A MICROSATELLITE is a tract of repetitive
DNA in which certain DNA
motifs (ranging in length from 2–13 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
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. A type of microsatellites called SHORT TANDEM REPEATS (STRS) are
often used by forensic geneticists because although the repeating
sequence of base pairs of a specific microsatellite does not change
from person to person, the number of times the sequence repeats does
change. This allows the number of repeats of a sequence to identify a
person through his/her
DNA if the number of sequence repeats matches
DNA basis used for comparison. STR s can also eliminate a
person from suspicion or reduce the suspicion of a person if he/she
does not have the same number of sequence repeats as the comparate DNA
. This also applies to all other organisms that have STRs.
Microsatellites are often called SIMPLE SEQUENCE REPEATS (SSRS) by
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
Mutation mechanisms and mutation rates
Microsatellite mutation rates
* 3 Biological effects of microsatellite mutations
* 3.1 Effects on proteins
* 3.2 Effects on gene regulation
* 3.3 Effects within introns
* 3.4 Effects within transposons
* 4 Analysis
* 4.1 Amplification
* 4.2 Design of microsatellite primers
* 4.3 ISSR-PCR
* 4.4 Limitations
* 5 Applications
* 5.1 Forensic analysis
* 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
MUTATION MECHANISMS AND MUTATION RATES
DNA strand slippage during replication of an STR locus. Boxes
DNA units. Arrows indicate the direction in which
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
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
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
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
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. 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. A number of
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
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
DNA from the focal species. These random segments are
inserted into a plasmid or bacteriophage vector , which is in turn
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
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
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
DNA sequencing . The use of PCR means that microsatellite
length analysis is prone to PCR limitations like any other
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
* 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
* 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 .
A partial human STR profile obtained using the Applied
Biosystems Identifiler kit
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
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
SGM+ system uses 10 loci and a sex marker , rather than the
American 13 loci.
Y-STRs (microsatellites on the
Y chromosome ) are often used in
DNA testing .
Consensus neighbor-joining tree of 249 human populations and six
chimpanzee populations. Created based on 246 microsatellite markers.
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.
* Long interspersed repetitive element
* Short interspersed repetitive element
Simple sequence length polymorphism (SSLP)
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* About microsatellites:
* Eremorph – web based resource for prediction and study of gene