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CTCF-mediated functional chromatin interactome in pluripotent cells

An Erratum to this article was published on 27 July 2011

This article has been updated

Abstract

Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, we identified 1,480 cis- and 336 trans-interacting loci with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function.

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Figure 1: Genome-wide CTCF-mediated chromatin interactome.
Figure 2: Validation of CTCF-mediated chromatin interactions.
Figure 3: Cumulative histone modification patterns of CTCF loops.
Figure 4: Distinct types of chromatin domains defined by CTCF-tethered interactions.
Figure 5: Promoter-p300 communications facilitated by CTCF-associated chromatin interactions.
Figure 6: Lamin-associated domains (LADs) in embryonic stem cells.

Accession codes

Accessions

Gene Expression Omnibus

Change history

  • 11 July 2011

    In the version of this article initially published, the accession codes section contained inaccuracies. The raw sequences and processed data generated from this study can be downloaded with accession number GSE28247. The previously published histone modification data used in this study are found under accession numbers GSE12241 and GSE11172. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We acknowledge the Genome Technology and Biology Group, particularly the sequencing team, for technical support. We also thank C. Xi and H.H. Ng who provided technical guidance for p300 ChIP optimization, M. Fullwood and B. Han for their 4C assay protocol, L.M. Hui and E. Cheung for 3C optimization and discussion, Z. Jingyao for BAC clone preparation and K. Zawack for reading the manuscript. This work was supported by the Agency for Science, Technology and Research (A*STAR), Singapore, and US National Institutes of Health (NIH) ENCODE grants (R01 HG004456-01, R01HG003521-01 and 1U54HG004557-01) to Y.R. and C.-L.W.

Author information

Authors and Affiliations

Authors

Contributions

Y.R. and C.-L.W. designed the study. L.H., H.X. and G.L. conducted experiments and data analyses. C.Y.N., C.Y. and E.W. performed the ChIA-PET and ChIP-Seq experiments. L.H., E.C., M.S., C.Y., J.L.H.P., J.S. and V.C.-R. coordinated all the validation experiments. C.S.C. and A.S. provided sequencing data processing and management. F.M. and W.-K.S. provided ChIA-PET data processing and bioinformatics support. C.W.H.L., Y.Z., G.K. and G.B. carried out additional global bioinformatic analyses. T.P. offered high-throughput sequencing support. L.H., H.X., G.L. and C.L.W. analyzed the data and wrote the manuscript. Y.R. provided critical review of the manuscript.

Corresponding authors

Correspondence to Yijun Ruan or Chia-Lin Wei.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1–11 and Supplementary Tables 1, 4, 7 and 10. (PDF 4404 kb)

Supplementary Table 2

CTCF binding sites (XLS 3510 kb)

Supplementary Table 3

Intra-and inter-chromosomal interactions detected by CTCF ChIA-PET (XLS 2214 kb)

Supplementary Table 5

List of 5 categories assigned to intra-chromosomal interactions (XLS 729 kb)

Supplementary Table 6

RNA Pol II, p300 and LADs sites defined by ChIP-Seq (XLS 4340 kb)

Supplementary Table 8

RNAP II interactions defined by ChIA-PET (XLS 177 kb)

Supplementary Table 9

SALL4 interactions defined by ChIA-PET (XLS 179 kb)

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Handoko, L., Xu, H., Li, G. et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 43, 630–638 (2011). https://doi.org/10.1038/ng.857

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