Project Description

A Table of Short Tandem Repeats in Regulatory Regions of the Human Genome

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 regulatory regions, TRs can modify chromatin structure, affecting transcription and resulting in altered gene expression and protein abundance.

The most common TRs are short tandem repeats (STRs), or microsatellites. Promoter located STRs are more polymorphic than coding region STRs and may be common drivers of phenotypic variation.

The research team performed genome-wide analysis to identify all STRs present in a 3 kilobase region overlapping the transcription start sites of genes (see figure above).

The Short Tandem Repeats in Regulatory Regions Table, STaRRRT, contains the results of this analysis, outlining the characteristics of 5,264 STRs present in the upstream regulatory region of 4,441 human genes.

This is a readily-searchable resource for investigating potentially polymorphic STRs that could influence the expression of any gene of interest. Gene set enrichment analysis has revealed significant enrichment for STRs in cellular, transcriptional and neurological system gene promoters and genes important in calcium homeostasis.

The processes enriched for STRs provide potential novel targets for diagnosing and treating disease and support a role for STRs in evolution of the human genome.

Access the complete article in BMC Genomics here

Please cite this article as: Bolton et al.: STaRRRT: a table of short tandem repeats in regulatory regions of the human genome. BMC Genomics 2013 14:795

Download the resource by clicking on the link below:

STaRRRT_final

The research team includes:

Katherine A. Bolton1,2*, Jason P. Ross3,4*, Desma M. Grice1,2,3,4, Nikola A. Bowden1,2, Elizabeth G. Holliday1,5, Kelly A. Avery-Kiejda1,2 and Rodney J. Scott1,2,6,7

1 Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, NSW Australia

2 Priority Research Centre for Cancer, School of Biomedical Sciences and Pharmacy, University of Newcastle, NSW Australia

3 Preventative Health National Research Flagship, CSIRO, North Ryde, NSW Australia

4 Animal Food and Health Sciences, CSIRO, North Ryde, NSW Australia

5 School of Medicine and Public Health, University of Newcastle, NSW Australia

6 Hunter Area Pathology Service, Hunter New England Health, Newcastle, NSW Australia

* These authors contributed equally

7 Corresponding author: Professor Rodney Scott, Head of Discipline, School of Biomedical Sciences and Pharmacy, University of Newcastle, NSW Australia