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E-GEOD-48965 - Cohesin is a key determinant of interphase chromosome domain architecture (RNA-seq)

Status
Released on 11 December 2013, last updated on 3 June 2014
Organism
Mus musculus
Samples (8)
Protocols (3)
Description
To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. These loops demarcate topological domains and form intricate internal structures within them. Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains. Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes. Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programs within them. Hi-C, ChIP-Seq and RNA-Seq experiments were conducted in mouse neural stem cells and mouse astrocytes
Experiment type
RNA-seq of coding RNA 
Contacts
Amos Tanay, Dimitra Georgopoulou, Eitan Yaffe, Gary P Schroth, Matteo Vietri-Rudan, Sevil Sofueva, Steven M Pollard, Suzana Hadjur, Wen-Ching Chan
Citation
Cohesin-mediated interactions organize chromosomal domain architecture. Sofueva S, Yaffe E, Chan WC, Georgopoulou D, Vietri Rudan M, Mira-Bontenbal H, Pollard SM, Schroth GP, Tanay A, Hadjur S. , PMID:24185899
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-48965.idf.txt
Sample and data relationshipE-GEOD-48965.sdrf.txt
Additional data (1)E-GEOD-48965.additional.1.zip
Links