in Ecology & Evolution | volume = 11 | issue = 10 | pages = 424–9 | date = October 1996 | pmid = 21237902 | doi = 10.1016/0169-5347(96)10049-5 }}</ref> Most slippage results in a change of just one repeat unit, and slippage rates vary for different allele lengths and repeat unit sizes,<ref name="Brinkmann-1998">{{cite journal | vauthors = Brinkmann B, Klintschar M, Neuhuber F, Hühne J, Rolf B | title = Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat | journal = American Journal of Human Genetics | volume = 62 | issue = 6 | pages = 1408–15 | date = June 1998 | pmid = 9585597 | pmc = 1377148 | doi = 10.1086/301869 }}</ref> and within different species.<ref name="Kruglyak 1998">{{cite journal | vauthors = Kruglyak S, Durrett RT, Schug MD, Aquadro CF | title = Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 18 | pages = 10774–8 | date = September 1998 | pmid = 9724780 | pmc = 27971 | doi = 10.1073/pnas.95.18.10774 | bibcode = 1998PNAS...9510774K | doi-access = free }}</ref><ref>{{cite journal | vauthors = Laidlaw J, Gelfand Y, Ng KW, Garner HR, Ranganathan R, Benson G, Fondon JW | title = Elevated basal slippage mutation rates among the Canidae | journal = The Journal of Heredity | volume = 98 | issue = 5 | pages = 452–460 | date = 1 July 2007 | pmid = 17437958 | doi = 10.1093/jhered/esm017 | doi-access = free }}</ref><ref name="Mutation mechanisms and rates">{{cite journal | vauthors = Lian Y, Garner HR | title = Evidence for the regulation of alternative splicing via complementary DNA sequence repeats | journal = Bioinformatics | volume = 21 | issue = 8 | pages = 1358–1364 | date = April 2005 | pmid = 15673565 | doi = 10.1093/bioinformatics/bti180 | doi-access = free }}</ref> If there is a large size difference between individual alleles, then there may be increased instability during recombination at meiosis.<ref name="Jarne 1996"/>

Another possible cause of microsatellite mutations are point mutations, where only one nucleotide is incorrectly copied during replication. A study comparing human and primate genomes found that most changes in repeat number in short microsatellites appear due to point mutations rather than slippage.<ref name="Amos-2010">{{cite journal | vauthors = Amos W | title = Mutation biases and mutation rate variation around very short human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments | journal = Journal of Molecular Evolution | volume = 71 | issue = 3 | pages = 192–201 | date = September 2010 | pmid = 20700734 | doi = 10.1007/s00239-010-9377-4 | bibcode = 2010JMolE..71..192A | s2cid = 1424625 }}</ref>

===Microsatellite mutation rates===
Direct estimates of microsatellite mutation rates have been made in numerous organisms, from insects to humans. In the [[desert locust]] ''Schistocerca gregaria'', the microsatellite mutation rate was estimated at 2.1&nbsp;× 10<sup>−4</sup> per generation per locus.<ref name="Chapuis-2015">{{cite journal | vauthors = Chapuis MP, Plantamp C, Streiff R, Blondin L, Piou C | title = Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations | journal = Molecular Ecology | volume = 24 | issue = 24 | pages = 6107–19 | date = December 2015 | pmid = 26562076 | doi = 10.1111/mec.13465 | s2cid = 33307624 | doi-access = free | bibcode = 2015MolEc..24.6107C }}</ref> The microsatellite mutation rate in human male germ lines is five to six times higher than in female germ lines and ranges from 0 to 7&nbsp;× 10<sup>−3</sup> per locus per gamete per generation.<ref name="Brinkmann-1998"/> In the nematode ''[[Pristionchus pacificus]]'', the estimated microsatellite mutation rate ranges from 8.9&nbsp;× 10<sup>−5</sup> to 7.5&nbsp;× 10<sup>−4</sup> per locus per generation.<ref name="Molnar-2012">{{cite journal | vauthors = Molnar RI, Witte H, Dinkelacker I, Villate L, Sommer RJ | title = Tandem-repeat patterns and mutation rates in microsatellites of the nematode model organism Pristionchus pacificus | journal = G3 | volume = 2 | issue = 9 | pages = 1027–34 | date = September 2012 | pmid = 22973539 | pmc = 3429916 | doi = 10.1534/g3.112.003129 }}</ref>

Microsatellite mutation rates vary with base position relative to the microsatellite, repeat type, and base identity.<ref name="Amos-2010"/> Mutation rate rises specifically with repeat number, peaking around six to eight repeats and then decreasing again.<ref name="Amos-2010"/> Increased heterozygosity in a population will also increase microsatellite mutation rates,<ref name="Amos-2016">{{cite journal | vauthors = Amos W | title = Heterozygosity increases microsatellite mutation rate | journal = Biology Letters | volume = 12 | issue = 1 | pages = 20150929 | date = January 2016 | pmid = 26740567 | pmc = 4785931 | doi = 10.1098/rsbl.2015.0929 }}</ref> especially when there is a large length difference between alleles. This is likely due to [[homologous chromosomes]] with arms of unequal lengths causing instability during meiosis.<ref name="Amos-Rubinsztein-1996">{{cite journal | vauthors = Amos W, Sawcer SJ, Feakes RW, Rubinsztein DC | title = Microsatellites show mutational bias and heterozygote instability | journal = Nature Genetics | volume = 13 | issue = 4 | pages = 390–1 | date = August 1996 | pmid = 8696328 | doi = 10.1038/ng0896-390 | s2cid = 6086527 }}</ref>

==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>

==Applications==
Microsatellites are used for assessing chromosomal DNA deletions in cancer diagnosis. Microsatellites are widely used for [[DNA profiling]], also known as "genetic fingerprinting", of crime stains (in forensics) and of tissues (in transplant patients).  They are also widely used in [[kinship]] analysis (most commonly in paternity testing). Also, microsatellites are used for mapping locations  within the genome, specifically in [[genetic linkage]] analysis to locate a gene or a mutation responsible for a given trait or disease. As a special case of mapping, they can be used for studies of [[gene duplication]] or [[genetic deletion|deletion]]. Researchers use microsatellites in [[population genetics]] and in species conservation projects. Plant geneticists have proposed the use of microsatellites for [[marker assisted selection]] of desirable traits in plant breeding.

===Cancer diagnosis===
In [[tumour]] cells, whose controls on replication are damaged, microsatellites may be gained or lost at an especially high frequency during each round of [[mitosis]]. Hence a tumour cell line might show a different [[genetic fingerprint]] from that of the host tissue, and, especially in [[colorectal cancer]], might present with [[loss of heterozygosity]].<ref name="Cancer Diagnostics">{{cite journal | vauthors = Wistuba II, Behrens C, Virmani AK, Mele G, Milchgrub S, Girard L, Fondon JW, Garner HR, McKay B, Latif F, Lerman MI, Lam S, Gazdar AF, Minna JD | display-authors = 6 | title = High resolution chromosome 3p allelotyping of human lung cancer and preneoplastic/preinvasive bronchial epithelium reveals multiple, discontinuous sites of 3p allele loss and three regions of frequent breakpoints | journal = Cancer Research | volume = 60 | issue = 7 | pages = 1949–1960 | date = April 2000 | pmid = 10766185 }}</ref><ref>{{cite journal | vauthors = Forgacs E, Wren JD, Kamibayashi C, Kondo M, Xu XL, Markowitz S, Tomlinson GE, Muller CY, Gazdar AF, Garner HR, Minna JD | display-authors = 6 | title = Searching for microsatellite mutations in coding regions in lung, breast, ovarian and colorectal cancers | journal = Oncogene | volume = 20 | issue = 8 | pages = 1005–1009 | date = February 2001 | pmid = 11314036 | doi = 10.1038/sj.onc.1204211 | s2cid = 22893621 | doi-access = free }}</ref> Microsatellites analyzed in primary tissue therefore been routinely used in cancer diagnosis to assess tumour progression.<ref name="vanTilborg2012">{{cite journal | vauthors = van Tilborg AA, Kompier LC, Lurkin I, Poort R, El Bouazzaoui S, van der Keur K, Zuiverloon T, Dyrskjot L, Orntoft TF, Roobol MJ, Zwarthoff EC | display-authors = 6 | title = Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood | journal = PLOS ONE | volume = 7 | issue = 8 | pages = e43345 | year = 2012 | pmid = 22927958 | pmc = 3425555 | doi = 10.1371/journal.pone.0043345 | doi-access = free | bibcode = 2012PLoSO...743345V }}</ref><ref name="Sideris&Papagrigoriadis2014">{{cite journal | vauthors = Sideris M, Papagrigoriadis S | title = Molecular biomarkers and classification models in the evaluation of the prognosis of colorectal cancer | journal = Anticancer Research | volume = 34 | issue = 5 | pages = 2061–2068 | date = May 2014 | pmid = 24778007 }}</ref><ref name="Boland1998">{{cite journal | vauthors = Boland CR, Thibodeau SN, Hamilton SR, Sidransky D, Eshleman JR, Burt RW, Meltzer SJ, Rodriguez-Bigas MA, Fodde R, Ranzani GN, Srivastava S | display-authors = 6 | title = A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer | journal = Cancer Research | volume = 58 | issue = 22 | pages = 5248–5257 | date = November 1998 | pmid = 9823339 }}</ref> Genome Wide Association Studies (GWAS) have been used to identify microsatellite biomarkers as a source of genetic predisposition in a variety of cancers.<ref name="Rivero et al">{{cite journal | vauthors = Rivero-Hinojosa S, Kinney N, Garner HR, Rood BR | title = Germline microsatellite genotypes differentiate children with medulloblastoma | journal = Neuro-Oncology | volume = 22 | issue = 1 | pages = 152–162 | date = January 2020 | pmid = 31562520 | doi = 10.1093/neuonc/noz179 | pmc = 6954392 }}</ref><ref name="Kinney">{{cite journal | vauthors = Kinney N, Varghese RT, Anandakrishnan R, Garner HR | title = ''ZDHHC3'' as a Risk and Mortality Marker for Breast Cancer in African American Women | journal = Cancer Informatics | volume = 16 | pages = 1176935117746644 | date = 2017 | pmid = 29276372 | doi = 10.1177/1176935117746644 | pmc = 5734450 | s2cid = 32129259 }}</ref><ref name="Velmurugan">{{cite journal | vauthors = Velmurugan KR, Varghese RT, Fonville NC, Garner HR | title = High-depth, high-accuracy microsatellite genotyping enables precision lung cancer risk classification | journal = Oncogene | volume = 36 | issue = 46 | pages = 6383–6390 | date = November 2017 | pmid = 28759038 | doi = 10.1038/onc.2017.256 | pmc = 5701090 | s2cid = 21655592 }}</ref>

[[File:Str profile.jpg|thumb|400px|A partial human STR profile obtained using the [[Applied Biosystems]] Identifiler kit]]

=== Forensic and medical fingerprinting ===
Microsatellite analysis became popular in the field of [[forensics]] in the 1990s.<ref name=":0" /> It is used for the [[genetic fingerprinting]] of individuals where it permits forensic identification (typically matching a crime stain to a victim or perpetrator). It is also used to follow up [[bone marrow transplant]] patients.<ref name="pmid11669214">{{cite journal | vauthors = Antin JH, Childs R, Filipovich AH, Giralt S, Mackinnon S, Spitzer T, Weisdorf D | title = Establishment of complete and mixed donor chimerism after allogeneic lymphohematopoietic transplantation: recommendations from a workshop at the 2001 Tandem Meetings of the International Bone Marrow Transplant Registry and the American Society of Blood and Marrow Transplantation | journal = Biology of Blood and Marrow Transplantation | volume = 7 | issue = 9 | pages = 473–85 | year = 2001 | pmid = 11669214 | doi = 10.1053/bbmt.2001.v7.pm11669214 | doi-access = free }}</ref>

The microsatellites in use today for forensic analysis are all tetra- or penta-nucleotide repeats, as these give a high degree of error-free data while being short enough to survive degradation in non-ideal conditions.  Even shorter repeat sequences would tend to suffer from artifacts such as PCR stutter and preferential amplification, while longer repeat sequences would suffer more highly from environmental degradation and would amplify less well by [[polymerase chain reaction|PCR]].<ref name="interpol">{{cite web |title=DNA Profiling  | vauthors = Carracedo A |url= http://www.interpol.int/public/Forensic/dna/conference/DNAProfiling01.asp#note41 |archive-url=http://webarchive.loc.gov/all/20010927081712/http://www.interpol.int/public/forensic/dna/conference/dnaprofiling01.asp |archive-date=2001-09-27 |access-date=2010-09-20}}</ref> Another forensic consideration is that the person's [[medical privacy]] must be respected, so that forensic STRs are chosen which are non-coding, do not influence gene regulation, and are not usually trinucleotide STRs which could be involved in [[Trinucleotide repeat disorder|triplet expansion diseases]] such as [[Huntington's disease]]. Forensic STR profiles are stored in DNA databanks such as the [[UK National DNA Database]] (NDNAD), the American [[CODIS]] or the Australian NCIDD.

===Kinship analysis (paternity testing)===
[[Autosomal]] microsatellites are widely used for [[DNA profiling]] in [[kinship]] analysis (most commonly in paternity testing).<ref>{{cite journal | vauthors = Lászik A, Brinkmann B, Sótonyi P, Falus A | title = Automated fluorescent detection of a 10 loci multiplex for paternity testing | journal = Acta Biologica Hungarica | volume = 51 | issue = 1 | pages = 99–105 | date = 2000 | pmid = 10866366 | doi =  10.1007/BF03542970| s2cid = 28270630 }}</ref> Paternally inherited [[Y-STR]]s (microsatellites on the [[Y chromosome]]) are often used in [[genealogical DNA test]]ing.

===Genetic linkage analysis===
During the 1990s and the first several years of this millennium, microsatellites were the workhorse genetic markers for genome-wide scans to locate any gene responsible for a given phenotype or disease, using [[Mendelian inheritance#Law of Segregation of genes (the "First Law")|segregation]] observations across generations of a sampled pedigree. Although the rise of higher throughput and cost-effective [[single-nucleotide polymorphism]] (SNP) platforms led to the era of the SNP for genome scans, microsatellites remain highly informative measures of genomic variation for linkage and association studies. Their continued advantage lies in their greater allelic diversity than biallelic SNPs, thus microsatellites can differentiate alleles within a SNP-defined linkage disequilibrium block of interest. Thus, microsatellites have successfully led to discoveries of type 2 diabetes ([[TCF7L2]]) and prostate cancer genes (the 8q21 region).<ref name="Gulcher2012">{{cite journal | vauthors = Lu W, Zhang Y, Liu D, Songyang Z, Wan M | title = Telomeres-structure, function, and regulation | journal = Experimental Cell Research | volume = 319 | issue = 2 | pages = 133–141 | date = January 2013 | pmid = 23006819 | pmc = 4051234 | doi = 10.1016/j.yexcr.2012.09.005 }}</ref><ref name="Ott2015">{{cite journal | vauthors = Ott J, Wang J, Leal SM | title = Genetic linkage analysis in the age of whole-genome sequencing | journal = Nature Reviews. Genetics | volume = 16 | issue = 5 | pages = 275–284 | date = May 2015 | pmid = 25824869 | pmc = 4440411 | doi = 10.1038/nrg3908 }}</ref>

=== Population genetics ===
[[File:Consensus neighbor-joining tree of the 249 human populations and six chimpanzee populations.svg|thumb|[[Computational phylogenetics#Consensus Tree|Consensus]] [[neighbor-joining]] tree of 249 human populations and six chimpanzee populations. Created based on 246 microsatellite markers.<ref name="PembertonDeGiorgio2013">{{cite journal | vauthors = Pemberton TJ, DeGiorgio M, Rosenberg NA | title = Population structure in a comprehensive genomic data set on human microsatellite variation | journal = G3 | volume = 3 | issue = 5 | pages = 891–907 | date = May 2013 | pmid = 23550135 | pmc = 3656735 | doi = 10.1534/g3.113.005728 }}</ref>]]
Microsatellites were popularized in [[population genetics]] during the 1990s because as [[Polymerase chain reaction|PCR]] became ubiquitous in laboratories researchers were able to design primers and amplify sets of microsatellites at low cost. Their uses are wide-ranging.<ref>{{Cite journal| vauthors = Manel S, Schwartz MK, Luikart G, Taberlet P |date=2003-04-01|title=Landscape genetics: combining landscape ecology and population genetics | journal=Trends in Ecology & Evolution|volume=18|issue=4|pages=189–197|doi=10.1016/S0169-5347(03)00008-9|s2cid=2984426 }}</ref> A microsatellite with a neutral evolutionary history makes it applicable for measuring or inferring [[Population bottleneck|bottlenecks]],<ref>{{cite journal | vauthors = Spencer CC, Neigel JE, Leberg PL | title = Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks | journal = Molecular Ecology | volume = 9 | issue = 10 | pages = 1517–28 | date = October 2000 | pmid = 11050547 | doi = 10.1046/j.1365-294x.2000.01031.x | bibcode = 2000MolEc...9.1517S | s2cid = 22244000 }}</ref> [[local adaptation]],<ref>{{cite journal | vauthors = Nielsen R | title = Molecular signatures of natural selection | journal = Annual Review of Genetics | volume = 39 | issue = 1 | pages = 197–218 | date = 2005-01-01 | pmid = 16285858 | doi = 10.1146/annurev.genet.39.073003.112420 | s2cid = 3063754 }}</ref> the allelic [[fixation index]] (F<sub>ST</sub>),<ref>{{cite journal | vauthors = Slatkin M | title = A measure of population subdivision based on microsatellite allele frequencies | journal = Genetics | volume = 139 | issue = 1 | pages = 457–62 | date = January 1995 | doi = 10.1093/genetics/139.1.457 | pmid = 7705646 | pmc = 1206343 | url = http://www.genetics.org/content/139/1/457 }}</ref> [[population size]],<ref>{{cite journal | vauthors = Kohn MH, York EC, Kamradt DA, Haught G, Sauvajot RM, Wayne RK | title = Estimating population size by genotyping faeces | journal = Proceedings. Biological Sciences | volume = 266 | issue = 1420 | pages = 657–63 | date = April 1999 | pmid = 10331287 | pmc = 1689828 | doi = 10.1098/rspb.1999.0686 }}</ref> and [[gene flow]].<ref>{{cite journal | vauthors = Waits L, Taberlet P, Swenson JE, Sandegren F, Franzén R | title = Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos) | journal = Molecular Ecology | volume = 9 | issue = 4 | pages = 421–31 | date = April 2000 | pmid = 10736045 | doi = 10.1046/j.1365-294x.2000.00892.x | bibcode = 2000MolEc...9..421W | s2cid = 46475635 }}</ref> As [[next generation sequencing]] becomes more affordable the use of microsatellites has decreased, however they remain a crucial tool in the field.<ref>{{cite journal | vauthors = Allendorf FW, Hohenlohe PA, Luikart G | title = Genomics and the future of conservation genetics | journal = Nature Reviews. Genetics | volume = 11 | issue = 10 | pages = 697–709 | date = October 2010 | pmid = 20847747 | doi = 10.1038/nrg2844 | s2cid = 10811958 }}</ref>

===Plant breeding===
[[Marker assisted selection]] or marker aided selection (MAS) is an indirect selection process where a [[Trait (biology)|trait]] of interest is selected based on a [[Biological marker|marker]] ([[Morphology (biology)|morphological]], [[biochemical]] or [[DNA]]/[[RNA]] variation) linked to a trait of interest (e.g. productivity, disease resistance, stress tolerance, and quality), rather than on the trait itself. Microsatellites have been proposed to be used as such markers to assist plant breeding.<ref name="Miah2013">{{cite journal | vauthors = Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam K, Latif MA | title = A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance | journal = International Journal of Molecular Sciences | volume = 14 | issue = 11 | pages = 22499–528 | date = November 2013 | pmid = 24240810 | pmc = 3856076 | doi = 10.3390/ijms141122499 | doi-access = free }}</ref>

==Analysis==
[[File:Short Tandem Repeat (STR) analysis.png|thumb|300px|Short Tandem Repeat (STR) analysis on a simplified model using [[polymerase chain reaction]] (PCR): First, a DNA sample undergoes PCR with [[Primer (molecular biology)|primers]] targeting certain STRs (which vary in lengths between individuals and their [[allele]]s). The resultant fragments are separated by size (such as [[electrophoresis]]).<ref>Image by Mikael Häggström, MD, using following source image: [https://www.researchgate.net/figure/Principles-of-STR-analysis-STRs-loci-comprise-repetitive-sequences-of-2-7-bp-which-are_fig1_26513043 Figure 1 - available via license: Creative Commons Attribution 4.0 International"], from the following article:<br />{{cite journal|title=Using PCR for molecular monitoring of post-transplantation chimerism|url=https://www.researchgate.net/publication/26513043 |vauthors=Sitnik R, Torres MA, Bacal NS, Rebello Pinho JR|journal=Einstein |location=Sao Paulo |year=2006|volume=4|issue=2 |via=ResearchGate}}</ref>]]
Repetitive DNA is not easily analysed by [[DNA sequencing|next generation DNA sequencing]] methods, for some technologies struggle with [[Polymer#Structure|homopolymeric]] tracts. A variety of software approaches have been created for the analysis or raw nextgen DNA sequencing reads to determine the genotype and variants at repetitive loci.<ref name="Analysis">{{cite journal | author1 = Halman A| author2 = Oshlack A| author-link2 = Alicia Oshlack | title = Accuracy of short tandem repeats genotyping tools in whole exome sequencing data | journal = F1000Research | volume = 9 | pages = 200 | date = 2020 | pmid = 32665844 | doi = 10.12688/f1000research.22639.1 | pmc = 7327730 | s2cid = 213733005 | doi-access = free }}</ref><ref name="Rajan-Babu">{{cite journal | vauthors = Rajan-Babu IS, Peng JJ, Chiu R, Li C, Mohajeri A, Dolzhenko E, Eberle MA, Birol I, Friedman JM | display-authors = 6 | title = Correction to: Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions | journal = Genome Medicine | volume = 13 | issue = 1 | pages = 151 | date = September 2021 | pmid = 34517885 | doi = 10.1186/s13073-021-00961-4 | pmc = 8439056 | s2cid = 256019433 | doi-access = free }}</ref> Microsatellites can be analysed and verified by established PCR amplification and amplicon size determination, sometimes followed by [[DNA sequencing|Sanger DNA sequencing]].

In forensics, the analysis is performed by extracting [[nuclear DNA]] from the cells of a sample of interest, then amplifying specific [[polymorphism (biology)|polymorphic]] regions of the extracted DNA by means of the [[polymerase chain reaction]]. Once these sequences have been amplified, they are resolved either through [[gel electrophoresis]] or [[capillary electrophoresis]], which will allow the analyst to determine how many repeats of the microsatellites sequence in question there are.  If the DNA was resolved by gel electrophoresis, the DNA can be visualized either by [[silver stain]]ing (low sensitivity, safe, inexpensive), or an [[DNA intercalation|intercalating dye]] such as [[ethidium bromide]] (fairly sensitive, moderate health risks, inexpensive), or as most modern forensics labs use, [[Fluorescence|fluorescent dyes]] (highly sensitive, safe, expensive).<ref name="nist">{{cite web |title=Technology for Resolving STR Alleles |url=http://www.cstl.nist.gov/strbase/tech.htm |access-date=2010-09-20}}</ref> Instruments built to resolve microsatellite fragments by capillary electrophoresis also use fluorescent dyes.<ref name="nist"/> Forensic profiles are stored in major databanks. The [[United Kingdom|British]] data base for microsatellite loci identification was originally based on the British [[SGM+]] system<ref>{{cite web |title=The National DNA Database |url=http://www.parliament.uk/documents/post/postpn258.pdf |archive-url=https://web.archive.org/web/20101013140110/http://www.parliament.uk/documents/post/postpn258.pdf |archive-date=2010-10-13 |url-status=live |access-date=2010-09-20}}</ref><ref>{{cite web |title=House of Lords Select Committee on Science and Technology Written Evidence  |url=https://publications.parliament.uk/pa/ld199900/ldselect/ldsctech/115/115we20.htm |access-date=2010-09-20}}</ref> using 10 loci and a [[Amelogenin|sex marker]]. The Americans<ref>{{cite web |title=FBI CODIS Core STR Loci |url=http://www.cstl.nist.gov/strbase/fbicore.htm |access-date=2010-09-20}}</ref> increased this number to 13 loci.<ref name="Butler 2005">{{cite book | vauthors = Butler JM |date=2005|title=Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers, Second Edition |location=New York |publisher=Elsevier Academic Press}}</ref> The Australian database is called the NCIDD, and since 2013 it has been using 18 core markers for DNA profiling.<ref name=":0">{{Cite news |url= https://theconversation.com/from-the-crime-scene-to-the-courtroom-the-journey-of-a-dna-sample-82250 |title=From the crime scene to the courtroom: the journey of a DNA sample | vauthors = Curtis C, Hereward J |date=August 29, 2017|work=The Conversation }}</ref>

===Amplification===
Microsatellites can be amplified for identification by the [[polymerase chain reaction]] (PCR) process, using the unique sequences of flanking regions as [[Primer (molecular biology)|primers]].  DNA is repeatedly denatured at a high temperature to separate the double strand, then cooled to allow [[Annealing (biology)|annealing]] of primers and the extension of nucleotide sequences through the microsatellite.  This process results in production of enough DNA to be visible on [[Agarose gel electrophoresis|agarose]] or [[acrylamide|polyacrylamide]] gels; only small amounts of DNA are needed for amplification because in this way thermocycling creates an exponential increase in the replicated segment.<ref name="Griffiths">{{cite book |vauthors=Griffiths AJ, Miller JF, Suzuki DT, Lewontin RC, Gelbart WM |year=1996 |title=Introduction to Genetic Analysis |edition=5th |publisher=W.H. Freeman |location=New York}}</ref> With the abundance of PCR technology, primers that flank microsatellite loci are simple and quick to use, but the development of correctly functioning primers is often a tedious and costly process.[[File:PAGE AgStain Microsat.jpg|thumb|right|A number of DNA samples from specimens of ''[[Littorina plena]]'' amplified using polymerase chain reaction with primers targeting a variable simple sequence repeat (SSR, a.k.a. microsatellite) locus. Samples were run on a 5% polyacrylamide gel and visualized using silver staining.]]

===Design of microsatellite primers===
If searching for microsatellite markers in specific regions of a genome, for example within a particular [[intron]], primers can be designed manually. This involves searching the genomic DNA sequence for microsatellite repeats, which can be done by eye or by using automated tools such as [http://www.repeatmasker.org/ repeat masker]. Once the potentially useful microsatellites are determined, the flanking sequences can be used to design [[oligonucleotide]] primers which will amplify the specific microsatellite repeat in a PCR reaction.

Random microsatellite primers can be developed by [[cloning]] random segments of DNA from the focal species. These random segments are inserted into a [[plasmid]] or [[bacteriophage]] [[Cloning vector|vector]], which is in turn implanted into ''[[Escherichia coli]]'' bacteria. Colonies are then developed, and screened with fluorescently–labelled oligonucleotide sequences that will hybridize to a microsatellite repeat, if present on the DNA segment. If positive clones can be obtained from this procedure, the DNA is sequenced and PCR primers are chosen from sequences flanking such regions to determine a specific [[locus (genetics)|locus]]. This process involves significant trial and error on the part of researchers, as microsatellite repeat sequences must be predicted and primers that are randomly isolated may not display significant polymorphism.<ref name="Jarne 1996" /><ref name="Queller">{{cite journal | vauthors = Queller DC, Strassmann JE, Hughes CR | title = Microsatellites and kinship | journal = Trends in Ecology & Evolution | volume = 8 | issue = 8 | pages = 285–8 | date = August 1993 | pmid = 21236170 | doi = 10.1016/0169-5347(93)90256-O }}</ref> Microsatellite loci are widely distributed throughout the genome and can be isolated from semi-degraded DNA of older specimens, as all that is needed is a suitable substrate for amplification through PCR.

More recent techniques involve using oligonucleotide sequences consisting of repeats complementary to repeats in the microsatellite to "enrich" the DNA extracted ([[microsatellite enrichment]]). The oligonucleotide probe hybridizes with the repeat in the microsatellite, and the probe/microsatellite complex is then pulled out of solution. The enriched DNA is then cloned as normal, but the proportion of successes will now be much higher, drastically reducing the time required to develop the regions for use. However, which probes to use can be a trial and error process in itself.<ref name="Kaukinen">{{cite journal |vauthors=Kaukinen KH, Supernault KJ, and Miller KM |year=2004 |title=Enrichment of tetranucleotide microsatellite loci from invertebrate species |journal=Journal of Shellfish Research |volume=23 |issue=2 |page=621}}</ref>

===ISSR-PCR===
'''ISSR''' (for '''inter-simple sequence repeat''') is a general term for a genome region between microsatellite loci. The complementary sequences to two neighboring microsatellites are used as PCR primers<!-- Theor. Appl. Genet. 89, 998–1006. -->; the variable region between them gets amplified. The limited length of amplification cycles during PCR prevents excessive replication of overly long contiguous DNA sequences, so the result will be a mix of a variety of amplified DNA strands which are generally short but vary much in length.

Sequences amplified by ISSR-PCR can be used for DNA fingerprinting. Since an ISSR may be a conserved or nonconserved region, this technique is not useful for distinguishing individuals, but rather for [[phylogeography]] analyses<!-- Biota 3, 109–118. --> or maybe delimiting [[species]]<!-- Molecular Phylogenetics and Evolution 37 (2005) 389–401 -->; sequence diversity is lower than in SSR-PCR, but still higher than in actual gene sequences. In addition, microsatellite sequencing and ISSR sequencing are mutually assisting, as one produces primers for the other.

===Limitations===
Repetitive DNA is not easily analysed by [[DNA sequencing|next generation DNA sequencing]] methods, which struggle with homopolymeric tracts.<ref>{{cite journal | vauthors = Tytgat O, Gansemans Y, Weymaere J, Rubben K, Deforce D, Van Nieuwerburgh F | title = Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling | journal = Genes | volume = 11 | issue = 4 | pages = 381 | date = April 2020 | pmid = 32244632 | pmc = 7230633 | doi = 10.3390/genes11040381 | s2cid = 214786277 | doi-access = free }}</ref> Therefore, microsatellites are normally analysed by conventional PCR amplification and amplicon size determination. The use of PCR means that microsatellite length analysis is prone to PCR limitations like any other PCR-amplified DNA locus. A particular concern is the occurrence of '[[null allele]]s':
* Occasionally, within a sample of individuals such as in paternity testing casework, a mutation in the DNA flanking the microsatellite can prevent the PCR primer from binding and producing an amplicon (creating a "null allele" in a gel assay), thus only one allele is amplified (from the non-mutated sister chromosome), and the individual may then falsely appear to be homozygous. This can cause confusion in paternity casework. It may then be necessary to amplify the microsatellite using a different set of primers.<ref name="Jarne 1996"/><ref name="Dakin">{{cite journal | vauthors = Dakin EE, Avise JC | title = Microsatellite null alleles in parentage analysis | journal = Heredity | volume = 93 | issue = 5 | pages = 504–9 | date = November 2004 | pmid = 15292911 | doi = 10.1038/sj.hdy.6800545 | doi-access = free }}</ref> Null alleles are caused especially by mutations at the 3' section, where extension commences.
* In species or population analysis, for example in conservation work, PCR primers which amplify microsatellites in one individual or species can work in other species. However, the risk of applying PCR primers across different species is that null alleles become likely, whenever sequence divergence is too great for the primers to bind. The species may then artificially appear to have a reduced diversity. Null alleles in this case can sometimes be indicated by an excessive frequency of homozygotes causing deviations from Hardy-Weinberg equilibrium expectations.

== See also ==
{{cmn|
* [[Genetic marker]]
* [[Junk DNA]]
* [[LASARsat]]
* [[List of biological databases]]
* [[Long interspersed nucleotide elements]]
* [[Microsatellite instability]]
* [[Mobile element]]
* [[Satellite DNA]]
* [[Short interspersed element|Short interspersed repetitive element]]
* [[Simple sequence length polymorphism]] (SSLP)—a search tool
* [[Snpstr]]
* [[Strbase]]
* [[Earth Human STR Allele Frequencies Database]]
* [[Transposon]]
* [[UgMicroSatdb]]
}}

== References ==
{{Reflist|32em}}

== Further reading ==
{{Refbegin|32em}}
* {{cite journal | vauthors = Caporale LH | title = Natural selection and the emergence of a mutation phenotype: an update of the evolutionary synthesis considering mechanisms that affect genome variation | journal = Annual Review of Microbiology | volume = 57 | pages = 467–85 | year = 2003 | pmid = 14527288 | doi = 10.1146/annurev.micro.57.030502.090855 | url = https://zenodo.org/record/896811 }}
* {{cite journal  |vauthors=Kashi Y, etal |year=1997 |title=Simple sequence repeats as a source of quantitative genetic variation  | journal=Trends Genet. |volume=13 |issue=2 |pages=74–78 |doi=10.1016/S0168-9525(97)01008-1|pmid=9055609 }}
* {{cite journal | vauthors = Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJ, Koornneef M, Kakutani T | title = Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats | journal = The Plant Journal | volume = 49 | issue = 1 | pages = 38–45 | date = January 2007 | pmid = 17144899 | doi = 10.1111/j.1365-313X.2006.02936.x | hdl = 11858/00-001M-0000-0012-38D2-5 | url = http://edoc.mpg.de/get.epl?fid=61177&did=293463&ver=0 | hdl-access = free }}
* {{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 | doi-access = free | bibcode = 2002MolEc..11.2453L }}
* {{cite journal | vauthors = Li YC, Korol AB, Fahima T, Nevo E | title = Microsatellites within genes: structure, function, and evolution | journal = Molecular Biology and Evolution | volume = 21 | issue = 6 | pages = 991–1007 | date = June 2004 | pmid = 14963101 | doi = 10.1093/molbev/msh073 | doi-access = free }}
* {{cite journal | vauthors = Mattick JS | title = Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms | journal = BioEssays | volume = 25 | issue = 10 | pages = 930–9 | date = October 2003 | pmid = 14505360 | doi = 10.1002/bies.10332 | citeseerx = 10.1.1.476.7561 }}
* {{cite journal | vauthors = Meagher TR, Vassiliadis C | title = Phenotypic impacts of repetitive DNA in flowering plants | journal = The New Phytologist | volume = 168 | issue = 1 | pages = 71–80 | date = October 2005 | pmid = 16159322 | doi = 10.1111/j.1469-8137.2005.01527.x | doi-access = free }}
* {{cite journal | vauthors = Müller KJ, Romano N, Gerstner O, Garcia-Maroto F, Pozzi C, Salamini F, Rohde W | title = The barley Hooded mutation caused by a duplication in a homeobox gene intron | journal = Nature | volume = 374 | issue = 6524 | pages = 727–30 | date = April 1995 | pmid = 7715728 | doi = 10.1038/374727a0 | bibcode = 1995Natur.374..727M | s2cid = 4344876 }}
* {{cite journal | vauthors = Pumpernik D, Oblak B, Borstnik B | title = Replication slippage versus point mutation rates in short tandem repeats of the human genome | journal = Molecular Genetics and Genomics | volume = 279 | issue = 1 | pages = 53–61 | date = January 2008 | pmid = 17926066 | doi = 10.1007/s00438-007-0294-1 | s2cid = 20542422 }}
* {{cite journal |vauthors=Streelman JT, Kocher TD |year=2002 |title=Microsatellite variation associated with prolactin expression and growth of salt-challenged ''Tilapia'' | journal=Physiol. Genomics |volume=9 |issue= 1|pages=1–4|doi=10.1152/physiolgenomics.00105.2001 |pmid=11948285 |s2cid=8360732 }}
* {{cite journal | vauthors = Vinces MD, Legendre M, Caldara M, Hagihara M, Verstrepen KJ | title = Unstable tandem repeats in promoters confer transcriptional evolvability | journal = Science | volume = 324 | issue = 5931 | pages = 1213–6 | date = May 2009 | pmid = 19478187 | pmc = 3132887 | doi = 10.1126/science.1170097 | bibcode = 2009Sci...324.1213V }}
{{Refend}}

== External links ==
* [https://stripy.org/database All known disease-causing short tandem repeats]
* [https://data.ccmb.res.in/msdb/ MicroSatellite DataBase]
* Search tools:
** [http://www.dna-algo.co.za/downloads.htm FireMuSat2+] {{Webarchive|url=https://web.archive.org/web/20140221191007/http://www.dna-algo.co.za/downloads.htm |date=2014-02-21 }}
** [http://www.cdfd.org.in/imex IMEx] {{Webarchive|url=https://web.archive.org/web/20130914212105/http://www.cdfd.org.in/imex/ |date=2013-09-14 }}
** [http://ssr.nwisrl.ars.usda.gov/ Imperfect SSR Finder] {{Webarchive|url=https://web.archive.org/web/20210723015637/https://ssr.nwisrl.ars.usda.gov/ |date=2021-07-23 }}—find perfect or imperfect SSRs in [[FASTA format|FASTA]] sequences.
** [https://web.archive.org/web/20060404015058/http://bioinf.dms.med.uniroma1.it/JSTRING/ JSTRING—Java Search for Tandem Repeats In Genomes]
** [https://web.archive.org/web/20060709203109/http://www.biophp.org/minitools/microsatellite_repeats_finder/demo.php Microsatellite repeats finder]
** [http://pgrc.ipk-gatersleben.de/misa/misa.html MISA—MIcroSAtellite identification tool]
** [http://alggen.lsi.upc.edu/recerca/search/mrepatt/ MREPATT] {{Webarchive|url=https://web.archive.org/web/20090209132756/http://alggen.lsi.upc.edu/recerca/search/mrepatt/ |date=2009-02-09 }}
** [http://bioinfo.lifl.fr/mreps Mreps] {{Webarchive|url=https://web.archive.org/web/20110929023604/http://bioinfo.lifl.fr/mreps/ |date=2011-09-29 }}
** [http://www.rub.de/spezzoo/cm/cm_phobos.htm Phobos]—a tandem repeat search tool for perfect and imperfect repeats—the maximum pattern size depends only on computational power
** [http://www.bioinformatics.org/poly/ Poly]
** [http://www.kofler.or.at/bioinformatics/SciRoKo/index.html SciRoKo]
** [https://web.archive.org/web/20101020172857/http://www.csufresno.edu/ssrfinder/ SSR Finder]
** [http://atgc.lirmm.fr/star STAR]
** [https://bioserf.org SERF] De Novo Genome Analysis and Tandem Repeats Finder
** [http://tandem.bu.edu/trf/trf.html Tandem Repeats Finder]
** [https://web.archive.org/web/20060712070732/http://strand.imb.ac.ru/swan/index.html TandemSWAN]
** [http://www.sci.brooklyn.cuny.edu/~sokol/tandem TRED]
** [http://finder.sourceforge.net/ TROLL]
** [http://kbrin.a-bldg.louisville.edu/cgi-bin/Zv8/getRepeats.cgi?LinkageGroup=ALL&SeqBeg=47697593&SeqEnd=49399415&RptLen=ALL/ Zebrafish Repeats] {{Webarchive|url=https://web.archive.org/web/20190912163917/http://kbrin.a-bldg.louisville.edu/cgi-bin/Zv8/getRepeats.cgi?LinkageGroup=ALL&SeqBeg=47697593&SeqEnd=49399415&RptLen=ALL%2F |date=2019-09-12 }}

{{Repeated sequence}}
{{Authority control}}

[[Category:Genetics]]
[[Category:Forensic genetics]]
[[Category:Repetitive DNA sequences]]