An in vivo cis-regulatory screen at the type 2 diabetes associated TCF7L2 locus identifies multiple tissue-specific enhancers

• Published in: PloS one 2012-05, Vol.7 (5), p.e36501-e36501
• Main Authors: Savic, Daniel, Bell, Graeme I, Nobrega, Marcelo A
• Format: Article
• Language: English
• Subjects: Alleles; Animals; Artificial chromosomes; Atherosclerosis; Bacteria; Bacterial artificial chromosomes; Beta cells; Biology; Brain; Cardiovascular disease; Chromosomes, Artificial, Bacterial - genetics; Cloning; Colorectal cancer; Comorbidity; Complexity; Conservation; Conserved sequence; Coronary vessels; Development and progression; Diabetes; Diabetes mellitus; Diabetes Mellitus, Type 2 - genetics; Diabetes Mellitus, Type 2 - metabolism; Diabetes Mellitus, Type 2 - pathology; Disruption; Enhancer Elements, Genetic; Enhancers; Etiology; Evolutionary conservation; Gene mapping; Genetic engineering; Genetic Loci; Genetic Predisposition to Disease; Genetics; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomic Library; Genomics; Health risks; Health screening; Insulin-Secreting Cells - metabolism; Insulin-Secreting Cells - pathology; Interrogation; Loci; Medicine; Metabolism; Mice; Mice, Transgenic; Mortality; Neurological disorders; Organ Specificity - genetics; Pancreas; Pancreatic beta cells; Polymorphism; Polymorphism, Single Nucleotide; Potassium; Regulatory sequences; Rodents; Schizophrenia; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Studies; Surveys; Transcription factors; Transgenic; Trends; Type 2 diabetes
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0036501

Genome-wide association studies (GWAS) have repeatedly shown an association between non-coding variants in the TCF7L2 locus and risk for type 2 diabetes (T2D), implicating a role for cis-regulatory variation within this locus in disease etiology. Supporting this hypothesis, we previously localized complex regulatory activity to the TCF7L2 T2D-associated interval using an in vivo bacterial artificial chromosome (BAC) enhancer-trapping reporter strategy. To follow-up on this broad initial survey of the TCF7L2 regulatory landscape, we performed a fine-mapping enhancer scan using in vivo mouse transgenic reporter assays. We functionally interrogated approximately 50% of the sequences within the T2D-associated interval, utilizing sequence conservation within this 92-kb interval to determine the regulatory potential of all evolutionary conserved sequences that exhibited conservation to the non-eutherian mammal opossum. Included in this study was a detailed functional interrogation of sequences spanning both protective and risk alleles of single nucleotide polymorphism (SNP) rs7903146, which has exhibited allele-specific enhancer function in pancreatic beta cells. Using these assays, we identified nine segments regulating various aspects of the TCF7L2 expression profile and that constitute nearly 70% of the sequences tested. These results highlight the regulatory complexity of this interval and support the notion that a TCF7L2 cis-regulatory disruption leads to T2D predisposition.