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Series GSE36203 Query DataSets for GSE36203
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.
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.
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
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)
GSM883646 Smc1_NPC_ChIPSeq
GSM883648 NPC_input DNA
SRA SRP011234
BioProject PRJNA152875

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Supplementary file Size Download File type/resource
GSE36203_RAW.tar 1.1 Mb (http)(custom) TAR (of BED)
GSE36203_processed_5C_seq_data.txt.gz 9.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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