Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other.[1] Several protein domains also form tandem repeats within their amino acid primary structure, such as Armadillo repeats. However, in proteins, perfect tandem repeats are unlikely in most in vivo proteins, and most known repeats are in proteins which have been designed.[2]
An example would be:
- ATTCG ATTCG ATTCG
in which the sequence ATTCG is repeated three times.
Contents
- 1 Terminology
- 2 Uses
- 3 See also
- 4 References
- 5 External links
Terminology
When between 10 and 60 nucleotides are repeated, it is called a minisatellite. Those with fewer are known as microsatellites or short tandem repeats.
When exactly two nucleotides are repeated, it is called a dinucleotide repeat (for example: ACACACAC…). The microsatellite instability in hereditary nonpolyposis colon cancer most commonly affects such regions.[3]
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.
When the repeat unit copy number is variable in the population being considered, it is called a variable number tandem repeat (VNTR). MeSH classifies variable number tandem repeats under minisatellites.[4]
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 repeats are used for certain genealogical DNA tests.
DNA is examined from microsatellites within the chromosomal DNA. Minisatellite is another way of saying special regions of the loci. Polymerase chain reaction (or PCR) is performed on the minisatellite areas. The PCR must be performed on each organism being tested. The amplified material is then run through electrophoresis. By checking the percentage of bands that match, parentage is determined.
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).
In the field of Computer Science, tandem repeats in strings (e.g., DNA sequences) can be efficiently detected using suffix trees or suffix arrays.
Studies in 2004 linked the unusual genetic plasticity of dogs to mutations in tandem repeats.[5]
See also
- Variable number tandem repeats
- Short tandem repeats
- Satellite DNA
- Minisatellite
- Microsatellite
- Tandem Repeats Database
- Amino acid tandem repeat
References
- ^ Tandem Repeat at the US National Library of Medicine Medical Subject Headings (MeSH)
- ^ Jorda J, Xue B, Uversky VN, Kajava AV (June 2010). "Protein tandem repeats - the more perfect, the less structured". The FEBS Journal 277 (12): 2673–82. doi:10.1111/j.1742-464X.2010.07684.x. PMC 2928880. PMID 20553501.
- ^ Oki E, Oda S, Maehara Y, Sugimachi K (March 1999). "Mutated gene-specific phenotypes of dinucleotide repeat instability in human colorectal carcinoma cell lines deficient in DNA mismatch repair". Oncogene 18 (12): 2143–7. doi:10.1038/sj.onc.1202583. PMID 10321739.
- ^ Variable Number of Tandem Repeats at the US National Library of Medicine Medical Subject Headings (MeSH)
- ^ Pennisi E (December 2004). "Genetics. A ruff theory of evolution: gene stutters drive dog shape". Science 306 (5705): 2172. doi:10.1126/science.306.5705.2172. PMID 15618495.
External links
- Examples:
- VNTRs - info and animated example
- Databases:
- The Microorganisms Tandem Repeats Database
- Short Tandem Repeats Database
- Search tools:
- TAPO: A combined method for the identification of tandem repeats in protein structures
- Tandem Repeats Finder
- Mreps
- STAR
- TRED - Tandem Repeats over the Edit Distance
- TandemSWAN
- Microsatellite repeats finder
- JSTRING - Java Search for Tandem Repeats in genomes
- Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power
- UGENE - an ultra fast and memory efficient open-source tandem repeats finder implementation.
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Genetics: repeated sequence
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Repeatome
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| Tandem repeats |
- Satellite DNA
- Variable number tandem repeat/Minisatellite
- Short tandem repeat/Microsatellite (Trinucleotide repeat disorders)
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| Interspersed repeats |
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Transposon
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Retrotransposon
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DNA transposon
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| Genomic island |
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- 1. 遺伝的変異の概要overview of genetic variation [show details]
…Disease-causing expansions of tandem repeat sequences (trinucleotide repeats) have been described in coding regions of genes, intronic sequences, and 5' untranslated regions (5’UTR) of sequence and are mutated in …
- 2. 遺伝学：用語集genetics glossary of terms [show details]
… single-cell RNA sequencing and exome sequencing. Barcoding also refers to methods for determining the species of origin of a DNA sample on the basis of the DNA sequence itself.… Microsatellites are also known as short tandem repeat markers (STRs) or short tandem repeat polymorphisms (STRPs).…
- 3. 着床前遺伝子検査preimplantation genetic testing [show details]
…cross over. Improved PGT-M protocols that include closely linked markers, STRs (Short Tandem Repeats), or SNPs (Simple Sequence Repeats) may alleviate those problems. The oocyte must either be fertilized …
- 4. ベックウィズ・ヴィーデマン症候群beckwith wiedemann syndrome [show details]
… CCCTC-binding factor (CTCF) to its consensus sequence within IC1. CTCF only binds to the unmethylated sequence (maternal allele) and modulates the… UPD can be confirmed by analysis of short tandem repeats when it is suggested by methylation alterations…
- 5. 薬理ゲノム学の概要overview of pharmacogenomics [show details]
…various components of the genome on response to a drug. Among the most commonly studied are genetic sequence variants, structural changes in chromosomes (eg, translocations), epigenetic variants (eg, changes … percent. Other forms of variation include insertions, deletions, copy number variants, and short tandem repeats. Variants that are seen at much lower prevalence than 1 percent of the population are often …