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Wikipedia

Tandem repeat

January 24, 2023

Not to be confused with Tandemly arrayed genes.

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.

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]

Mechanism

Tandem repeats can occur through different mechanisms. For example, slipped strand mispairing (SSM), (also known as replication slippage), 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.

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. 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).

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]

Nested tandem repeats are described as repeating unit lengths that are variable or unknown and frequently include an asymmetric hierarchy of smaller repeating units. These repeats are constructed from distinct groups of homologous-length monomers. An algorithm known as NTRprism was created by Oxford Nanopore Technologies researchers to enable for the annotation of repetitive structures in built satellite DNA arrays. The algorithm NTRprism is developed to find and display the satellite repeating periodicity.[6]

See also

References

  1. ^ Tandem+Repeat at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. ^ 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.1742-4658.2010.07684.x. PMC 2928880. PMID 20553501.
  3. ^ 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.
  4. ^ Variable+Number+of+Tandem+Repeats at the US National Library of Medicine Medical Subject Headings (MeSH)
  5. ^ 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. S2CID 10680162.
  6. ^ Altemose, Nicolas; Logsdon, Glennis A.; Bzikadze, Andrey V.; Sidhwani, Pragya; Langley, Sasha A.; Caldas, Gina V.; Hoyt, Savannah J.; Uralsky, Lev; Ryabov, Fedor D.; Shew, Colin J.; Sauria, Michael E. G.; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A. (April 2022). "Complete genomic and epigenetic maps of human centromeres". Science. 376 (6588): eabl4178. doi:10.1126/science.abl4178. ISSN 0036-8075. PMC 9233505. PMID 35357911.

External links

  • Examples:
    • VNTRs - info and animated example
  • Databases:
    • TRDB - The 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
    • Tandem Repeats Finder
    • Mreps
    • STAR
    • Splinter
    • Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power
    • - 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

January 24, 2023
tandem, repeat, confused, with, tandemly, arrayed, genes, occur, when, pattern, more, nucleotides, repeated, repetitions, directly, adjacent, each, other, several, protein, domains, also, form, tandem, repeats, within, their, amino, acid, primary, structure, s. Not to be confused with Tandemly arrayed genes 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 ATTCGin which the sequence ATTCG is repeated three times Contents 1 Terminology 2 Mechanism 3 Uses 4 See also 5 References 6 External linksTerminology EditWhen 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 Mechanism EditTandem repeats can occur through different mechanisms For example slipped strand mispairing SSM also known as replication slippage 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 Uses EditTandem 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 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 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 Nested tandem repeats are described as repeating unit lengths that are variable or unknown and frequently include an asymmetric hierarchy of smaller repeating units These repeats are constructed from distinct groups of homologous length monomers An algorithm known as NTRprism was created by Oxford Nanopore Technologies researchers to enable for the annotation of repetitive structures in built satellite DNA arrays The algorithm NTRprism is developed to find and display the satellite repeating periodicity 6 See also EditMicrosatellite Minisatellite ProRepeat Satellite DNA Tandem Repeats Database Tandem repeat locus Variable number tandem repeatsReferences Edit 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 4658 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 S2CID 10680162 Altemose Nicolas Logsdon Glennis A Bzikadze Andrey V Sidhwani Pragya Langley Sasha A Caldas Gina V Hoyt Savannah J Uralsky Lev Ryabov Fedor D Shew Colin J Sauria Michael E G Borchers Matthew Gershman Ariel Mikheenko Alla Shepelev Valery A April 2022 Complete genomic and epigenetic maps of human centromeres Science 376 6588 eabl4178 doi 10 1126 science abl4178 ISSN 0036 8075 PMC 9233505 PMID 35357911 External links EditExamples 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 Tandem Repeats Finder Mreps STAR Splinter 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 TRAL Tandem Repeat Annotation Library a meta predictor tool with statistical filtering with a range of functions for repeat annotation and analyses Retrieved from https en wikipedia org w index php title Tandem repeat amp oldid 1133898745, wikipedia, wiki, book, books, library,

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