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| Status |
Public on Nov 02, 2010 |
| Title |
Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Identifying cis-regulatory elements is important to understand how human pancreatic islets modulate gene expression in physiologic or pathophysiologic (e.g., diabetic) conditions. We conducted genome-wide analysis of DNase I hypersensitive sites, histone H3 lysine methylation marks (K4me1, K4me3, K79me2), and CCCTC factor (CTCF) binding in human islets. This identified ~18,000 putative promoters (several hundred novel and islet-active). Surprisingly, active promoter marks were absent at genes encoding islet-specific hormones, suggesting a distinct regulatory mechanism. Of 34,039 distal (non-promoter) regulatory elements, 47% are islet-unique and 22% are CTCF-bound. These findings present a global snapshot of the human islet epigenome and should provide functional context for non-coding variants emerging from genetic studies of T2D and other pancreatic islet disorders.
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| Overall design |
Three different islet samples were tested for DNase I hypersensitivity by DNase-Seq. Five different primary pancreatic islet samples were evaluated for several chromatin modifications (H3K4me3, H3K4me1, H3K79me2) by ChIP-seq. One islet sample was evaluated for CTCF binding via ChIP-seq, All ChIP-seq samples have both non-specific IP (GFP) and input DNA controls.
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| Contributor(s) |
Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS |
| Citation(s) |
21035756, 23997652 |
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| Submission date |
Aug 24, 2010 |
| Last update date |
Aug 13, 2019 |
| Contact name |
Francis S Collins |
| E-mail(s) |
collinsf@mail.nih.gov
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| Organization name |
NHGRI
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| Department |
Genome Technology Branch
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| Lab |
Molecular Genetics Section
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| Street address |
1 Center Drive, Rm 126
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (25)
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| Relations |
| SRA |
SRP003499 |
| BioProject |
PRJNA130725 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23784_RAW.tar |
888.6 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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