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Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)

Abstract

The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function1,2,3,4,5,6,7,8,9,10,11,12. We developed 4C technology (chromosome conformation capture (3C)-on-chip), which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active β-globin locus in fetal liver preferentially contacts transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, whereas the inactive locus in fetal brain contacts different transcriptionally silent loci. A housekeeping gene in a gene-dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture.

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Figure 1: 4C technology.
Figure 2: Long-range interactions with β-globin, as shown by 4C technology.
Figure 3: Active and inactive β-globin interact with active and inactive chromosomal regions, respectively.
Figure 4: Ubiquitously expressed Rad23a interacts with very similar active regions in fetal liver and brain.
Figure 5: Cryo-FISH confirms that 4C technology truly identifies interacting regions.
Figure 6: Interchromosomal interactions with Rad23a.

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Acknowledgements

We thank F. Grosveld for support and discussion and S. van Baal, M. Branco, A. Pombo, P. Verrijzer, J. Hou, B. Eussen, A. de Klein, T. de Vries Lentsch, D. Noordermeer and R.-J. Palstra for assistance. This work was supported by grants from the Dutch Scientific Organization (NWO) (912-04-082) and the Netherlands Genomics Initiative (050-71-324) to W.L.

Author information

Authors and Affiliations

Authors

Contributions

M.S. set up, performed and analyzed 4C experiments and wrote the paper; P.K. performed cryo-FISH experiments; E.S. helped set up 4C; Y.M. helped with statistical analysis; R.W. prepared cryosections; E.d.W. and B.v.S. provided probe sequences and helped with statistical analysis and W.d.L. designed experiments and wrote the paper.

Corresponding author

Correspondence to Wouter de Laat.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

4C analysis of HS2 and Hbb-b1 give highly similar results. (PDF 111 kb)

Supplementary Fig. 2

4C detects interactions previously identified by FISH. (PDF 85 kb)

Supplementary Fig. 3

Regions that interact with β-globin also frequently contact each other. (PDF 32 kb)

Supplementary Fig. 4

Rad23a colocalizes with gene-dense regions in cis. (PDF 48 kb)

Supplementary Table 1

Intrachromosomal interactions detected by 4C. (PDF 61 kb)

Supplementary Table 2

Overview of cryo-FISH results for intrachromosomal interactions. (PDF 16 kb)

Supplementary Table 3

Cryo-FISH results for interchromosomal interactions. (PDF 39 kb)

Supplementary Table 4

Interchromosomal interactions with Rad23a detected by 4C. (PDF 36 kb)

Supplementary Table 5

Primer sequences used for 4C analysis. (PDF 16 kb)

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Simonis, M., Klous, P., Splinter, E. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C). Nat Genet 38, 1348–1354 (2006). https://doi.org/10.1038/ng1896

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