Tandem repeats occur in
DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form
tandem repeats
Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form tandem repeats within their amino acid primary structure, such as armadil ...
within their amino acid primary structure, such as
armadillo repeat
An armadillo repeat is the name of a characteristic, repetitive amino acid sequence of about 40 residues in length that is found in many proteins. Proteins that contain armadillo repeats typically contain several tandemly repeated copies. Each ar ...
s. However, in proteins, perfect tandem repeats are unlikely in most ''in vivo'' proteins, and most known repeats are in proteins which have been designed.
An example would be:
: ATTCG ATTCG ATTCG
in which the sequence ATTCG is repeated three times.
Terminology
When between 10 and 60 nucleotides are repeated, it is called a
minisatellite
A minisatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 10–60 base pairs) are typically repeated 5-50 times. Minisatellites occur at more than 1,000 locations in the human genome and they are notable for ...
. Those with fewer are known as
microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...
s or
short tandem repeat
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome
...
s.
When exactly two nucleotides are repeated, it is called a ''dinucleotide repeat'' (for example: ACACACAC...). The
microsatellite instability
Microsatellite instability (MSI) is the condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR). The presence of MSI represents phenotypic evidence that MMR is not functioning normal ...
in
hereditary nonpolyposis colon cancer
Hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome is an autosomal dominant genetic condition that is associated with a high risk of colon cancer as well as other cancers including endometrial cancer (second most common), ova ...
most commonly affects such regions.
When three nucleotides are repeated, it is called a ''trinucleotide repeat'' (for example: CAGCAGCAGCAG...), and abnormalities in such regions can give rise to
trinucleotide repeat disorders
Trinucleotide repeat disorders, also known as microsatellite expansion diseases, are a set of over 50 genetic disorders caused by trinucleotide repeat expansion, a kind of mutation in which repeats of three nucleotides ( trinucleotide repeats) inc ...
.
When the repeat unit copy number is variable in the population being considered, it is called a
variable number tandem repeat
A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length (number of repeats) among individua ...
(VNTR).
MeSH
A mesh is a barrier made of connected strands of metal, fiber, or other flexible or ductile materials. A mesh is similar to a web or a net in that it has many attached or woven strands.
Types
* A plastic mesh may be extruded, oriented, ex ...
classifies variable number tandem repeats under minisatellites.
Mechanism
Tandem repeats can occur through different mechanisms. For example, slipped strand mispairing (SSM), (also known as
replication slippage
Replication may refer to:
Science
* Replication (scientific method), one of the main principles of the scientific method, a.k.a. reproducibility
** Replication (statistics), the repetition of a test or complete experiment
** Replication crisis
* ...
), is a mutation process which occurs during DNA replication. It involves denaturation and displacement of the DNA strands, resulting in mispairing of the complementary bases. Slipped strand mispairing is one explanation for the origin and evolution of repetitive DNA sequences.
Other mechanisms include
unequal crossover and
gene conversion
Gene conversion is the process by which one DNA sequence replaces a homologous sequence such that the sequences become identical after the conversion event. Gene conversion can be either allelic, meaning that one allele of the same gene replaces a ...
.
Uses
Tandem repeat describes a pattern that helps determine an individual's inherited traits.
Tandem repeats can be very useful in determining
parentage.
Short tandem repeat
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome
...
s are used for certain
genealogical DNA test
A genealogical DNA test is a DNA-based test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or (with lower reliability) to estimate the ethnic mixt ...
s.
DNA is examined from ''
microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...
s'' within the chromosomal DNA. Parentage can be determined through the similarity in these regions.
Polymorphic tandem repeats (alias VNTRs) are also present in microorganisms and can be used to trace the origin of an outbreak. The corresponding assay in which a collection of VNTRs is typed to characterize a strain is most often called
MLVA
Multiple loci VNTR analysis (MLVA) is a method employed for the genetic analysis of particular microorganisms, such as pathogenic bacteria, that takes advantage of the polymorphism of tandemly repeated DNA sequences. A "VNTR" is a "variable-number ...
(Multiple Loci VNTR Analysis).
In the field of
computer science
Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to Applied science, practical discipli ...
, tandem repeats in strings (e.g., DNA sequences) can be efficiently detected using
suffix tree
In computer science, a suffix tree (also called PAT tree or, in an earlier form, position tree) is a compressed trie containing all the suffixes of the given text as their keys and positions in the text as their values. Suffix trees allow particu ...
s or
suffix array
In computer science, a suffix array is a sorted array of all suffixes of a string. It is a data structure used in, among others, full-text indices, data-compression algorithms, and the field of bibliometrics.
Suffix arrays were introduced by as ...
s.
Studies in 2004 linked the unusual genetic plasticity of
dog
The dog (''Canis familiaris'' or ''Canis lupus familiaris'') is a domesticated descendant of the wolf. Also called the domestic dog, it is derived from the extinct Pleistocene wolf, and the modern wolf is the dog's nearest living relative. Do ...
s to mutations in tandem repeats.
See also
*
Microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...
*
Minisatellite
A minisatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 10–60 base pairs) are typically repeated 5-50 times. Minisatellites occur at more than 1,000 locations in the human genome and they are notable for ...
*
ProRepeat ProRepeat is a database of protein repeats.{{cite journal , last=Luo, first=Hong, author2=Lin Ke , author3=David Audrey , author4=Nijveen Harm , author5=Leunissen Jack A M , date=Jan 2012, title=ProRepeat: an integrated repository for studying amino ...
*
Satellite DNA Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA. Satellite DNA is the main component of functional centromeres, and form the main structural constituent of heterochromatin.
The name "satellite DNA" refers to the p ...
*
Tandem Repeats Database
The Tandem Repeats Database (TRDB) is a database of tandem repeats in genomic DNA.
See also
* Tandem repeat
Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other ...
*
Tandem repeat locus
Variable number of tandem repeat locus (VNTR locus) is any DNA sequence that exist in multiple copies strung together in a variety of tandem lengths. The number of repeat copies present at a locus can be visualized by means of a Multi-locus or Mul ...
*
Variable number tandem repeat
A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length (number of repeats) among individua ...
s
References
External links
*Examples:
*
VNTRs- info and animated example
*Databases:
*
TRDB - The Tandem Repeats Database *
The Microorganisms Tandem Repeats Database*
Short Tandem Repeats Database*
Tandem Repeats in major genomes *Search tools:
TAPO: A combined method for the identification of tandem repeats in protein structures*
*
Mreps*
STAR*
Splinter*
TRED - Tandem Repeats over the Edit Distance*
*
Microsatellite repeats finder*
JSTRING - Java Search for Tandem Repeats in genomes*
**
ttps://web.archive.org/web/20140606101328/http://ugene.unipro.ru/documentation/manual/plugins/repeat_finder.html#tandem-repeats UGENE - an ultra fast and memory efficient open-source tandem repeats finder implementation.
TRAL: Tandem Repeat Annotation Library - a meta-predictor tool with statistical filtering, with a range of functions for repeat annotation and analyses
{{Organisms et al.
Repetitive DNA sequences
de:Tandemwiederholung