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GEO help: Mouse over screen elements for information. |
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Status |
Public on Dec 11, 2013 |
Title |
Cohesin is a key determinant of interphase chromosome domain architecture (RNA-seq) |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
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.
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Overall design |
Hi-C, ChIP-Seq and RNA-Seq experiments were conducted in mouse neural stem cells and mouse astrocytes
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Contributor(s) |
Sofueva S, Yaffe E, Chan W, Georgopoulou D, Vietri-Rudan M, Pollard SM, Schroth GP, Tanay A, Hadjur S |
Citation(s) |
24185899 |
Submission date |
Jul 17, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Suzana Hadjur |
E-mail(s) |
s.hadjur@ucl.ac.uk
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Phone |
+44 7798957199
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Organization name |
Ucl
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Department |
Cancer biology
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Lab |
Genome organization
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Street address |
72 Huntley street
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City |
London |
ZIP/Postal code |
Wc1e6bt |
Country |
United Kingdom |
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Platforms (1) |
GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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Samples (8)
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GSM1187679 |
HadjurLab-RNASeq-mAST-Rad21-floxed-72hr, replicate 1 |
GSM1187680 |
HadjurLab-RNASeq-mAST-Rad21-floxed-72hr, replicate 2 |
GSM1187681 |
HadjurLab-RNASeq-mAST-Rad21-deleted-72hr, replicate 1 |
GSM1187682 |
HadjurLab-RNASeq-mAST-Rad21-deleted-72hr, replicate 2 |
GSM1187683 |
HadjurLab-RNASeq-mAST-Rad21-floxed-96hr, replicate 1 |
GSM1187684 |
HadjurLab-RNASeq-mAST-Rad21-floxed-96hr, replicate 2 |
GSM1187685 |
HadjurLab-RNASeq-mAST-Rad21-deleted-96hr, replicate 1 |
GSM1187686 |
HadjurLab-RNASeq-mAST-Rad21-deleted-96hr, replicate 2 |
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This SubSeries is part of SuperSeries: |
GSE49018 |
Cohesin is a key determinant of interphase chromosome domain architecture |
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Relations |
BioProject |
PRJNA212628 |
SRA |
SRP027571 |
Supplementary file |
Size |
Download |
File type/resource |
GSE48965_RNA_mAST.genes.fpkm_tracking.gz |
2.4 Mb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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