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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 24, 2011 |
| Title |
The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. |
| Organism |
Mus musculus |
| Experiment type |
Genome variation profiling by high throughput sequencing
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| Summary |
3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps of the active and inactive X-chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial re-folding of the inactive X into a conformation resembling the active X, without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X-chromosome independently of transcription.
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| Overall design |
Five or six 4C viewpoints were applied on the mouse female wild type active X-chromosome, the wild type inactive X-chromosome, the conditional Xist X-chromosome and the Xist knock out X-chromosome
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| Contributor(s) |
Splinter E, de Wit E, Nora EP, Klous P, van de Werken HJ, Zhu Y, Kaaij LJ, van Ijcken W, Gribnau J, Heard E, de Laat W |
| Citation(s) |
21690198 |
| Submission date |
May 24, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Erik Splinter |
| E-mail(s) |
w.laat@hubrecht.eu
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| Organization name |
Hubrecht Institute
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (28)
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| GSM730552 |
Slitrk4_Xa_NPC 129Xa-CASTXi (#169) |
| GSM730553 |
Pcdh11x_Xa_NPC 129Xi-CASTXa (#170) |
| GSM730554 |
Jarid1C_Xa_NPC 129Xa-CASTXi (#132) |
| GSM730555 |
R23a_NPC 129Xi-CASTXa (#137) |
| GSM730556 |
Pctk1_Xi_NPC 129Xi-CASTXa (#137) |
| GSM730557 |
MeCP2_Xi_NPC 129Xi-CASTXa (#170) |
| GSM730558 |
Slitrk4 _Xi_NPC 129Xi-CASTXa (#170) |
| GSM730559 |
Pcdh11x_Xi_NPC 129Xa-CASTXi (#169) |
| GSM730560 |
Xist_Xi_NPC 129Xi-CASTXa (#170) |
| GSM730561 |
Jarid1C_Xi_NPC 129Xi-CASTXa (#137) |
| GSM730562 |
R23a_NPC 129Xi-CastXa (#179) |
| GSM730563 |
Pctk1_condXi_NPC 129Xi-CastXa (#179) |
| GSM730564 |
Mecp2_condXi_NPC 129Xi-CastXa (#177) |
| GSM730565 |
Pcdh11X_condXi_NPC 129Xi-CastXa (#178) |
| GSM730566 |
Slitrk4_condXi_NPC 129Xi-CastXa (#177) |
| GSM730567 |
Xist_condXi_NPC 129Xi-CastXa (#177) |
| GSM730568 |
Jarid1C_condXi_NPC 129Xi-CastXa (#178) |
| GSM730569 |
Sox3_condXi_NPC 129Xi-CastXa (#177) |
| GSM730570 |
R23a_KOXi_NPC 129Xi-CastXa (#182) |
| GSM730571 |
Pctk1_KOXi_NPC 129Xi-CastXa (#182) |
| GSM730572 |
Mecp2_KOXi_NPC 129Xi-CastXa (#180) |
| GSM730573 |
Pcdh11X_KOXi_NPC 129Xi-CastXa (#181) |
| GSM730574 |
Slitrk4_KOXi_NPC 129Xi-CastXa (#180) |
| GSM730575 |
Jarid1C_KOXi_NPC 129Xi-CastXa (#181) |
| GSM730576 |
Sox3_KOXi_NPC 129Xi-CastXa (#180) |
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| Relations |
| SRA |
SRP006842 |
| BioProject |
PRJNA141457 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE29509_RAW.tar |
122.1 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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