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A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers

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In vitro scan for enhancers at the TCF7L2 locus.

D Savic¹, S Y Park, K A Bailey

¹Department of Human Genetics, University of Chicago, 920 E. 58th St, CLSC 319A, Chicago, IL 60637, USA.

|September 27, 2012

Summary

This summary is machine-generated.

This study mapped cis-regulatory elements in the TCF7L2 gene region, identifying sequences linked to type 2 diabetes risk. Allele-specific effects at SNP rs7903146 were confirmed, suggesting peripheral defects contribute to disease.

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Area of Science:

Genetics
Molecular Biology
Endocrinology

Background:

Genome-wide association studies (GWAS) increasingly identify cis-regulatory variation as a driver of complex disease susceptibility.
The transcription factor 7-like 2 (TCF7L2) gene locus is strongly associated with type 2 diabetes risk, with evidence suggesting regulatory mechanisms.

Purpose of the Study:

To systematically fine-map cis-regulatory sequences within the TCF7L2 type 2 diabetes GWAS locus.
To investigate the functional impact of the type 2 diabetes-associated single nucleotide polymorphism (SNP) rs7903146.

Main Methods:

A cell-based enhancer assay was used to screen a 92 kb interval of the TCF7L2 locus across multiple cell lines (HCT-116, Neuro-2a, C2C12, U2OS, MIN6, HepG2).
Chromatin state was evaluated in select regions, and allelic-specific enhancer activity was assessed at SNP rs7903146.

Main Results:

Approximately 30% of tested sequences exhibited cis-regulatory activity, with some enhancers active across multiple cell types and overlapping epigenetic markers.
Allele-specific enhancer properties at rs7903146 were replicated in pancreatic beta cells and observed in other cell lines.

Conclusions:

A detailed map of cis-regulatory elements within the TCF7L2 GWAS locus was generated, supporting the role of cis-regulatory variation in type 2 diabetes predisposition.
The consistent allelic-specific enhancer effects at rs7903146 across cell types suggest a potential peripheral defect in type 2 diabetes etiology.