Microsatellite




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 1–6 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


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 8-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


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 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.[9]


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




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.[10]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.[11][12] Typically, slippage in each microsatellite occurs about once per 1,000 generations.[13] Thus, slippage changes in repetitive DNA are three orders of magnitude more common than point mutations in other parts of the genome.[14] Most slippage results in a change of just one repeat unit, and slippage rates vary for different allele lengths and repeat unit sizes,[15] 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.[14]


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


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.[15] 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


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


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


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]



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


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.[40]



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



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 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. Microsatellites have therefore been routinely used in cancer diagnosis to assess tumour progression.[43][44][45]




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.[46] 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.[47]


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.[48] 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)


Autosomal microsatellites are widely used for DNA profiling in kinship analysis (most commonly in paternity testing).[49] Paternally inherited Y-STRs (microsatellites on the Y chromosome) are often used in genealogical DNA testing.



Genetic linkage analysis


During the 1990s and the first several years of this millenium, 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][50]



Population genetics





Consensus neighbor-joining tree of 249 human populations and six chimpanzee populations. Created based on 246 microsatellite markers.[51]


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.[52] A microsatellite with a neutral evolutionary history makes it applicable for measuring or inferring bottlenecks,[53]local adaptation,[54] the allelic fixation index (FST),[55]population size,[56] and gene flow.[57] As next generation sequencing becomes more affordable the use of microsatellites has decreased, however they remain a crucial tool in the field.[58]



Plant breeding


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;[59] nevertheless, as of 2012, "breeding programs based on DNA markers for improving quantitative traits in plants are rare".[60]



Analysis


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).[61] Instruments built to resolve microsatellite fragments by capillary electrophoresis also use fluorescent dyes.[61] Forensic profiles are stored in major databanks. The British data base for microsatellite loci identification was originally based on the British SGM+ system[62][63] using 10 loci and a sex marker. The Americans[64] increased this number to 13 loci.[65] The Australian database is called the NCIDD, and since 2013 it has been using 18 core markers for DNA profiling.[46]



Amplification



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 agaroseor polyacrylamide gels; only small amounts of DNA are needed for amplification because in this way thermocycling creates an exponential increase in the replicated segment.[66] 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.




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 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.[14][67] 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.[68]



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; 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


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. 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.[14][69] 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



  • Genetic marker

  • Junk DNA

  • Long interspersed repetitive element

  • Microsatellite instability

  • Mobile element

  • Short interspersed repetitive element


  • Simple sequence length polymorphism (SSLP)

  • Snpstr

  • Transposon



References





  1. ^ abcde 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 2593564. PMID 19052325..mw-parser-output cite.citation{font-style:inherit}.mw-parser-output q{quotes:"""""""'""'"}.mw-parser-output code.cs1-code{color:inherit;background:inherit;border:inherit;padding:inherit}.mw-parser-output .cs1-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/6/65/Lock-green.svg/9px-Lock-green.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-limited a,.mw-parser-output .cs1-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/d/d6/Lock-gray-alt-2.svg/9px-Lock-gray-alt-2.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/a/aa/Lock-red-alt-2.svg/9px-Lock-red-alt-2.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration{color:#555}.mw-parser-output .cs1-subscription span,.mw-parser-output .cs1-registration span{border-bottom:1px dotted;cursor:help}.mw-parser-output .cs1-hidden-error{display:none;font-size:100%}.mw-parser-output .cs1-visible-error{font-size:100%}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration,.mw-parser-output .cs1-format{font-size:95%}.mw-parser-output .cs1-kern-left,.mw-parser-output .cs1-kern-wl-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right,.mw-parser-output .cs1-kern-wl-right{padding-right:0.2em}


  2. ^ abc Gulcher, J. (2012). "Microsatellite markers for linkage and association studies". Cold Spring Harb Protoc. 4: 425–432. doi:10.1101/pdb.top068510.


  3. ^ 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 1377148. PMID 9585597.


  4. ^ Short+Tandem+Repeat at the US National Library of Medicine Medical Subject Headings (MeSH)


  5. ^ ab Kit, S. (1961). "Equilibrium sedimentation in density gradients of DNA preparations from animal tissues". J. Mol. Biol. 3 (6): 711–716. doi:10.1016/S0022-2836(61)80075-2. ISSN 0022-2836. PMID 14456492.


  6. ^ King, David G.; Soller, Morris; Kashi, Yechezkel (1997). "Evolutionary tuning knobs". Endeavour. 21 (1): 36–40. doi:10.1016/S0160-9327(97)01005-3.


  7. ^ 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.


  8. ^ Turnpenny P, Ellard S (2005). Emery's Elements of Medical Genetics (12th ed.). London: Elsevier.CS1 maint: Uses authors parameter (link)


  9. ^ ab Pearson C. E.; et al. (2005). "Repeat instability: mechanisms of dynamic mutations". Nature Reviews Genetics. 6 (10): 729–742. doi:10.1038/nrg1689.


  10. ^ 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.CS1 maint: Uses authors parameter (link)


  11. ^ 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.


  12. ^ 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 4345458. PMID 25694621.CS1 maint: Uses authors parameter (link)


  13. ^ 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.CS1 maint: Uses authors parameter (link)


  14. ^ abcd 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.CS1 maint: Uses authors parameter (link)


  15. ^ ab 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 1377148. PMID 9585597.CS1 maint: Uses authors parameter (link)


  16. ^ 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 27971. PMID 9724780.


  17. ^ abc 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. Bibcode:2010JMolE..71..192A. doi:10.1007/s00239-010-9377-4. PMID 20700734.


  18. ^ Amos W (2016). "Heterozygosity increases microsatellite mutation rate". Biol. Lett. 12: 20150929. doi:10.1098/rsbl.2015.0929. PMC 4785931.


  19. ^ Amos W, Rubinsztein DC (1996). "Microsatellites show mutational bias and heterozygote instability". Nature Genetics. 13: 390–391. doi:10.1038/ng0896-390.CS1 maint: Uses authors parameter (link)


  20. ^ 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.CS1 maint: Uses authors parameter (link)


  21. ^ 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 3429916. PMID 22973539.


  22. ^ ab Gymrek, Melissa; Willems, Thomas; Guilmatre, Audrey; Zeng, Haoyang; Markus, Barak; Georgiev, Stoyan; Daly, Mark J; Price, Alkes L; Pritchard, Jonathan K (January 2016). "Abundant contribution of short tandem repeats to gene expression variation in humans". Nature Genetics. 48: 22–29. doi:10.1038/ng.3461. PMC 4909355. PMID 26642241.


  23. ^ 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.


  24. ^ 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 42017. PMID 7731957.


  25. ^ 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.CS1 maint: Uses authors parameter (link)


  26. ^ 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 539791. PMID 15596718.


  27. ^ 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.


  28. ^ 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. Genet. 110 (5): 488–494. doi:10.1007/s00439-002-0712-8. PMID 12073020.


  29. ^ 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.CS1 maint: Uses authors parameter (link)


  30. ^ Verstrepen K. J.; et al. (2005). "Intragenic tandem repeats generate functional variability". Nat. Genet. 37 (9): 986–990. doi:10.1038/ng1618. PMC 1462868. PMID 16086015.


  31. ^ ab Moxon E. R.; et al. (1994). "Adaptive evolution of highly mutable loci in pathogenic bacteria". Curr. Biol. 4: 24–32. doi:10.1016/S0960-9822(00)00005-1.


  32. ^ 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 1949147. PMID 17726525.
    open access publication – free to read


  33. ^ ab 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.CS1 maint: Uses authors parameter (link)


  34. ^ 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.


  35. ^ Grünewald, Thomas G P; Bernard, Virginie; Gilardi-Hebenstreit, Pascale; Raynal, Virginie; Surdez, Didier; Aynaud, Marie-Ming; Mirabeau, Olivier; Cidre-Aranaz, Florencia; Tirode, Franck (July 2015). "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 4591073. PMID 26214589.


  36. ^ 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 1376805. PMID 9443873.


  37. ^ 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 2731768. PMID 19054556.


  38. ^ 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.


  39. ^ 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.


  40. ^ 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 4691745. PMID 26566657.


  41. ^ Scherer S. (2008). A short guide to the human genome. New York: Cold Spring Harbor University Press.


  42. ^ 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.


  43. ^ van Tilborg, Angela; kompier, Lucy; Lurkin, Irene; Poort, riccardo; El Bouazzaoui, Samira; van der Keur, Kirstin; Zuiverloon, Tahlita; Dyrskjot, Lars; Orntoft, torben; Roobol, Monique; Zwarthoff, Ellen (2012). "Selection of Microsatellite Markers for Bladder Cancer Diagnosis without the Need for Corresponding Blood". PLOS One. 7: e43345. Bibcode:2012PLoSO...743345V. doi:10.1371/journal.pone.0043345. PMC 3425555. PMID 22927958.


  44. ^ Sideris, M; Papagrigoriadis, S (2014). "Molecular biomarkers and classification models in the evaluation of the prognosis of colorectal cancer. Review". Anticancer Res. 34 (5): 2061–2068. PMID 24778007.


  45. ^ Boland CR, Thibodeau SN, Hamilton SR, Sidransky D, Eshleman JR, Burt RW, Meltzer SJ, Rodriguez-Bigas MA, Fodde R, Ranzani GN, Srivastava S (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 Res. 58 (22): 5248–5257. PMID 9823339.CS1 maint: Uses authors parameter (link)


  46. ^ ab Curtis, Caitlin; Hereward, James (August 29, 2017). "From the crime scene to the courtroom: the journey of a DNA sample". The Conversation.


  47. ^ 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.


  48. ^ Angel Carracedo. "DNA Profiling". Archived from the original on 2001-09-27. Retrieved 2010-09-20.


  49. ^ Lászik, A; Brinkmann, B; Sótonyi, P; Palus, A (2000). "Automated fluorescent detection of a 10 loci multiplex for paternity testing". Acta Biologica Hungarica. 51 (1): 99–105. PMID 10866366.


  50. ^ Ott, J.; Wang, J.; Leal, S.M. (2015). "Genetic linkage analysis in the age of whole-genome sequencing". Nat Rev Genet. 16 (5): 275–284. doi:10.1038/nrg3908. PMC 4440411. PMID 25824869.


  51. ^ 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.


  52. ^ 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.


  53. ^ 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.


  54. ^ 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.


  55. ^ Slatkin, M. (1995-01-01). "A measure of population subdivision based on microsatellite allele frequencies". Genetics. 139 (1): 457–462. ISSN 0016-6731. PMC 1206343. PMID 7705646.


  56. ^ 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 1689828. PMID 10331287.


  57. ^ 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.


  58. ^ 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.


  59. ^ Gous Miah, Mohd Y. Rafii, Mohd R. Ismail, Adam B. Puteh, Harun A. Rahim, Kh. Nurul Islam, Mohammad Abdul Latif (2013). "A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance". Int. J. Mol. Sci. 14 (11): 22499–22528. doi:10.3390/ijms141122499. PMID 3856076.CS1 maint: Uses authors parameter (link)


  60. ^ Ben-Ari, Giora; Lavi, Uri (2012). Plant Biotechnology and Agriculture. Chapter 11: Marker-assisted selection in plant breeding. Science Direct. pp. 163–184.


  61. ^ ab "Technology for Resolving STR Alleles". Retrieved 2010-09-20.


  62. ^ "The National DNA Database" (PDF). Retrieved 2010-09-20.


  63. ^ "House of Lords Select Committee on Science and Technology Written Evidence". Retrieved 2010-09-20.


  64. ^ "FBI CODIS Core STR Loci". Retrieved 2010-09-20.


  65. ^ Butler J.M. (2005). Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers, Second Edition. New York: Elsevier Academic Press.


  66. ^ 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.CS1 maint: Uses authors parameter (link)


  67. ^ 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.CS1 maint: Uses authors parameter (link)


  68. ^ Kaukinen KH, Supernault KJ, and Miller KM (2004). "Enrichment of tetranucleotide microsatellite loci from invertebrate species". Journal of Shellfish Research. 23 (2): 621.CS1 maint: Uses authors parameter (link)


  69. ^ Dakin, EE; Avise, JC (2004). "Microsatellite null alleles in parentage analysis". Heredity. 93 (5): 504–509. doi:10.1038/sj.hdy.6800545. PMID 15292911.




Further reading




  • 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 Genet. 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. Biol. 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 Phytol. 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. (2008). "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.CS1 maint: Uses authors parameter (link)


  • 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 3132887. PMID 19478187.



External links



  • About microsatellites:

    • Microsatellite DNA Methodology

    • MicrosatDB

    • Eremorph – web based resource for prediction and study of gene variations



  • 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

    • MREPATT

    • Mreps

    • IMEx

    • FireMuSat2+

    • Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power

    • Poly

    • Tandem Repeats Finder

    • STAR

    • TandemSWAN

    • TRED

    • TROLL

    • SciRoKo

    • SSLP

    • Zebrafish Repeats











-

Popular posts from this blog

Florida Star v. B. J. F.

Image
Florida Star v. B. J. F. From Wikipedia, the free encyclopedia Jump to navigation Jump to search United States Supreme Court case Florida Star v. B. J. F. Supreme Court of the United States Argued March 21, 1989 Decided June 21, 1989 Full case name The Florida Star v. B. J. F. Citations 491 U.S. 524 ( more ) 109 S. Ct. 2603; 105 L. Ed. 2d 443; 1989 U.S. LEXIS 3120; 57 U.S.L.W. 4816; 16 Media L. Rep. 1801 Prior history The Florida Star v. B.J.F., 530 So.2d 286 (1988) Supreme Court of Florida; Florida Star v. B.J.F., 499 So.2d 883 (1986) Fla. Dist. Court of Appeals Holding Florida Stat. § 794.03 is unconstitutional to the extent it makes the truthful reporting of information that was a matter of public record unlawful, as it violates the First Amendment. Court membership Chief Justice William Rehnquist Associate Justices William J. Brennan Jr.  · Byron White Thurgood Marshall  · Harry Blac
Read more

Danny Elfman

Image
Danny Elfman From Wikipedia, the free encyclopedia Jump to navigation Jump to search Danny Elfman Elfman at the 2010 San Diego Comic-Con Born Daniel Robert Elfman ( 1953-05-29 ) May 29, 1953 (age 65) Los Angeles, California, U.S. Spouse(s) Bridget Fonda ( m.  2003) Children 1 Musical career Genres Rock [1] ska [2] new wave film music video game music Occupation(s) Composer, singer, songwriter, record producer Instruments Trombone guitar percussion vocals keyboards [3] Years active 1972–present Associated acts Oingo Boingo James Newton Howard Daniel Robert Elfman (born May 29, 1953) is an American composer, singer, songwriter, and record producer. Elfman first became known for being the lead singer and songwriter for the band Oingo Boingo from 1974 to 1995. He is well known for scoring films and television shows, particularly his frequent collabora
Read more

Retrieve a Users Dashboard in Tumblr with R and TumblR. Oauth Issues

Image
.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ height:90px;width:728px;box-sizing:border-box; } 0 I am trying to use the TumblR package in R to set up the Oauth Authentication to Retrieve a user's dashboard using the second example in tumblR documentation However I get the following error, it seems that using twitter others have been able to use a different function to get around this, but I am not finding the same function available for Tumblr. See twitter package for R authentication: error 401 My code consumer_key <- OKey consumer_secret <- SKey appname <- App_name tokenURL <- 'http://www.tumblr.com/oauth/request_token' accessTokenURL <- 'http://www.tumblr.com/oauth/acces_token'
Read more