Letter | Published:

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

Nature volume 504, pages 306310 (12 December 2013) | Download Citation


In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination1. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements2. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space3. However, the dynamic nature of chromatin connectivity has not been characterized at the genome-wide level. Here, through a chromatin interaction analysis with paired-end tagging approach3,4,5 using an antibody that primarily recognizes the pre-initiation complexes of RNA polymerase II6, we explore the transcriptional interactomes of three mouse cells of progressive lineage commitment, including pluripotent embryonic stem cells7, neural stem cells8 and neurosphere stem/progenitor cells9. Our global chromatin connectivity maps reveal approximately 40,000 long-range interactions, suggest precise enhancer–promoter associations and delineate cell-type-specific chromatin structures. Analysis of the complex regulatory repertoire shows that there are extensive colocalizations among promoters and distal-acting enhancers. Most of the enhancers associate with promoters located beyond their nearest active genes, indicating that the linear juxtaposition is not the only guiding principle driving enhancer target selection. Although promoter–enhancer interactions exhibit high cell-type specificity, promoters involved in interactions are found to be generally common and mostly active among different cells. Chromatin connectivity networks reveal that the pivotal genes of reprogramming functions are transcribed within physical proximity to each other in embryonic stem cells, linking chromatin architecture to coordinated gene expression. Our study sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orchestrating development.

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Gene Expression Omnibus

Data deposits

All data described in this study have been deposited in the GEO under accession number GSE44067.


  1. 1.

    et al. Circuitry and dynamics of human transcription factor regulatory networks. Cell 150, 1274–1286 (2012)

  2. 2.

    et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854–858 (2009)

  3. 3.

    et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012)

  4. 4.

    et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nature Genet. 43, 630–638 (2011)

  5. 5.

    et al. An oestrogen-receptor-α-bound human chromatin interactome. Nature 462, 58–64 (2009)

  6. 6.

    & Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20, 2922–2936 (2006)

  7. 7.

    & Establishment in culture of pluripotential cells from mouse embryos. Nature 292, 154–156 (1981)

  8. 8.

    et al. Niche-independent symmetrical self-renewal of a mammalian tissue stem cell. PLoS Biol. 3, e283 (2005)

  9. 9.

    et al. Sox2 regulatory sequences direct expression of a β-geo transgene to telencephalic neural stem cells and precursors of the mouse embryo, revealing regionalization of gene expression in CNS stem cells. Development 127, 2367–2382 (2000)

  10. 10.

    , , , & Interchromosomal associations between alternatively expressed loci. Nature 435, 637–645 (2005)

  11. 11.

    et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116–120 (2012)

  12. 12.

    et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106–1117 (2008)

  13. 13.

    et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010)

  14. 14.

    & Genomic approaches towards finding cis-regulatory modules in animals. Nature Rev. Genet. 13, 469–483 (2012)

  15. 15.

    et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)

  16. 16.

    et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011)

  17. 17.

    et al. A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev. Biol. 337, 484–495 (2010)

  18. 18.

    et al. Transcription factors mediate long-range enhancer–promoter interactions. Proc. Natl Acad. Sci. USA 106, 20222–20227 (2009)

  19. 19.

    et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917–1920 (2007)

  20. 20.

    & Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132, 567–582 (2008)

  21. 21.

    et al. Direct reprogramming of mouse and human fibroblasts into multipotent neural stem cells with a single factor. Cell Stem Cell 11, 100–109 (2012)

  22. 22.

    , , , & Fibroblast growth factor induces a neural stem cell phenotype in foetal forebrain progenitors and during embryonic stem cell differentiation. Mol. Cell. Neurosci. 38, 393–403 (2008)

  23. 23.

    et al. Olig2-regulated lineage-restricted pathway controls replication competence in neural stem cells and malignant glioma. Neuron 53, 503–517 (2007)

  24. 24.

    Paused RNA polymerase II as a developmental checkpoint. Cell 145, 502–511 (2011)

  25. 25.

    et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012)

  26. 26.

    et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 11, R22 (2010)

  27. 27.

    , & Gephi: an open source software for exploring and manipulating networks and (International AAAI Conference on Weblogs and Social Media, 2009)

  28. 28.

    et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008)

  29. 29.

    et al. Expression of the cytoplasmic NPM1 mutant (NPMc+) causes the expansion of hematopoietic cells in zebrafish. Blood 115, 3329–3340 (2010)

  30. 30.

    et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005)

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The authors thank J. Mariani for the preparation of RNA from NPC; K. Murphy and A. Ku for their assistance with zebrafish enhancer assays; and A. Visel and A. Nord for discussion and their comments on the manuscript. S.N. and R.F. were supported by grants from ASTIL Regione Lombardia (SAL-19 ref. no. 16874), Telethon (GGP12152), Cariplo (Rif. 2010-0673) and AIRC (IG-5801). N.A. is supported by NINDS grant number R01NS079231, NICHD grant number R01HD059862, NHGRI grant numbers R01HG005058 and R01HG006768, NIDDK award number R01DK090382, NIGMS award number GM61390 and Simons Foundation SFARI no. 256769. R.Y.B. is supported by NINDS grant number R01NS079231 and the UCSF Program for Biomedical Breakthrough Research (PBBR). This work was supported by Agency for Science, Technology and Research (A*STAR), Singapore, the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231 and National Institutes of Health ENCODE grants (R01 HG004456-01, R01HG003521-01 and 1U54HG004557-01) to Y.R. and C.-L.W.

Author information

Author notes

    • Yubo Zhang
    • , Chee-Hong Wong
    •  & Ramon Y. Birnbaum

    These authors contributed equally to this work.

    • Yubo Zhang
    •  & Ramon Y. Birnbaum

    Present addresses: Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel (R.Y.B.); National Heart, Lung, and Blood Institute, National Institutes of Health, Systems Biology Center, 9000 Rockville Pike, Bethesda, Maryland 20892, USA (Y.Z.).


  1. Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA

    • Yubo Zhang
    • , Chee-Hong Wong
    • , Chew Yee Ngan
    •  & Chia-Lin Wei
  2. Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, UCSF, San Francisco, California 94158, USA

    • Ramon Y. Birnbaum
    •  & Nadav Ahituv
  3. The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA

    • Guoliang Li
    •  & Yijun Ruan
  4. Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore

    • Guoliang Li
    • , Joanne Lim
    • , Eunice Tai
    • , Huay Mei Poh
    • , Eleanor Wong
    • , Fabianus Hendriyan Mulawadi
    • , Wing-Kin Sung
    •  & Chia-Lin Wei
  5. Department of Biological Sciences and Biotechnology, University of Milano-Bicocca, 20126 Milano, Italy

    • Rebecca Favaro
    •  & Silvia Nicolis


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Y.Z. constructed ChIA-PET experiments and data evaluation. R.Y.B. and N.A. designed and performed zebrafish enhancer assays. C.-H.W. carried out data analysis. C.-Y.N. and Y.Z. performed the RNA-seq experiments. J.L. performed DNA-FISH. H.M.P., E.T., R.F. and E.W. prepared the cells and ChIP material. G.L., F.H.M., W.-K.S. and Y.R. designed the data processing pipeline. C.-L.W. and S.N. designed the experiments. Y.Z. and C.-L.W. wrote the paper. All authors provided intellectual input and approved the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Chia-Lin Wei.

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