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Series GSE51311 Query DataSets for GSE51311
Status Public on Nov 08, 2013
Title Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (ChIP-seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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 pro- filing in human pancreatic islets. Integrated analysis of islet data with those generated by the ENCODE project in 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 rele- vant to a particular cell type are more enriched in stretch enhancers compared with short enhancers. Reporter constructs containing stretch enhancer sequences exhibited tissue-specific activity in cell culture experiments and in transgenic mice. These results suggest that stretch enhancers are critical chromatin elements for coordinating cell type–specific regulatory programs and that sequence variation in stretch enhancers affects risk of major common human diseases.
 
Overall design Integrated analysis of islet chromatin modification and transcriptome data with those generated by the ENCODE project.

NISC Comparative Sequencing Program
Web link http://research.nhgri.nih.gov/manuscripts/Collins/islet_chromatin
 
Contributor(s) Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N, Black BL, Visel A, Pennacchio LA, Collins FS
Citation(s) 24127591
Submission date Sep 30, 2013
Last update date Dec 03, 2018
Contact name Francis S Collins
E-mail collinsf@mail.nih.gov
Organization name NHGRI
Department Genome Technology Branch
Lab Molecular Genetics Section
Street address 1 Center Drive, Rm 126
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (9)
GSM1261670 UG3360_H3K36me3
GSM1261671 UG3360_Input
GSM1261672 ULI102_H3K27ac
This SubSeries is part of SuperSeries:
GSE51312 Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants
Relations
BioProject PRJNA227219
SRA SRP032815

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE51311_Islets_chromHMM.bed.gz 6.2 Mb (ftp)(http) BED
Raw data are available in SRA
Processed data is available on Series record

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