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| Status |
Public on May 24, 2013 |
| Title |
Architectural protein subclasses shape 3-D organization of genomes during lineage commitment |
| Organism |
Mus musculus |
| Experiment type |
Genome variation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Understanding the topological configurations of chromatin can reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in architecture at different length scales. CTCF/cohesin anchor long-range constitutive interactions that might form the topological basis for invariant sub-domains. Conversely, Mediator/cohesin together with pioneer factors bridge short-range enhancer-promoter interactions within and between larger sub-domains. Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions. We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales.
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| |
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| Overall design |
Analysis of higher-order chromatin chromatin architecture in mouse ES cells and ES-derived NPCs. Analysis of CTCF and Smc1 occupied sites in ES-derived NPCs.
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| |
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| Contributor(s) |
Phillips-Cremins JE |
| Citation(s) |
23706625 |
| |
| Submission date |
Mar 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Elizabeth Phillips-Cremins |
| E-mail(s) |
Jennifer.Phillips-Cremins@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School and Emory University
|
| Department |
Program in Systems Biology and Department of Biology
|
| Lab |
Job Dekker Laboratory and Victor Corces Laboratory
|
| Street address |
364 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (7)
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| Relations |
| SRA |
SRP011234 |
| BioProject |
PRJNA152875 |
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