STaRRRT: a table of short tandem repeats in regulatory regions of the human genome
- PMID: 24228761
- PMCID: PMC3840602
- DOI: 10.1186/1471-2164-14-795
STaRRRT: a table of short tandem repeats in regulatory regions of the human genome
Abstract
Background: Tandem repeats (TRs) are unstable regions commonly found within genomes that have consequences for evolution and disease. In humans, polymorphic TRs are known to cause neurodegenerative and neuromuscular disorders as well as being associated with complex diseases such as diabetes and cancer. If present in upstream regulatory regions, TRs can modify chromatin structure and affect transcription; resulting in altered gene expression and protein abundance. The most common TRs are short tandem repeats (STRs), or microsatellites. Promoter located STRs are considerably more polymorphic than coding region STRs. As such, they may be a common driver of phenotypic variation. To study STRs located in regulatory regions, we have performed genome-wide analysis to identify all STRs present in a region that is 2 kilobases upstream and 1 kilobase downstream of the transcription start sites of genes.
Results: The Short Tandem Repeats in Regulatory Regions Table, STaRRRT, contains the results of the genome-wide analysis, outlining the characteristics of 5,264 STRs present in the upstream regulatory region of 4,441 human genes. Gene set enrichment analysis has revealed significant enrichment for STRs in cellular, transcriptional and neurological system gene promoters and genes important in ion and calcium homeostasis. The set of enriched terms has broad similarity to that seen in coding regions, suggesting that regulatory region STRs are subject to similar evolutionary pressures as STRs in coding regions and may, like coding region STRs, have an important role in controlling gene expression.
Conclusions: STaRRRT is a readily-searchable resource for investigating potentially polymorphic STRs that could influence the expression of any gene of interest. The processes and genes enriched for regulatory region STRs provide potential novel targets for diagnosing and treating disease, and support a role for these STRs in the evolution of the human genome.
Figures
Similar articles
-
Evolutionary trend of exceptionally long human core promoter short tandem repeats.Gene. 2012 Oct 1;507(1):61-7. doi: 10.1016/j.gene.2012.07.001. Epub 2012 Jul 13. Gene. 2012. PMID: 22796130
-
Genome-scale portrait and evolutionary significance of human-specific core promoter tri- and tetranucleotide short tandem repeats.Hum Genomics. 2018 Apr 5;12(1):17. doi: 10.1186/s40246-018-0149-3. Hum Genomics. 2018. PMID: 29622039 Free PMC article.
-
Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements.PLoS One. 2013;8(2):e54710. doi: 10.1371/journal.pone.0054710. Epub 2013 Feb 6. PLoS One. 2013. PMID: 23405090 Free PMC article.
-
A genomic view of short tandem repeats.Curr Opin Genet Dev. 2017 Jun;44:9-16. doi: 10.1016/j.gde.2017.01.012. Epub 2017 Feb 16. Curr Opin Genet Dev. 2017. PMID: 28213161 Review.
-
Variable tandem repeats accelerate evolution of coding and regulatory sequences.Annu Rev Genet. 2010;44:445-77. doi: 10.1146/annurev-genet-072610-155046. Annu Rev Genet. 2010. PMID: 20809801 Review.
Cited by
-
Native functions of short tandem repeats.Elife. 2023 Mar 20;12:e84043. doi: 10.7554/eLife.84043. Elife. 2023. PMID: 36940239 Free PMC article.
-
Looking beyond the cytogenetics in haematological malignancies: decoding the role of tandem repeats in DNA repair genes.Mol Biol Rep. 2022 Nov;49(11):10293-10305. doi: 10.1007/s11033-022-07761-y. Epub 2022 Sep 12. Mol Biol Rep. 2022. PMID: 36097110
-
Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species.PLoS Genet. 2022 Jan 10;18(1):e1009604. doi: 10.1371/journal.pgen.1009604. eCollection 2022 Jan. PLoS Genet. 2022. PMID: 35007277 Free PMC article.
-
A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.Genet Sel Evol. 2021 Apr 23;53(1):39. doi: 10.1186/s12711-021-00631-4. Genet Sel Evol. 2021. PMID: 33892623 Free PMC article.
-
Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition.BMC Genomics. 2020 Nov 30;21(1):842. doi: 10.1186/s12864-020-07222-5. BMC Genomics. 2020. PMID: 33256598 Free PMC article.
References
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials