Oct 16, 2013

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

Proceedings of the National Academy of Sciences of the United States of America
Stephen C J ParkerNISC Comparative Sequencing Program Authors


Chromatin-based functional genomic analyses and genomewide association studies (GWASs) together implicate enhancers as critical elements influencing gene expression and risk for common diseases. Here, we performed systematic chromatin and transcriptome profiling in human pancreatic islets. Integrated analysis of islet data with those from nine cell types identified specific and significant enrichment of type 2 diabetes and related quantitative trait GWAS variants in islet enhancers. Our integrated chromatin maps reveal that most enhancers are short (median = 0.8 kb). Each cell type also contains a substantial number of more extended (≥ 3 kb) enhancers. Interestingly, these stretch enhancers are often tissue-specific and overlap locus control regions, suggesting that they are important chromatin regulatory beacons. Indeed, we show that (i) tissue specificity of enhancers and nearby gene expression increase with enhancer length; (ii) neighborhoods containing stretch enhancers are enriched for important cell type-specific genes; and (iii) GWAS variants associated with traits relevant to a particular cell type are more enriched in stretch enhancers compared with short enhancers. Reporter constructs containing stretch enhancer seque...Continue Reading

Mentioned in this Paper

Genome-Wide Association Study
Diabetes Mellitus, Non-Insulin-Dependent
Structure of Beta Cell of Islet
Locus Control Region
Tissue Specificity
Cell Culture Techniques
House mice
Chromatin Immunoprecipitation
Gene Expression

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