STaRRRT: a table of short tandem repeats in regulatory regions of the human genome

BMC Genomics

Research Article

Nikola A Bowden¹  Katherine A Bolton¹  Kelly A Avery-Kiejda¹  Rodney J Scott²  Desma M Grice³  Elizabeth G Holliday⁴  Jason P Ross⁵ 

[1] Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, NSW, Australia;Priority Research Centre for Cancer, School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia;Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, NSW, Australia;Priority Research Centre for Cancer, School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia;Hunter Area Pathology Service, Hunter New England Health, Newcastle, NSW, Australia;Head of the Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, University Drive, 2305, Callaghan, NSW, Australia;Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, NSW, Australia;Priority Research Centre for Cancer, School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia;Preventative Health National Research Flagship, CSIRO, North Ryde, NSW, Australia;Animal Food and Health Sciences, CSIRO, North Ryde, NSW, Australia;Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, NSW, Australia;School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia;Preventative Health National Research Flagship, CSIRO, North Ryde, NSW, Australia;Animal Food and Health Sciences, CSIRO, North Ryde, NSW, Australia;

关键词: Short tandem repeats;    STR;    Microsatellites;    Simple sequence repeats;    SSR;    Promoter;    Regulatory region;    Neurological disease;    Neural genes;    Evolution;   

DOI  :  10.1186/1471-2164-14-795

 received in 2013-05-27, accepted in 2013-11-05,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundTandem 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.ResultsThe 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.ConclusionsSTaRRRT 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.

【 授权许可】

Unknown   
© Bolton et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.