A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 2–5 base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome; additionally, they have a higher mutation rate than other areas of DNA leading to high genetic diversity.
Microsatellites and their longer cousins, the minisatellites, together are classified as VNTR (variable number of tandem repeats) DNA. The name "satellite" 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. Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists, or as simple sequence repeats (SSRs) by plant geneticists.
They are widely used for DNA profiling in kinship analysis (especially paternity testing) and in forensic identification. They are also used in genetic linkage analysis/marker assisted selection 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.
- 1 Structures, locations, and functions
- 2 Mutation mechanisms and mutation rates
- 3 Biological effects of microsatellite mutations
- 4 Analysis
- 5 Applications
- 6 See also
- 7 References
- 8 Further reading
- 9 External links
Structures, locations, and functions
A microsatellite is a tract of tandemly repeated (i.e. adjacent) DNA motifs that range in length from two to five nucleotides, 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. Microsatellites are distributed throughout the genome. 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 within the coding region.
Microsatellites in non-coding regions do not have any specific function, and therefore cannot 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.
The telomeres at the ends of the chromosomes, thought to be involved in ageing/senescence, consist of repetitive DNA, with the hexanucleotide repeat motif TTAGGG in vertebrates. They are thus classified as minisatellites. Similarly, insects have shorter repeat motifs in their telomeres that could arguably be considered microsatellites.
Mutation mechanisms and mutation rates
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. 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. Typically, slippage in each microsatellite occurs about once per 1,000 generations. Thus, slippage changes in repetitive DNA are three orders of magnitude more common than point mutations in other parts of the genome. Most slippage results in a change of just one repeat unit, and slippage rates vary for different allele lengths and repeat unit sizes, and within different species. If there is a large size difference between individual alleles, then there may be increased instability during recombination at meiosis.
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.
Microsatellite mutation rates
Microsatellite mutation rates vary with base position relative to the microsatellite, repeat type, and base identity. Mutation rate rises specifically with repeat number, peaking around six to eight repeats and then decreasing again. Increased heterozygosity in a population will also increase microsatellite mutation rates, 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.
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. 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. 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.
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 - microsatellite mutations in such cases can lead to phenotypic changes and diseases. Recent studies provided evidence that microsatellites may act as enhancers regulating disease-relevant genes.
Effects on proteins
In mammals, 20% to 40% of proteins contain repeating sequences of amino acids encoded by short sequence repeats. 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. 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. 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. This association also applies to a wider range of Carnivora species. Length changes in polyalanine tracts within the HoxA13 gene are linked to Hand-Foot-Genital Syndrome, a developmental disorder in humans. Length changes in other triplet repeats are linked to more than 40 neurological diseases in humans. 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. Specifically, length changes in the FLO1 gene control the level of adhesion to substrates. 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. Length changes in short sequence repeats in a fungus (Neurospora crassa) control the duration of its circadian clock cycles.
Effects on gene regulation
Length changes of microsatellites within promoters and other cis-regulatory regions can also 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.
Length changes in bacterial SSRs can affect fimbriae formation in Haemophilus influenzae, by altering promoter spacing. Minisatellites are also linked to abundant variations in cis-regulatory control regions in the human genome. And microsatellites in control regions of the Vasopressin 1a receptor gene in voles influence their social behavior, and level of monogamy.
Effects within introns
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. Tandem repeats in the first intron of the Asparagine synthetase gene are linked to acute lymphoblastic leukaemia. A repeat polymorphism in the fourth intron of the NOS3 gene is linked to hypertension in a Tunisian population. Reduced repeat lengths in the EGFR gene are linked with osteosarcomas.
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.
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. It is probable that short sequence repeats in those locations are also involved in the regulation of gene expression.
Microsatellites are widely used for DNA profiling in kinship analysis (most commonly in paternity testing), in forensic identification (typically matching a crime stain to a victim or perpetrator), and in population genetics. Also, microsatellites are used for mapping locations within the genome, specifically in genetic linkage analysis/marker assisted selection 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. These applications are realized by various technical methods.
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. 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.
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 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. 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.
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.
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 amplication and amplicon size determination, sometimes followed by Sanger DNA sequencing. 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. 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.
- 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. Microsatellites have therefore been routinely used in cancer research to assess loss of heterozygosity.
Microsatellite analysis became popular in the field of forensics in the 1990s. It is used for the genetic fingerprinting of individuals. 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 robust enough to survive degradation in non-ideal conditions. Shorter repeat sequences tend to suffer from artifacts such as PCR stutter and preferential amplification, as well as the fact that several genetic diseases are associated with tri-nucleotide repeats such as Huntington's disease. Longer repeat sequences will suffer more highly from environmental degradation and do not amplify by PCR as well as shorter sequences.
The analysis is performed by extracting nuclear DNA from the cells of a forensic 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). Instruments built to resolve microsatellite fragments by capillary electrophoresis also use fluorescent dyes. It is also used to follow up bone marrow transplant patients. In the United States, 13 core microsatellite loci have been decided upon to be the basis by which an individual genetic profile can be generated.
These profiles are stored on a local, state and national level in DNA databanks such as CODIS. The British data base for microsatellite loci identification is the UK National DNA Database (NDNAD). The British SGM+ system uses 10 loci and a sex marker, rather than the American 13 loci.
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. A microsatellite with a neutral evolutionary history makes it applicable for measuring or inferring bottlenecks, local adaptation, the allelic fixation index (FST), population size, and gene flow. As next generation sequencing becomes more affordable the use of microsatellites has decreased, however they remain a crucial tool in the field.
- Genetic marker
- Junk DNA
- Long interspersed repetitive element
- Microsatellite instability
- Mobile element
- Short interspersed repetitive element
- Simple sequence length polymorphism (SSLP)
- Turnpenny P, Ellard S (2005). Emery's Elements of Medical Genetics (12th ed.). London: Elsevier.
- Brinkmann, Bernd; Klintschar, Michael; Neuhuber, Franz; Hühne, Julia; Rolf, Burkhard (1998-06-01). "Mutation Rate in Human Microsatellites: Influence of the Structure and Length of the Tandem Repeat". The American Journal of Human Genetics. 62 (6): 1408–1415. doi:10.1086/301869. PMC . PMID 9585597.
- King, David G.; Soller, Morris; Kashi, Yechezkel (1997). "Evolutionary tuning knobs". Endeavour. 21 (1): 36–40. doi:10.1016/S0160-9327(97)01005-3.
- Richard, Guy-Franck; Kerrest, Alix; Dujon, Bernard (2008). "Comparative genomics and molecular dynamics of DNA repeats in Eukaryotes". Micr. Mol. Bio. Rev. 72 (4): 686–727. doi:10.1128/MMBR.00011-08. PMC . PMID 19052325.
- Chistiakov, Dimitry A.; Hellemans, Bart; Volckaert, Filip A. M. (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.
- Tautz D., Schlötterer C. (1994). "Simple sequences". Current Opinion in Genetics & Development. 4 (6): 832–837. doi:10.1016/0959-437X(94)90067-1. PMID 7888752.
- Klintschar M, et al. (2004). "Haplotype studies support slippage as the mechanism of germline mutations in short tandem repeats". Electrophoresis. 25: 3344–3348. doi:10.1002/elps.200406069. PMID 15490457.
- Forster P., Hohoff C., Dunkelmann B., Schürenkamp M., Pfeiffer H., Neuhuber F., Brinkmann B. (2015). "Elevated germline mutation rate in teenage fathers". Proc. R. Soc. B. 282 (1803): 20142898. doi:10.1098/rspb.2014.2898. PMC . PMID 25694621.
- Weber J.L., Wong C. (1993). "Mutation of human short tandem repeats". Hum. Mol. Genet. 2 (8): 1123–1128. doi:10.1093/hmg/2.8.1123. PMID 8401493.
- Jarne P., Lagoda P. J. L. (1996). "Microsatellites, from molecules to populations and back". Trends Ecol. Evol. 11 (10): 424–429. doi:10.1016/0169-5347(96)10049-5. PMID 21237902.
- Brinkmann B, Klintschar M, Neuhuber F, Huhne J, Rolf B (1998). "Mutation Rate in Human Microsatellites: Influence of the Structure and Length of the Tandem Repeat". Am J Hum Genet. 62 (6): 1408–1415. doi:10.1086/301869. PMC . PMID 9585597.
- Kruglyak S, et al. (1998). "Equilibrium distributions of microstellite repeat length resulting from a balance between slippage events and point mutations". Proc. Natl. Acad. Sci. U.S.A. 95 (18): 10774–10778. Bibcode:1998PNAS...9510774K. doi:10.1073/pnas.95.18.10774. PMC . PMID 9724780.
- Amos W (2010). "Mutation biases and mutation rate variation around very short human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments". J. Mol. Evol. 71: 192–201. doi:10.1007/s00239-010-9377-4. PMID 20700734.
- Amos W (2016). "Heterozygosity increases microsatellite mutation rate". Biol. Lett. 12: 20150929. doi:10.1098/rsbl.2015.0929.
- Amos W, Rubinsztein DC (1996). "Microsatellites show mutational bias and heterozygote instability". Nature Genetics. 13: 390–391. doi:10.1038/ng0896-390.
- Chapuis, M-P, Plantamp, C, Streiff, R, Blondin, L, Piou, C (2015). "Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations". Mol Ecol. 24: 6107–6119. doi:10.1111/mec.13465.
- Molnar, Ruxandra I.; Witte, Hanh; Dinkelacker, Iris; Villate, Laure; Sommer, Ralf J. (September 2012). "Tandem-Repeat Patterns and Mutation Rates in Microsatellites of the Nematode Model Organism Pristionchus pacificus". G3: Genes, Genomes, Genetics. 2 (9): 1027–1034. doi:10.1534/g3.112.003129. PMC . PMID 22973539.
- Gymrek, Melissa; Willems, Thomas; Guilmatre, Audrey; Zeng, Haoyang; Markus, Barak; Georgiev, Stoyan; Daly, Mark J; Price, Alkes L; Pritchard, Jonathan K. "Abundant contribution of short tandem repeats to gene expression variation in humans". Nature Genetics. 48: 22–29. doi:10.1038/ng.3461. PMC . PMID 26642241.
- Grünewald, Thomas G P; Bernard, Virginie; Gilardi-Hebenstreit, Pascale; Raynal, Virginie; Surdez, Didier; Aynaud, Marie-Ming; Mirabeau, Olivier; Cidre-Aranaz, Florencia; Tirode, Franck. "Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite". Nature Genetics. 47 (9): 1073–1078. doi:10.1038/ng.3363. PMC . PMID 26214589.
- Marcotte E. M.; et al. (1998). "A census of protein repeats". J. Mol. Biol. 293 (1): 151–160. doi:10.1006/jmbi.1999.3136. PMID 10512723.
- Sutherland, Grant R.; Richards, Robert I. (April 1995). "Simple tandem DNA repeats and human genetic disease". Proc. Natl. Acad. Sci. U.S.A. 92 (9): 3636–3641. Bibcode:1995PNAS...92.3636S. doi:10.1073/pnas.92.9.3636. PMC . PMID 7731957.
- Hancock J. M., Simon M. (2005). "Simple sequence repeats in proteins and their significance for network evolution". Gene. 345 (1): 113–118. doi:10.1016/j.gene.2004.11.023. PMID 15716087.
- Fondon, John W., III; Garner, Harold R. (2004). "Molecular origins of rapid and continuous morphological evolution". Proc. Natl. Acad. Sci. U.S.A. 101 (52): 18058–18063. Bibcode:2004PNAS..10118058F. doi:10.1073/pnas.0408118101. PMC . PMID 15596718.
- Sears K. E.; et al. (2007). "The correlated evolution of Runx2 tandem repeats, transcriptional activity, and facial length in Carnivora". Evol. & Dev. 9 (6): 555–565. doi:10.1111/j.1525-142X.2007.00196.x.
- Utsch B, et al. (2002). "A novel stable 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?". Hum. Gen. 110 (5): 488–494. doi:10.1007/s00439-002-0712-8. PMID 12073020.
- Pearson C. E.; et al. (2005). "Repeat instability: mechanisms of dynamic mutations". Nature Reviews Genetics. 6 (10): 729–742. doi:10.1038/nrg1689.
- Bowen S., Wheals A. E. (2006). "Ser//Thr-rich domains are associated with genetic variation and morphogenesis in Saccharomyces cerevisiae". Yeast. 23 (8): 633–640. doi:10.1002/yea.1381. PMID 16823884.
- Verstrepen K. J.; et al. (2005). "Intragenic tandem repeats generate functional variability". Nat. Genet. 37 (9): 986–990. doi:10.1038/ng1618.
- Moxon E. R.; et al. (1994). "Adaptive evolution of highly mutable loci in pathogenic bacteria". Curr. Bio. 4: 24–32. doi:10.1016/S0960-9822(00)00005-1.
- Michael T. P.; et al. (2007). Redfield, Rosemary, ed. "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 . PMID 17726525.
- Rockman M. V., Wray G. A. (2002). "Abundant raw material for cis-regulatory evolution in humans". Mol. Biol. Evol. 19 (11): 1991–2004. doi:10.1093/oxfordjournals.molbev.a004023. PMID 12411608.
- Hammock, Elizabeth A. D.; Young, Larry J. (2005). "Microsatellite instability generates diversity in brain and sociobehavioral traits". Science. 308 (5728): 1630–1634. Bibcode:2005Sci...308.1630H. doi:10.1126/science.1111427. PMID 15947188.
- Bidichandani S. I.; et al. (1998). "The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA structure". Am. J. Hum. Genet. 62 (1): 111–121. doi:10.1086/301680. PMC . PMID 9443873.
- Akagi T, et al. (2008). "Functional analysis of a novel DNA polymorphism of a tandem repeated sequence in the asparagine synthetase gene in acute lymphoblastic leukemia cells". Leuk. Res. 33 (7): 991–996. doi:10.1016/j.leukres.2008.10.022. PMC . PMID 19054556.
- Jemaa R, et al. (2008). "Association of a 27-bp repeat polymorphism in intron 4 of endothelial constitutive nitric oxide synthase gene with hypertension in a Tunisian population". Clin. Biochem. 42 (9): 852–856. doi:10.1016/j.clinbiochem.2008.12.002. PMID 19111531.
- Kersting C, et al. (2008). "Biological importance of a polymorphic CA sequence within intron I of the epidermal growth factor receptor gene (EGFR) in high grade central osteosarcomas". Gene Chrom. & Cancer. 47 (8): 657–664. doi:10.1002/gcc.20571.
- Lin, Chien-Ling; Taggart, Allison J.; Lim, Kian Huat; Cygan, Kamil J.; Ferraris, Luciana; Creton, Robbert; Huang, Yen-Tsung; Fairbrother, William G. (2016-01-01). "RNA structure replaces the need for U2AF2 in splicing". Genome Research. 26 (1): 12–23. doi:10.1101/gr.181008.114. ISSN 1549-5469. PMC . PMID 26566657.
- Scherer S. (2008). A short guide to the human genome. New York: Cold Spring Harbor University Press.
- Tomilin N. V. (2008). "Regulation of mammalian gene expression by retroelements and non-coding tandem repeats". BioEssays. 30 (4): 338–348. doi:10.1002/bies.20741. PMID 18348251.
- 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.
- Queller, D.C., Strassman,,J.E. & Hughes, C.R. (1993). "Microsatellites and Kinship". Trends in Ecology and Evolution. 8 (8): 285–288. doi:10.1016/0169-5347(93)90256-O. PMID 21236170.
- Kaukinen KH, Supernault KJ, and Miller KM (2004). "Enrichment of tetranucleotide microsatellite loci from invertebrate species". Journal of Shellfish Research. 23 (2): 621.
- Dakin, EE; Avise, JC (2004). "Microsatellite null alleles in parentage analysis". Heredity. 93 (5): 504–509. doi:10.1038/sj.hdy.6800545. PMID 15292911.
- Angel Carracedo. "DNA Profiling". Archived from the original on 2001-09-27. Retrieved 2010-09-20.
- "Technology for Resolving STR Alleles". Retrieved 2010-09-20.
- Antin JH, Childs R, Filipovich AH, et al. (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". Biol. Blood Marrow Transplant. 7 (9): 473–85. doi:10.1053/bbmt.2001.v7.pm11669214. PMID 11669214.
- Butler J.M. (2005). Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers, Second Edition. New York: Elsevier Academic Press.
- "The National DNA Database" (PDF). Retrieved 2010-09-20.
- "House of Lords Select Committee on Science and Technology Written Evidence". Retrieved 2010-09-20.
- "FBI CODIS Core STR Loci". Retrieved 2010-09-20.
- Pemberton, T. J.; DeGiorgio, M.; Rosenberg, N. A. (2013). "Population Structure in a Comprehensive Genomic Data Set on Human Microsatellite Variation". G3: Genes, Genomes, Genetics. 3 (5): 891–907. doi:10.1534/g3.113.005728. ISSN 2160-1836.
- Manel, Stéphanie; Schwartz, Michael K.; Luikart, Gordon; Taberlet, Pierre (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.
- Spencer, C. C.; Neigel, J. E.; Leberg, P. L. (2000-10-01). "Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks". Molecular Ecology. 9 (10): 1517–1528. doi:10.1046/j.1365-294x.2000.01031.x. ISSN 1365-294X.
- Nielsen, Rasmus (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.
- Slatkin, M. (1995-01-01). "A measure of population subdivision based on microsatellite allele frequencies.". Genetics. 139 (1): 457–462. ISSN 0016-6731. PMC . PMID 7705646.
- Kohn, Michael H.; York, Eric C.; Kamradt, Denise A.; Haught, Gary; Sauvajot, Raymond M.; Wayne, Robert K. (1999-04-07). "Estimating population size by genotyping faeces". Proceedings of the Royal Society of London B: Biological Sciences. 266 (1420): 657–663. doi:10.1098/rspb.1999.0686. ISSN 0962-8452. PMC . PMID 10331287.
- Waits, Lisette; Taberlet, Pierre; Swenson, Jon E.; Sandegren, Finn; Franzén, Robert (2000-04-01). "Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos)". Molecular Ecology. 9 (4): 421–431. doi:10.1046/j.1365-294x.2000.00892.x. ISSN 1365-294X.
- Allendorf, Fred W.; Hohenlohe, Paul A.; Luikart, Gordon (2010-10-01). "Genomics and the future of conservation genetics". Nature Reviews Genetics. 11 (10): 697–709. doi:10.1038/nrg2844. ISSN 1471-0056.
- Caporale L. H. (2003). "Natural selection and the emergence of a mutation phenotype: an update of the evolutionary synthesis considering mechanisms that affect genome variation". Annu. Rev. Microbiol. 57: 467–485. doi:10.1146/annurev.micro.57.030502.090855.
- Kashi Y, et al. (1997). "Simple sequence repeats as a source of quantitative genetic variation". Trends Gen. 13 (2): 74–78. doi:10.1016/S0168-9525(97)01008-1.
- Kinoshita Y, et al. (2007). "Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats". Plant. J. 49 (1): 38–45. doi:10.1111/j.1365-313X.2006.02936.x. PMID 17144899.
- Li Y-C.; et al. (2002). "Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review". Mol. Ecol. 11 (12): 2453–2465. doi:10.1046/j.1365-294X.2002.01643.x. PMID 12453231.
- Li Y-C.; et al. (2003). "Microsatellites within genes: structure, function and evolution". Mol. Bio. Evol. 21 (6): 991–1007. doi:10.1093/molbev/msh073. PMID 14963101.
- Mattick J. S. (2003). "Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms". BioEssays. 25 (10): 930–939. doi:10.1002/bies.10332. PMID 14505360.
- Meagher T., Vassiliadis C. (2005). "Phenotypic impacts of repetitive DNA in flowering plants". New Phyto. 168: 71–80. doi:10.1111/j.1469-8137.2005.01527.x.
- Müller K. J.; Romano; Gerstner; Garcia-Marotot; Pozzi; Salamini; Rohde; et al. (1995). "The barley Hooded mutation caused by a duplication in a homeobox gene intron". Nature. 374 (6524): 727–730. Bibcode:1995Natur.374..727M. doi:10.1038/374727a0. PMID 7715728.
- Pumpernik D, et al. ", Replication slippage versus point mutation rates in short tandem repeats of the human genome. 2008. Mol. Genet". Genomics. 279 (1): 53–61. doi:10.1007/s00438-007-0294-1. PMID 17926066.
- Streelman J. T., Kocher T. D. (2002). "Microsatellite variation associated with prolactin expression and growth of salt-challenged Tilapia". Phys. Genom. 9: 1–4.
- Vinces M. D.; Legendre; Caldara; Hagihara; Verstrepen; et al. (2009). "Unstable tandem repeats in promoters confer transcriptional evolvability". Science. 324 (5931): 1213–1216. Bibcode:2009Sci...324.1213V. doi:10.1126/science.1170097. PMC . PMID 19478187.
- About microsatellites:
- Search tools :
- SSR Finder
- 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
- Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power
- Tandem Repeats Finder
- Zebrafish Repeats