Abstract

The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes1. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization2,3,4,5,6,7,8,9. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks. The strongest spatial network is composed of the four Hox gene clusters and early developmental transcription factor genes, the majority of which contact poised enhancers. Removal of Polycomb repression leads to disruption of promoter-promoter contacts in the Hox gene network. In contrast, promoter-enhancer contacts are maintained in the absence of Polycomb repression, with accompanying widespread acquisition of active chromatin signatures at network enhancers and pronounced transcriptional upregulation of network genes. Thus, PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network. We propose that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.

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Acknowledgements

We thank members of the Elderkin, Fraser and Luscombe groups for discussions and J. Houseley and P. Rugg-Gunn for commenting on the manuscript. We thank F. Krueger for help with data processing and formatting. We thank R.J. Klose and N. Brockdorff for sequencing. We thank D. Bolland, J. Martins and A. Corcoran for help and advice with the three-dimensional DNA FISH and MetaCyte data analyses. This work was funded by the Wellcome Trust (WT085102MA) (S.E.), the Biotechnology and Biological Science Research Council, the Medical Research Council UK (P.F.) and the European Union Framework Programme 7 Epigenesys Network of Excellence (N.M.L.).

Author information

Author notes

    • Filipe Tavares-Cadete

    Present address: Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan.

    • Stefan Schoenfelder
    • , Robert Sugar
    • , Andrew Dimond
    • , Biola-Maria Javierre
    •  & Harry Armstrong

    These authors contributed equally to this work.

Affiliations

  1. Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK.

    • Stefan Schoenfelder
    • , Andrew Dimond
    • , Biola-Maria Javierre
    • , Harry Armstrong
    • , Emilia Dimitrova
    • , Louise Matheson
    • , Mayra Furlan-Magaril
    • , Wiktor Jurkowski
    • , Steven W Wingett
    • , Kristina Tabbada
    • , Cameron S Osborne
    • , Peter Fraser
    •  & Sarah Elderkin
  2. European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.

    • Robert Sugar
    •  & Nicholas M Luscombe
  3. Cancer Research UK London Research Institute, London, UK.

    • Borbala Mifsud
    • , Filipe Tavares-Cadete
    •  & Nicholas M Luscombe
  4. Department of Genetics, Evolution and Environment, University College London, London, UK.

    • Borbala Mifsud
    •  & Nicholas M Luscombe
  5. Department of Biochemistry, Oxford University, Oxford, UK.

    • Emilia Dimitrova
  6. Bioinformatics Group, The Babraham Institute, Cambridge, UK.

    • Anne Segonds-Pichon
    • , Steven W Wingett
    •  & Simon Andrews
  7. Agilent Technologies, Inc., Santa Clara, California, USA.

    • Bram Herman
    •  & Emily LeProust
  8. Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

    • Haruhiko Koseki
  9. Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan.

    • Nicholas M Luscombe

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Contributions

S.S. conceptualized, designed and performed promoter CHi-C and helped with data interpretation and writing of the manuscript. R.S. analyzed promoter-promoter (promoter CHi-C) data and performed network analysis. A.D. performed nuclear RNA-seq, analyzed promoter-genome (promoter CHi-C) data, gene expression and ChIP-seq data, and helped write the manuscript. B.-M.J. performed 3C-PCR and commented on the manuscript. H.A. performed three-dimensional DNA FISH, analyzed MetaCyte data and helped with CHi-C data analysis. B.M. analyzed ChIP-seq data, performed promoter-promoter contact enrichment analysis and commented on the manuscript. E.D. performed experiments and histone ChIP-seq. L.M. performed three-dimensional DNA FISH, analyzed MetaCyte data and helped with CHi-C data analysis. F.T.-C. mapped ChIP-seq data and analyzed promoter-genome enrichments. M.F.-M. helped with promoter CHi-C protocol development and wild-type ESC promoter CHi-C. W.J. analyzed ChIP-seq data. A.S.-P. analyzed three-dimensional DNA FISH data. S.W.W. helped with the mapping and analysis of promoter CHi-C data. K.T. carried out sequencing. B.H., E.L., C.S.O., S.A. and S.W.W. designed and provided the capture system. H.K. provided RING1A-knockout ESCs and helped with manuscript preparation. P.F. helped with study design, data interpretation and manuscript preparation. N.M.L. was involved in study design, data interpretation and manuscript preparation. S.E. conceptualized and designed the study, designed and performed experiments, interpreted data and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Sarah Elderkin.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8.

  2. 2.

    Supplementary Data Set

    Full-length gels for 3C analysis in the main figures.

Excel files

  1. 1.

    Supplementary Table 1

    Promoter fragment baits in different categories.

  2. 2.

    Supplementary Table 2

    Next-generation sequencing statistics for promoter CHi-C, nuclear RNA-seq and ChIP-seq.

  3. 3.

    Supplementary Table 3

    Publically available data sets used.

  4. 4.

    Supplementary Table 4

    Enhancer fragment baits in different enhancer classes.

  5. 5.

    Supplementary Table 5

    BACs and primer sequences used for 3C-PCR and 3D DNA FISH.

  6. 6.

    Supplementary Table 6

    Interprobe distances for 3D DNA FISH.

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DOI

https://doi.org/10.1038/ng.3393

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