ArticleGenome biology2005
Tandem repeat copy-number variation in protein-coding regions of human genes.
Article in Genome biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 67 citations in OpenAlex.
- Epigenetic dysregulation and the etiology of spina bifida.Neurochemistry international · 2025Review
- Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms.Briefings in bioinformatics · 2025Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Phytophthora sojae effector PsAvh113 associates with the soybean transcription factor GmDPB to inhibit catalase-mediated immunity.Plant biotechnology journal · 2023Article
- Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species.Journal of evolutionary biology · 2023Review
- A guide for the diagnosis of rare and undiagnosed disease: beyond the exome.Genome medicine · 2022Review
- Losing DNA methylation at repetitive elements and breaking bad.Epigenetics & chromatin · 2021Review
- Immune activation by a multigene family of lectins with variable tandem repeats in oriental river prawn (Open biology · 2020Article
- Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification.Epigenetics · 2019Article
- Microsatellite Stability in STR AnalysisFrontiers in cellular and infection microbiology · 2019Article
- The Ustilago maydis repetitive effector Rsp3 blocks the antifungal activity of mannose-binding maize proteins.Nature communications · 2018Article
- MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals.Genome research · 2015Article
- Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing.PloS one · 2015Article
- The overdue promise of short tandem repeat variation for heritability.Trends in genetics : TIG · 2014Review
- Large-scale analysis of tandem repeat variability in the human genome.Nucleic acids research · 2014Article
- HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.Bioinformatics (Oxford, England) · 2012Article
- Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences.Genes · 2012Article
- Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.BMC bioinformatics · 2012Article
- Variable numbers of tandem repeats in Plasmodium falciparum genes.Journal of molecular evolution · 2010Article
- TRStalker: an efficient heuristic for finding fuzzy tandem repeats.Bioinformatics (Oxford, England) · 2010Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTandem repeat variation in protein-coding regions will alter protein length and may introduce frameshifts. Tandem repeat variants are associated with variation in pathogenicity in bacteria and with human disease. We characterized tandem repeat polymorphism in human proteins, using the UniGene database, and tested whether these were associated with host defense roles.
resultsProtein-coding tandem repeat copy-number polymorphisms were detected in 249 tandem repeats found in 218 UniGene clusters; observed length differences ranged from 2 to 144 nucleotides, with unit copy lengths ranging from 2 to 57. This corresponded to 1.59% (218/13,749) of proteins investigated carrying detectable polymorphisms in the copy-number of protein-coding tandem repeats. We found no evidence that tandem repeat copy-number polymorphism was significantly elevated in defense-response proteins (p = 0.882). An association with the Gene Ontology term 'protein-binding' remained significant after covariate adjustment and correction for multiple testing. Combining this analysis with previous experimental evaluations of tandem repeat polymorphism, we estimate the approximate mean frequency of tandem repeat polymorphisms in human proteins to be 6%. Because 13.9% of the polymorphisms were not a multiple of three nucleotides, up to 1% of proteins may contain frameshifting tandem repeat polymorphisms.
conclusionAround 1 in 20 human proteins are likely to contain tandem repeat copy-number polymorphisms within coding regions. Such polymorphisms are not more frequent among defense-response proteins; their prevalence among protein-binding proteins may reflect lower selective constraints on their structural modification. The impact of frameshifting and longer copy-number variants on protein function and disease merits further investigation.
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Registered trials
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