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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2013 |
| Title |
Distinct properties of cell type-specific and shared transcription factor binding sites |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Most human transcription factors bind a small subset of potential genomic sites and often use different subsets in different cell types. To identify mechanisms that govern cell type-specific transcription factor binding, we used an integrative approach to study estrogen receptor α (ER). We found that ER exhibits two distinct modes of binding. Shared sites, bound in multiple cell types, are characterized by high affinity estrogen response elements (EREs), inaccessible chromatin and a lack of DNA methylation, while cell-specific sites are characterized by a lack of EREs, co-occurrence with other transcription factors and cell type-specific chromatin accessibility and DNA methylation. These observations enabled accurate quantitative models of ER binding that suggest tethering of ER to one-third of cell-specific sites. The distinct properties of cell-specific binding were also observed with glucocorticoid receptor and for ER in primary mouse tissues, representing an elegant genomic encoding scheme for generating cell type-specific gene regulation.
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| Overall design |
ChIP-seq of transcription factors in mouse tissues
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| Contributor(s) |
Gertz J, Myers RM |
| Citation(s) |
24076218 |
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| Submission date |
Aug 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Gertz |
| E-mail(s) |
jgertz@hudsonalpha.com
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| Organization name |
HudsonAlpha Institute
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| Street address |
601 Genome Way
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| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA215762 |
| SRA |
SRP028899 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE49993_RAW.tar |
630.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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