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| Status |
Public on Mar 01, 2014 |
| Title |
Clustering of CpG islands constitutes an important determinant of the interphase chromosome 3D organization [ChIP-Seq] |
| Organism |
Gallus gallus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Using 4C-Seq experimental procedure we have characterized, in cultured chicken lymphoid and erythroid cells, genome-wide patterns of spatial contacts of several CpG islands scattered along the chromosome 14. A clear tendency for interaction of CpG islands present within the same and different chromosomes has been observed. Accordingly, preferential spatial contacts between Sp1 binding motifs, and other GC-rich genomic elements including DNA sequence motifs capable to form G-quadruplexes were demonstrated. On the other hand, an anchor placed in gene/CpG islands-poor area was found to form spatial contacts with other gene/CpG islands-poor areas within chromosome 14 and other chromosomes. These results corroborate the two compartments model of interphase chromosome spatial organization and suggest that clustering of CpG islands harboring promoters and origins of DNA replication constitutes an important determinant of the 3D organization of eukaryotic genome in the cell nucleus. Using ChIP-Seq experimental procedure we have mapped genome-wide the CTCF deposition sites in chicken lymphoid and erythroid cells subjected to the 4C analysis. A good correlation between the density of these sites and the level of 4C signals was observed for the anchors located in CpG islands. It is thus possible that CTCF contributes to the clustering of CpG islands revealed in our experiments.
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| Overall design |
Using ChIP-Seq experimental procedure we have mapped genome-wide the CTCF deposition sites in chicken lymphoid and erythroid cells subjected to the 4C analysis.
CTCF deposition sites in chicken lymphoid and erythroid (induced and non-induced) cells.
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| Contributor(s) |
Kotova ES, Akopov SB, Nikolaev LG, Sverdlov ED, Iarovaia OV, Razin SV |
| Citation(s) |
24736527 |
| |
| Submission date |
Oct 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Artem V Artemov |
| Organization name |
Medical University of Vienna
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| Department |
Center for Brain Research
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| Street address |
Spitalgasse 4
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platforms (1) |
| GPL16133 |
Illumina HiSeq 2000 (Gallus gallus) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE51939 |
Clustering of CpG islands constitutes an important determinant of the interphase chromosome 3D organization |
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| Relations |
| BioProject |
PRJNA225600 |
| SRA |
SRP032347 |
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