Format

Send to

Choose Destination
Epigenetics. 2014 Jul;9(7):951-63. doi: 10.4161/epi.28794. Epub 2014 Apr 15.

The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes.

Author information

1
Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Molecular Biology; Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia.
2
Faculty of Bioengineering and Bioinformatics; Lomonosov Moscow State University; Moscow, Russia; Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow, Russia.
3
Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia.
4
Laboratory of Evolutionary Genomics; Lomonosov Moscow State University; Moscow, Russia.
5
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia.
6
Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia.

Abstract

We used the 4C-Seq technique to characterize the genome-wide patterns of spatial contacts of several CpG islands located on chromosome 14 in cultured chicken lymphoid and erythroid cells. We observed a clear tendency for the spatial clustering of CpG islands present on the same and different chromosomes, regardless of the presence or absence of promoters within these CpG islands. Accordingly, we observed preferential spatial contacts between Sp1 binding motifs and other GC-rich genomic elements, including the DNA sequence motifs capable of forming G-quadruplexes. However, an anchor placed in a gene/CpG island-poor area formed spatial contacts with other gene/CpG island-poor areas on chromosome 14 and other chromosomes. These results corroborate the two-compartment model of the spatial organization of interphase chromosomes and suggest that the clustering of CpG islands constitutes an important determinant of the 3D organization of the eukaryotic genome in the cell nucleus. Using the ChIP-Seq technique, we mapped the genome-wide CTCF deposition sites in the chicken lymphoid and erythroid cells that were used for the 4C analysis. We observed a good correlation between the density of CTCF deposition sites and the level of 4C signals for the anchors located in CpG islands but not for an anchor located in a gene desert. It is thus possible that CTCF contributes to the clustering of CpG islands observed in our experiments.

KEYWORDS:

4C; CTCF; CpG island; genome spatial organization; housekeeping gene

PMID:
24736527
PMCID:
PMC4143410
DOI:
10.4161/epi.28794
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Taylor & Francis Icon for PubMed Central
Loading ...
Support Center