Microsatellite

Repeating sequences of 2-13 base pairs of DNA

This article is about the DNA sequence. For small orbiting spacecraft, see Microsatellite (spaceflight).

A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times.[1][2] Microsatellites occur at thousands of locations within an organism's genome. They have a higher mutation rate than other areas of DNA[3] leading to high genetic diversity. Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as simple sequence repeats (SSRs) by plant geneticists.[4]

Microsatellites and their longer cousins, the minisatellites, together are classified as VNTR (variable number of tandem repeats) DNA. The name "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.[5]

They are widely used for DNA profiling in cancer diagnosis, in kinship analysis (especially 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.

## Contents

* 1 History
* 2 Structures, locations, and functions
* 3 Mutation mechanisms and mutation rates
* 3.1 Microsatellite mutation rates
* 4 Biological effects of microsatellite mutations
* 4.1 Effects on proteins
* 4.2 Effects on gene regulation
* 4.3 Effects within introns
* 4.4 Effects within transposons
* 5 Applications
* 5.1 Cancer diagnosis
* 5.2 Forensic and medical fingerprinting
* 5.3 Kinship analysis (paternity testing)
* 5.4 Genetic linkage analysis
* 5.5 Population genetics
* 5.6 Plant breeding
* 6 Analysis
* 6.1 Amplification
* 6.2 Design of microsatellite primers
* 6.3 ISSR-PCR
* 6.4 Limitations
* 7 See also
* 8 References
* 9 Further reading
* 10 External links

## History[edit | edit source]

Although the first microsatellite was characterised in 1984 at the University of Leicester by Weller, 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.[1] The name "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.[5] 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 (Hagelberg et al. 1991), and of the Auschwitz concentration camp doctor Josef Mengele who escaped to South America following World War II (Jeffreys et al. 1992).[1]

## Structures, locations, and functions[edit | edit source]

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),[1][2] 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 eukaryotes have microsatellites, with the notable exception of some yeast species. Microsatellites are distributed throughout the genome.[6][1][7] The human genome for example contains 50,000–100,000 dinucleotide microsatellites, and lesser numbers of tri-, tetra- and pentanucleotide microsatellites.[8] 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 regions.

Microsatellites in non-coding regions may not have any specific function, and therefore might not be 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 codons of genes – microsatellite mutations in such cases can lead to phenotypic changes and diseases, notably in triplet expansion diseases such as fragile X syndrome and Huntington's disease.[9]

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".[2] In white blood cells, the gradual shortening of telomeric DNA has been shown to inversely correlate with aging in several sample types.[10] Telomeres consist of repetitive DNA, with the hexanucleotide repeat motif TTAGGG in vertebrates.[citation needed] They are thus classified as minisatellites. Similarly, insects have shorter repeat motifs in their telomeres that could arguably be considered microsatellites.[citation needed]

## Mutation mechanisms and mutation rates[edit | edit source]

File:STR-Slippage Dr.Peter Forster.jpg

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 loci is expected to differ from other mutation rates, such as base substitution rates. 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.[11] 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.[12][13] Typically, slippage in each microsatellite occurs about once per 1,000 generations.[14] Thus, slippage changes in repetitive DNA are three orders of magnitude more common than point mutations in other parts of the genome.[15] Most slippage results in a change of just one repeat unit, and slippage rates vary for different allele lengths and repeat unit sizes,[3] and within different species.[16] If there is a large size difference between individual alleles, then there may be increased instability during recombination at meiosis.[15]

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.[17]

### Microsatellite mutation rates[edit | edit source]

Microsatellite mutation rates vary with base position relative to the microsatellite, repeat type, and base identity.[17] Mutation rate rises specifically with repeat number, peaking around six to eight repeats and then decreasing again.[17] Increased heterozygosity in a population will also increase microsatellite mutation rates,[18] 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.[19]

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 x 10−4 per generation per locus.[20] 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 x 10−3 per locus per gamete per generation.[3] In the nematode Pristionchus pacificus, the estimated microsatellite mutation rate ranges from 8.9 × 10−5 to 7.5 × 10−4 per locus per generation.[21]

## Biological effects of microsatellite mutations[edit | edit source]

Many microsatellites are located in non-coding DNA and are biologically silent. Others are located in regulatory or even coding DNA – 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.[22]

### Effects on proteins[edit | edit source]

In mammals, 20% to 40% of proteins contain repeating sequences of amino acids encoded by short sequence repeats.[23] 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.[24] 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.[25] 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.[26] This association also applies to a wider range of Carnivora species.[27] Length changes in polyalanine tracts within the HoxA13 gene are linked to Hand-Foot-Genital Syndrome, a developmental disorder in humans.[28] Length changes in other triplet repeats are linked to more than 40 neurological diseases in humans, notably triplet expansion diseases such as fragile X syndrome and Huntington's disease.[9] 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.[29] Specifically, length changes in the FLO1 gene control the level of adhesion to substrates.[30] 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.[31] Length changes in short sequence repeats in a fungus (Neurospora crassa) control the duration of its circadian clock cycles.[32]

### Effects on gene regulation[edit | edit source]

Length changes of microsatellites within promoters and other 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.[22][33]

Length changes in bacterial SSRs can affect fimbriae formation in Haemophilus influenzae, by altering promoter spacing.[31] Dinucleotide microsatellites are linked to abundant variation in cis-regulatory control regions in the human genome.[33] Microsatellites in control regions of the Vasopressin 1a receptor gene in voles influence their social behavior, and level of monogamy.[34]

In Ewing's 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.[35] In addition, other GGAA microsatellites may influence the expression of genes that contribute to the clinical outcome of Ewing sarcoma patients.[36]

### Effects within introns[edit | edit source]

Microsatellites within introns 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 Ataxia.[37] Tandem repeats in the first intron of the Asparagine synthetase gene are linked to acute lymphoblastic leukaemia.[38] A repeat polymorphism in the fourth intron of the NOS3 gene is linked to hypertension in a Tunisian population.[39] Reduced repeat lengths in the EGFR gene are linked with osteosarcomas.[40]

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 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 tetrapods and to represent an artifact of an RNA world.[41]

### Effects within transposons[edit | edit source]

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.[42] It is probable that short sequence repeats in those locations are also involved in the regulation of gene expression.[43]

## Applications[edit | edit source]

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 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[edit | edit source]

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. Microsatellites have therefore been routinely used in cancer diagnosis to assess tumour progression.[44][45][46]

File:Str profile.jpg

A partial human STR profile obtained using the Applied Biosystems Identifiler kit

### Forensic and medical fingerprinting[edit | edit source]

Microsatellite analysis became popular in the field of forensics in the 1990s.[47] 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.[48]

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 PCR.[49] 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 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)[edit | edit source]

Autosomal microsatellites are widely used for DNA profiling in kinship analysis (most commonly in paternity testing).[50] Paternally inherited Y-STRs (microsatellites on the Y chromosome) are often used in genealogical DNA testing.

### Genetic linkage analysis[edit | edit source]

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 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).[2][51]

### Population genetics[edit | edit source]

File:Consensus neighbor-joining tree of the 249 human populations and six chimpanzee populations.svg

Consensus neighbor-joining tree of 249 human populations and six chimpanzee populations. Created based on 246 microsatellite markers.[52]

Microsatellites were popularized in population genetics during the 1990s because as PCR became ubiquitous in laboratories researchers were able to design primers and amplify sets of microsatellites at low cost. Their uses are wide-ranging.[53] A microsatellite with a neutral evolutionary history makes it applicable for measuring or inferring bottlenecks,[54] local adaptation,[55] the allelic fixation index (FST),[56] population size,[57] and gene flow.[58] As next generation sequencing becomes more affordable the use of microsatellites has decreased, however they remain a crucial tool in the field.[59]

### Plant breeding[edit | edit source]

Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a trait of interest is selected based on a marker (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.[60]

## Analysis[edit | edit source]

File:Short Tandem Repeat (STR) analysis.png

Short Tandem Repeat (STR) analysis on a simplified model using polymerase chain reaction (PCR): First, a DNA sample undergoes PCR with primers targeting certain STRs (which vary in lengths between individuals and their alleles). The resultant fragments are separated by size (such as electrophoresis).[61]

Repetitive DNA is not easily analysed by next generation DNA sequencing methods, which struggle with homopolymeric tracts. Therefore, microsatellites are normally analysed by conventional PCR amplification and amplicon size determination, sometimes followed by Sanger DNA sequencing.

In forensics, the analysis is performed by extracting nuclear DNA from the cells of a sample of interest, then amplifying specific 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 staining (low sensitivity, safe, inexpensive), or an intercalating dye such as ethidium bromide (fairly sensitive, moderate health risks, inexpensive), or as most modern forensics labs use, fluorescent dyes (highly sensitive, safe, expensive).[62] Instruments built to resolve microsatellite fragments by capillary electrophoresis also use fluorescent dyes.[62] Forensic profiles are stored in major databanks. The British data base for microsatellite loci identification was originally based on the British SGM+ system[63][64] using 10 loci and a sex marker. The Americans[65] increased this number to 13 loci.[66] The Australian database is called the NCIDD, and since 2013 it has been using 18 core markers for DNA profiling.[47]

### Amplification[edit | edit source]

Microsatellites can be amplified for identification by the polymerase chain reaction (PCR) process, using the unique sequences of flanking regions as primers. DNA is repeatedly denatured at a high temperature to separate the double strand, then cooled to allow 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 or polyacrylamide gels; only small amounts of DNA are needed for amplification because in this way thermocycling creates an exponential increase in the replicated segment.[67] 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

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[edit | edit source]

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 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 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. 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.[15][68] 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.[69]

### ISSR-PCR[edit | edit source]

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; 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 or maybe delimiting species; 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[edit | edit source]

Repetitive DNA is not easily analysed by next generation DNA sequencing methods, which struggle with homopolymeric tracts.[70] 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 alleles’:

* 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.[15][71] 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[edit | edit source]

* Genetic marker
* Junk DNA
* List of biological databases
* Long interspersed nucleotide elements
* Microsatellite instability
* Mobile element
* Satellite DNA
* Short interspersed repetitive element
* Simple sequence length polymorphism (SSLP)—a search tool
* Snpstr
* Strbase
* Transposon
* UgMicroSatdb

## References[edit | edit source]

1. ^ a b c d e Richard GF, Kerrest A, Dujon B (December 2008). "Comparative genomics and molecular dynamics of DNA repeats in eukaryotes". Microbiology and Molecular Biology Reviews. 72 (4): 686–727. doi:10.1128/MMBR.00011-08. PMC 2593564. PMID 19052325.
2. ^ a b c d Lu, Weisi; Zhang, Yi; Liu, Dan; Songyang, Zhou; Wan, Ma (2013-01-15). "Telomeres - Structure, Function, and Regulation". Experimental Cell Research. 319 (2): 133–141. doi:10.1016/j.yexcr.2012.09.005. ISSN 0014-4827. PMC 4051234. PMID 23006819.
3. ^ a b c Brinkmann B, Klintschar M, Neuhuber F, Hühne J, Rolf B (June 1998). "Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat". American Journal of Human Genetics. 62 (6): 1408–15. doi:10.1086/301869. PMC 1377148. PMID 9585597.
4. ^ Short+Tandem+Repeat at the US National Library of Medicine Medical Subject Headings (MeSH)
5. ^ a b Kit S (December 1961). "Equilibrium sedimentation in density gradients of DNA preparations from animal tissues". Journal of Molecular Biology. 3 (6): 711–6. doi:10.1016/S0022-2836(61)80075-2. PMID 14456492.
6. ^ King DG, Soller M, Kashi Y (1997). "Evolutionary tuning knobs". Endeavour. 21 (1): 36–40. doi:10.1016/S0160-9327(97)01005-3.
7. ^ Chistiakov DA, Hellemans B, Volckaert FA (2006-05-31). "Microsatellites and their genomic distribution, evolution, function and applications: A review with special reference to fish genetics". Aquaculture. 255 (1–4): 1–29. doi:10.1016/j.aquaculture.2005.11.031.
8. ^ Turnpenny P, Ellard S (2005). Emery's Elements of Medical Genetics (12th ed.). London: Elsevier. ISBN 9780443100451.`{{cite book}}`: CS1 maint: uses authors parameter (link)
9. ^ a b Pearson CE, Nichol Edamura K, Cleary JD (October 2005). "Repeat instability: mechanisms of dynamic mutations". Nature Reviews. Genetics. 6 (10): 729–42. doi:10.1038/nrg1689. PMID 16205713. S2CID 26672703.
10. ^ Goldman, EA; Eick, GN; Compton, D; Kowal, P; Snodgrass, JJ; Eisenberg, DTA; Sterner, KN (2017-09-26). "Evaluating minimally invasive sample collection methods for telomere length measurement". American Journal of Human Biology. 30 (1): e23062. doi:10.1002/ajhb.23062. ISSN 1042-0533. PMC 5785450. PMID 28949426.
11. ^ Tautz D (December 1994). "Simple sequences". Current Opinion in Genetics & Development. 4 (6): 832–7. doi:10.1016/0959-437X(94)90067-1. PMID 7888752.
12. ^ Klintschar M, Dauber EM, Ricci U, Cerri N, Immel UD, Kleiber M, Mayr WR (October 2004). "Haplotype studies support slippage as the mechanism of germline mutations in short tandem repeats". Electrophoresis. 25 (20): 3344–8. doi:10.1002/elps.200406069. PMID 15490457. S2CID 22298567.
13. ^ Forster P, Hohoff C, Dunkelmann B, Schürenkamp M, Pfeiffer H, Neuhuber F, Brinkmann B (March 2015). "Elevated germline mutation rate in teenage fathers". Proceedings. Biological Sciences. 282 (1803): 20142898. doi:10.1098/rspb.2014.2898. PMC 4345458. PMID 25694621.
14. ^ Weber JL, Wong C (August 1993). "Mutation of human short tandem repeats". Human Molecular Genetics. 2 (8): 1123–8. doi:10.1093/hmg/2.8.1123. PMID 8401493.
15. ^ a b c d Jarne P, Lagoda PJ (October 1996). "Microsatellites, from molecules to populations and back". Trends in Ecology & Evolution. 11 (10): 424–9. doi:10.1016/0169-5347(96)10049-5. PMID 21237902.
16. ^ Kruglyak S, Durrett RT, Schug MD, Aquadro CF (September 1998). "Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations". Proceedings of the National Academy of Sciences of the United States of America. 95 (18): 10774–8. Bibcode:1998PNAS...9510774K. doi:10.1073/pnas.95.18.10774. PMC 27971. PMID 9724780.
17. ^ a b c Amos W (September 2010). "Mutation biases and mutation rate variation around very short human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments". Journal of Molecular Evolution. 71 (3): 192–201. Bibcode:2010JMolE..71..192A. doi:10.1007/s00239-010-9377-4. PMID 20700734. S2CID 1424625.
18. ^ Amos W (January 2016). "Heterozygosity increases microsatellite mutation rate". Biology Letters. 12 (1): 20150929. doi:10.1098/rsbl.2015.0929. PMC 4785931. PMID 26740567.
19. ^ Amos W, Sawcer SJ, Feakes RW, Rubinsztein DC (August 1996). "Microsatellites show mutational bias and heterozygote instability". Nature Genetics. 13 (4): 390–1. doi:10.1038/ng0896-390. PMID 8696328. S2CID 6086527.
20. ^ Chapuis MP, Plantamp C, Streiff R, Blondin L, Piou C (December 2015). "Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations". Molecular Ecology. 24 (24): 6107–19. doi:10.1111/mec.13465. PMID 26562076. S2CID 33307624.
21. ^ Molnar RI, Witte H, Dinkelacker I, Villate L, Sommer RJ (September 2012). "Tandem-repeat patterns and mutation rates in microsatellites of the nematode model organism Pristionchus pacificus". G3. 2 (9): 1027–34. doi:10.1534/g3.112.003129. PMC 3429916. PMID 22973539.
22. ^ a b Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, et al. (January 2016). "Abundant contribution of short tandem repeats to gene expression variation in humans". Nature Genetics. 48 (1): 22–9. doi:10.1038/ng.3461. PMC 4909355. PMID 26642241.
23. ^ Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D (October 1999). "A census of protein repeats". Journal of Molecular Biology. 293 (1): 151–60. doi:10.1006/jmbi.1999.3136. PMID 10512723. S2CID 11102561.
24. ^ Sutherland GR, Richards RI (April 1995). "Simple tandem DNA repeats and human genetic disease". Proceedings of the National Academy of Sciences of the United States of America. 92 (9): 3636–41. Bibcode:1995PNAS...92.3636S. doi:10.1073/pnas.92.9.3636. PMC 42017. PMID 7731957.
25. ^ Hancock JM, Simon M (January 2005). "Simple sequence repeats in proteins and their significance for network evolution". Gene. 345 (1): 113–8. doi:10.1016/j.gene.2004.11.023. PMID 15716087.
26. ^ Fondon JW, Garner HR (December 2004). "Molecular origins of rapid and continuous morphological evolution". Proceedings of the National Academy of Sciences of the United States of America. 101 (52): 18058–63. Bibcode:2004PNAS..10118058F. doi:10.1073/pnas.0408118101. PMC 539791. PMID 15596718.
27. ^ Sears KE, Goswami A, Flynn JJ, Niswander LA (2007). "The correlated evolution of Runx2 tandem repeats, transcriptional activity, and facial length in carnivora". Evolution & Development. 9 (6): 555–65. doi:10.1111/j.1525-142X.2007.00196.x. PMID 17976052. S2CID 26718314.
28. ^ Utsch B, Becker K, Brock D, Lentze MJ, Bidlingmaier F, Ludwig M (May 2002). "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?". Human Genetics. 110 (5): 488–94. doi:10.1007/s00439-002-0712-8. PMID 12073020. S2CID 22181414.
29. ^ Bowen S, Wheals AE (June 2006). "Ser/Thr-rich domains are associated with genetic variation and morphogenesis in Saccharomyces cerevisiae". Yeast. 23 (8): 633–40. doi:10.1002/yea.1381. PMID 16823884. S2CID 25142061.
30. ^ Verstrepen KJ, Jansen A, Lewitter F, Fink GR (September 2005). "Intragenic tandem repeats generate functional variability". Nature Genetics. 37 (9): 986–90. doi:10.1038/ng1618. PMC 1462868. PMID 16086015.
31. ^ a b Moxon ER, Rainey PB, Nowak MA, Lenski RE (January 1994). "Adaptive evolution of highly mutable loci in pathogenic bacteria". Current Biology. 4 (1): 24–33. doi:10.1016/S0960-9822(00)00005-1. PMID 7922307. S2CID 11203457.
32. ^ Michael TP, Park S, Kim TS, Booth J, Byer A, Sun Q, et al. (August 2007). "Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock". PLOS ONE. 2 (8): e795. Bibcode:2007PLoSO...2..795M. doi:10.1371/journal.pone.0000795. PMC 1949147. PMID 17726525.
33. ^ a b Rockman MV, Wray GA (November 2002). "Abundant raw material for cis-regulatory evolution in humans". Molecular Biology and Evolution. 19 (11): 1991–2004. doi:10.1093/oxfordjournals.molbev.a004023. PMID 12411608.
34. ^ Hammock EA, Young LJ (June 2005). "Microsatellite instability generates diversity in brain and sociobehavioral traits". Science. 308 (5728): 1630–4. Bibcode:2005Sci...308.1630H. doi:10.1126/science.1111427. PMID 15947188. S2CID 18899853.
35. ^ Grünewald TG, Bernard V, Gilardi-Hebenstreit P, Raynal V, Surdez D, Aynaud MM, et al. (September 2015). "Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite". Nature Genetics. 47 (9): 1073–8. doi:10.1038/ng.3363. PMC 4591073. PMID 26214589.
36. ^ Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MM, Mirabeau O, et al. (September 2019). "Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes". Nature Communications. 10 (1): 4128. Bibcode:2019NatCo..10.4128M. doi:10.1038/s41467-019-12071-2. PMC 6739408. PMID 31511524.
37. ^ Bidichandani SI, Ashizawa T, Patel PI (January 1998). "The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA structure". American Journal of Human Genetics. 62 (1): 111–21. doi:10.1086/301680. PMC 1376805. PMID 9443873.
38. ^ Akagi T, Yin D, Kawamata N, Bartram CR, Hofmann WK, Song JH, et al. (July 2009). "Functional analysis of a novel DNA polymorphism of a tandem repeated sequence in the asparagine synthetase gene in acute lymphoblastic leukemia cells". Leukemia Research. 33 (7): 991–6. doi:10.1016/j.leukres.2008.10.022. PMC 2731768. PMID 19054556.
39. ^ Jemaa R, Ben Ali S, Kallel A, Feki M, Elasmi M, Taieb SH, et al. (June 2009). "Association of a 27-bp repeat polymorphism in intron 4 of endothelial constitutive nitric oxide synthase gene with hypertension in a Tunisian population". Clinical Biochemistry. 42 (9): 852–6. doi:10.1016/j.clinbiochem.2008.12.002. PMID 19111531.
40. ^ Kersting C, Agelopoulos K, Schmidt H, Korsching E, August C, Gosheger G, et al. (August 2008). "Biological importance of a polymorphic CA sequence within intron 1 of the epidermal growth factor receptor gene (EGFR) in high grade central osteosarcomas". Genes, Chromosomes & Cancer. 47 (8): 657–64. doi:10.1002/gcc.20571. PMID 18464244. S2CID 19472307.
41. ^ Lin CL, Taggart AJ, Lim KH, Cygan KJ, Ferraris L, Creton R, et al. (January 2016). "RNA structure replaces the need for U2AF2 in splicing". Genome Research. 26 (1): 12–23. doi:10.1101/gr.181008.114. PMC 4691745. PMID 26566657.
42. ^ Scherer S. (2008). A short guide to the human genome. New York: Cold Spring Harbor University Press.
43. ^ Tomilin NV (April 2008). "Regulation of mammalian gene expression by retroelements and non-coding tandem repeats". BioEssays. 30 (4): 338–48. doi:10.1002/bies.20741. PMID 18348251.
44. ^ van Tilborg AA, Kompier LC, Lurkin I, Poort R, El Bouazzaoui S, van der Keur K, et al. (2012). "Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood". PLOS ONE. 7 (8): e43345. Bibcode:2012PLoSO...743345V. doi:10.1371/journal.pone.0043345. PMC 3425555. PMID 22927958.
45. ^ Sideris M, Papagrigoriadis S (May 2014). "Molecular biomarkers and classification models in the evaluation of the prognosis of colorectal cancer". Anticancer Research. 34 (5): 2061–8. PMID 24778007.
46. ^ Boland CR, Thibodeau SN, Hamilton SR, Sidransky D, Eshleman JR, Burt RW, et al. (November 1998). "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". Cancer Research. 58 (22): 5248–57. PMID 9823339.
47. ^ a b Curtis C, Hereward J (August 29, 2017). "From the crime scene to the courtroom: the journey of a DNA sample". The Conversation.
48. ^ Antin JH, Childs R, Filipovich AH, Giralt S, Mackinnon S, Spitzer T, Weisdorf D (2001). "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". Biology of Blood and Marrow Transplantation. 7 (9): 473–85. doi:10.1053/bbmt.2001.v7.pm11669214. PMID 11669214.
49. ^ Angel Carracedo. "DNA Profiling". Archived from the original on 2001-09-27. Retrieved 2010-09-20.
50. ^ Lászik A, Brinkmann B, Sótonyi P, Falus A (2000). "Automated fluorescent detection of a 10 loci multiplex for paternity testing". Acta Biologica Hungarica. 51 (1): 99–105. doi:10.1007/BF03542970. PMID 10866366.
51. ^ Ott J, Wang J, Leal SM (May 2015). "Genetic linkage analysis in the age of whole-genome sequencing". Nature Reviews. Genetics. 16 (5): 275–84. doi:10.1038/nrg3908. PMC 4440411. PMID 25824869.
52. ^ Pemberton TJ, DeGiorgio M, Rosenberg NA (May 2013). "Population structure in a comprehensive genomic data set on human microsatellite variation". G3. 3 (5): 891–907. doi:10.1534/g3.113.005728. PMC 3656735. PMID 23550135.
53. ^ Manel S, Schwartz MK, Luikart G, Taberlet P (2003-04-01). "Landscape genetics: combining landscape ecology and population genetics". Trends in Ecology & Evolution. 18 (4): 189–197. doi:10.1016/S0169-5347(03)00008-9.
54. ^ Spencer CC, Neigel JE, Leberg PL (October 2000). "Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks". Molecular Ecology. 9 (10): 1517–28. doi:10.1046/j.1365-294x.2000.01031.x. PMID 11050547. S2CID 22244000.
55. ^ Nielsen R (2005-01-01). "Molecular signatures of natural selection". Annual Review of Genetics. 39 (1): 197–218. doi:10.1146/annurev.genet.39.073003.112420. PMID 16285858. S2CID 3063754.
56. ^ Slatkin M (January 1995). "A measure of population subdivision based on microsatellite allele frequencies". Genetics. 139 (1): 457–62. doi:10.1093/genetics/139.1.457. PMC 1206343. PMID 7705646.
57. ^ Kohn MH, York EC, Kamradt DA, Haught G, Sauvajot RM, Wayne RK (April 1999). "Estimating population size by genotyping faeces". Proceedings. Biological Sciences. 266 (1420): 657–63. doi:10.1098/rspb.1999.0686. PMC 1689828. PMID 10331287.
58. ^ Waits L, Taberlet P, Swenson JE, Sandegren F, Franzén R (April 2000). "Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos)". Molecular Ecology. 9 (4): 421–31. doi:10.1046/j.1365-294x.2000.00892.x. PMID 10736045. S2CID 46475635.
59. ^ Allendorf FW, Hohenlohe PA, Luikart G (October 2010). "Genomics and the future of conservation genetics". Nature Reviews. Genetics. 11 (10): 697–709. doi:10.1038/nrg2844. PMID 20847747. S2CID 10811958.
60. ^ Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam K, Latif MA (November 2013). "A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance". International Journal of Molecular Sciences. 14 (11): 22499–528. doi:10.3390/ijms141122499. PMC 3856076. PMID 24240810.
61. ^ Image by Mikael Häggström, MD, using following source image: Figure 1 - available via license: Creative Commons Attribution 4.0 International", from the following article:
Roberta Sitnik, Margareth Afonso Torres, Nydia Strachman Bacal, João Renato Rebello Pinho (2006). "Using PCR for molecular monitoring of post-transplantation chimerism". Einstein (Sao Paulo).`{{cite web}}`: CS1 maint: multiple names: authors list (link)
62. ^ a b "Technology for Resolving STR Alleles". Retrieved 2010-09-20.
63. ^ "The National DNA Database" (PDF). Retrieved 2010-09-20.
64. ^ "House of Lords Select Committee on Science and Technology Written Evidence". Retrieved 2010-09-20.
65. ^ "FBI CODIS Core STR Loci". Retrieved 2010-09-20.
66. ^ Butler J.M. (2005). Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers, Second Edition. New York: Elsevier Academic Press.
67. ^ Griffiths, A.J.F., Miller, J.F., Suzuki, D.T., Lewontin, R.C. & Gelbart, W.M. (1996). Introduction to Genetic Analysis, 5th Edition. W.H. Freeman, New York.`{{cite book}}`: CS1 maint: uses authors parameter (link)
68. ^ Queller DC, Strassmann JE, Hughes CR (August 1993). "Microsatellites and kinship". Trends in Ecology & Evolution. 8 (8): 285–8. doi:10.1016/0169-5347(93)90256-O. PMID 21236170.
69. ^ Kaukinen KH, Supernault KJ, and Miller KM (2004). "Enrichment of tetranucleotide microsatellite loci from invertebrate species". Journal of Shellfish Research. 23 (2): 621.`{{cite journal}}`: CS1 maint: uses authors parameter (link)
70. ^ Tytgat, Olivier; Gansemans, Yannick; Weymaere, Jana; Rubben, Kaat; Deforce, Dieter; Van Nieuwerburgh, Filip (2020). "Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling". Genes. 11 (4): 381. doi:10.3390/genes11040381. PMC 7230633. PMID 32244632. S2CID 214786277.
71. ^ Dakin EE, Avise JC (November 2004). "Microsatellite null alleles in parentage analysis". Heredity. 93 (5): 504–9. doi:10.1038/sj.hdy.6800545. PMID 15292911.

## Further reading[edit | edit source]

* Caporale LH (2003). "Natural selection and the emergence of a mutation phenotype: an update of the evolutionary synthesis considering mechanisms that affect genome variation". Annual Review of Microbiology. 57: 467–85. doi:10.1146/annurev.micro.57.030502.090855. PMID 14527288.
* Kashi Y, et al. (1997). "Simple sequence repeats as a source of quantitative genetic variation". Trends Genet. 13 (2): 74–78. doi:10.1016/S0168-9525(97)01008-1. PMID 9055609.
* Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJ, Koornneef M, Kakutani T (January 2007). "Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats". The Plant Journal. 49 (1): 38–45. doi:10.1111/j.1365-313X.2006.02936.x. hdl:11858/00-001M-0000-0012-38D2-5. PMID 17144899.
* Li YC, Korol AB, Fahima T, Beiles A, Nevo E (December 2002). "Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review". Molecular Ecology. 11 (12): 2453–65. doi:10.1046/j.1365-294X.2002.01643.x. PMID 12453231.
* Li YC, Korol AB, Fahima T, Nevo E (June 2004). "Microsatellites within genes: structure, function, and evolution". Molecular Biology and Evolution. 21 (6): 991–1007. doi:10.1093/molbev/msh073. PMID 14963101.
* Mattick JS (October 2003). "Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms". BioEssays. 25 (10): 930–9. CiteSeerX 10.1.1.476.7561. doi:10.1002/bies.10332. PMID 14505360.
* Meagher TR, Vassiliadis C (October 2005). "Phenotypic impacts of repetitive DNA in flowering plants". The New Phytologist. 168 (1): 71–80. doi:10.1111/j.1469-8137.2005.01527.x. PMID 16159322.
* Müller KJ, Romano N, Gerstner O, Garcia-Maroto F, Pozzi C, Salamini F, Rohde W (April 1995). "The barley Hooded mutation caused by a duplication in a homeobox gene intron". Nature. 374 (6524): 727–30. Bibcode:1995Natur.374..727M. doi:10.1038/374727a0. PMID 7715728. S2CID 4344876.
* Pumpernik D, Oblak B, Borstnik B (January 2008). "Replication slippage versus point mutation rates in short tandem repeats of the human genome". Molecular Genetics and Genomics. 279 (1): 53–61. doi:10.1007/s00438-007-0294-1. PMID 17926066. S2CID 20542422.
* Streelman J. T., Kocher T. D. (2002). "Microsatellite variation associated with prolactin expression and growth of salt-challenged Tilapia". Physiol. Genomics. 9 (1): 1–4. doi:10.1152/physiolgenomics.00105.2001. PMID 11948285. S2CID 8360732.`{{cite journal}}`: CS1 maint: uses authors parameter (link)
* Vinces MD, Legendre M, Caldara M, Hagihara M, Verstrepen KJ (May 2009). "Unstable tandem repeats in promoters confer transcriptional evolvability". Science. 324 (5931): 1213–6. Bibcode:2009Sci...324.1213V. doi:10.1126/science.1170097. PMC 3132887. PMID 19478187.

## External links[edit | edit source]

* All known disease-causing short tandem repeats
* MicroSatellite DataBase
* Search tools:
* FireMuSat2+
* IMEx
* Imperfect SSR Finder—find perfect or imperfect SSRs in FASTA sequences.
* JSTRING—Java Search for Tandem Repeats In Genomes
* Microsatellite repeats finder
* MISA—MIcroSAtellite identification tool
* MREPATT
* Mreps
* Phobos—a tandem repeat search tool for perfect and imperfect repeats—the maximum pattern size depends only on computational power
* Poly
* SciRoKo
* SSR Finder
* STAR
* Tandem Repeats Finder
* TandemSWAN
* TRED
* TROLL
* Zebrafish Repeats

* v
* t
* e

Genetics: repeated sequence, transposon, gene duplication

Repeatome

Repeated sequence|

| Tandem repeats|

* Satellite DNA
* Variable number tandem repeat/Minisatellite
* Short tandem repeat/Microsatellite (Trinucleotide repeat disorders)
* Macrosatellite

|

Interspersed
repeat|

* Gene conversion
* Retrotransposon
* DNA transposon
* Polinton
* Helitron

Other|

* Inverted repeat
* Direct repeat

Transposon|

| Retrotransposon|

| SINEs|

* Alu sequence
* MIR

|

LINEs|

* LINE1
* LINE2

LTRs|

* HERV
* MER4
* retroposon

DNA transposon|

* Academ
* Crypton
* Dada
* EnSpm/CACTA
* Ginger1
* Ginger2
* Harbinger
* hAT
* Helitron
* IS3EU
* ISL2EU
* Kolobok
* Tc1/mariner
* Merlin
* MuDR
* Novosib
* P element
* PiggyBac
* Polinton
* Sola
* Transib
* Zator
* Zisupton

Gene duplication|

* Gene amplification
* Tandemly arrayed genes
* Ribosomal DNA
* Gene family
* Gene cluster
* Pseudogene

See also|

* Genomic island
* Pathogenicity island
* Symbiosis island
* Low copy repeats
* CRISPR
* Telomere

*[v]: View this template
*[t]: Discuss this template
*[e]: Edit this template