Our long-term goal is to understand the mechanisms by which sequence variations in enhancers affect gene expression. Genome-wide association study (GWAS) and expression quantitative trait loci (eQTL) mapping have revealed thousands of sequence variants that are associated with common diseases and gene expression variations. A large portion of the associated variants is located far away from genes, making them difficult to interpret. Given its abundance and essential role in gene regulation, sequence variants in transcriptional enhancers could be the cause of many phenotypic variations. Currently, identifying such variants remains a challenge because of several hurdles: i) rudimentary annotation of tissue-specific enhancers;ii) lack of strategies to precisely pinpoint the identity and location of transcription factor binding sites (TFBSs) within an enhancer;and iii lack of strategies to assign enhancer targets. By addressing these hurdles, the objective of this project is to design and test a computational framework that enables systematic and rapid screen of enhancer sequence variants that cause complex diseases. As an ultimate test of our approach, we will apply our computational strategy to screen and characterize enhancer variants that are associated with a common autoimmune disease, Type 1 Diabetes. To make the methods developed in this project useful to a much broader community of users, we will develop an open-source software suite and a database dedicated to the analysis and curation of regulatory mutations in enhancers. It is anticipated that the outcomes of this project will have an important positive impact because it promises to significantly accelerate the discovery and systematic documentation of causal genetic variants in the noncoding portion of the human genome.

Public Health Relevance

Thousands of genetic variants have been associated with human diseases but very few successful findings of actual etiologic variants have been reported. The need for computational and high throughput methods is essential to accelerate the discovery of disease-causing variants.

National Institute of Health (NIH)
Research Project (R01)
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Special Emphasis Panel (ZGM1)
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Krasnewich, Donna M
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University of Iowa
Internal Medicine/Medicine
Schools of Medicine
Iowa City
United States
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Steinke, Farrah C; Yu, Shuyang; Zhou, Xinyuan et al. (2014) TCF-1 and LEF-1 act upstream of Th-POK to promote the CD4(+) T cell fate and interact with Runx3 to silence Cd4 in CD8(+) T cells. Nat Immunol 15:646-56
He, Bing; Chen, Changya; Teng, Li et al. (2014) Global view of enhancer-promoter interactome in human cells. Proc Natl Acad Sci U S A 111:E2191-9