Accumulating evidence converges on the possibility that chromosomes interact with each other to regulate transcription in trans. To systematically explore the epigenetic dimension of such interactions, we devised a strategy termed circular chromosome conformation capture (4C). This approach involves a circularization step that enables high-throughput screening of physical interactions between chromosomes without a preconceived idea of the interacting partners. Here we identify 114 unique sequences from all autosomes, several of which interact primarily with the maternally inherited H19 imprinting control region. Imprinted domains were strongly overrepresented in the library of 4C sequences, further highlighting the epigenetic nature of these interactions. Moreover, we found that the direct interaction between differentially methylated regions was linked to epigenetic regulation of transcription in trans. Finally, the patterns of interactions specific to the maternal H19 imprinting control region underwent reprogramming during in vitro maturation of embryonic stem cells. These observations shed new light on development, cancer epigenetics and the evolution of imprinting.
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We thank A. Mattsson for expert technical assistance and M. Merkenschlager and P. Fraser for helpful advice. We are also grateful for the assistance of the Wallenberg microarray group at the Royal Technical University at Stockholm. This work was supported by the Swedish Science Research Council (V.R., R.O.), the Swedish Cancer Research Foundation (C.F., R.O.), the Swedish Pediatric Cancer Foundation (B.C.F, R.O.), HEROIC (European Union integrated project) and the Lundberg Foundation (R.O.).
The method described in the manuscript is the subject of a patent application. This has not influenced the results and discussion of this report.
3C validation of randomly picked sequences of the 4C library. (PDF 355 kb)
DNA FISH analysis of chromosomal interactions. (PDF 260 kb)
Markers of undifferentiated and differentiated embryonic stem (ES) cells. (PDF 59 kb)
The 4C library. (PDF 111 kb)
Primers for 3C and expression analysis. (PDF 83 kb)
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Zhao, Z., Tavoosidana, G., Sjölinder, M. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38, 1341–1347 (2006). https://doi.org/10.1038/ng1891
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