Abstract

The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation). GAM also reveals an abundance of three-way contacts across the genome, especially between regions that are highly transcribed or contain super-enhancers, providing a level of insight into genome architecture that, owing to the technical limitations of current technologies, has previously remained unattainable. Furthermore, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian nuclei.

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Acknowledgements

We thank J. Walter for critically reading the manuscript; C. Ferrai and E. Brookes for preparing mES cells; S. Robin, M.-F. Sagot and K. N. Natarajan for initial contributions to the statistical and bioinformatic analyses of GAM; T. Baslan and J. Hicks for suggestions on sequencing strategy; J. Pang from Illumina for help with HiSeq recipes; O. Clarke from Zeiss Microdissection Systems for advice on microdissection; K. Semrau from MYcroarray for advice on MYtag probes; P. A. Dear for advice about HAPPY mapping; T. Rito for help with ImageJ scripts; and D. Henrique and W. Bickmore for providing mES cell lines. The work was supported by the Medical Research Council, UK (A.P., R.A.B., M.C., S.Q.X., I.d.S., L.M.L., M.R.B., L.G., N.D.), by the Helmholtz Foundation (A.P., R.A.B., M.S., D.C.A.K., M.B.), by MRC-Technology (A.P., M.C., M.R.B.), by the Berlin Institute of Health (BIH; A.P., M.B.), by Breast Cancer Campaign (P.A.W.E.) and by Cancer Research UK (P.A.W.E.). Work by J.D. and J.F. was supported by grants from the Canadian Institutes of Health Research (CIHR) (MOP-86716, CAP-120350). Work by M.N. was supported by CINECA ISCRA grants no. HP10CYFPS5 and no. HP10CRTY8P. M.N. also acknowledges computer resources from INFN and Scope at the University of Naples.

Author information

Author notes

    • Antonio Scialdone
    • , Sheila Q. Xie
    • , Inês de Santiago
    •  & Miguel R. Branco

    Present addresses: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK (A.S.); Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK (S.Q.X.); Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK (I.d.S.); Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK (M.R.B.).

    • Robert A. Beagrie
    •  & Antonio Scialdone

    These authors contributed equally to this work.

    • Mario Nicodemi
    •  & Ana Pombo

    These authors jointly supervised this work.

Affiliations

  1. Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Robert-Rössle Straße, Berlin-Buch 13125, Germany

    • Robert A. Beagrie
    • , Markus Schueler
    • , Dorothee C. A. Kraemer
    • , Mariano Barbieri
    • , Liron-Mark Lavitas
    •  & Ana Pombo
  2. Genome Function Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK

    • Robert A. Beagrie
    • , Mita Chotalia
    • , Sheila Q. Xie
    • , Inês de Santiago
    • , Liron-Mark Lavitas
    • , Miguel R. Branco
    •  & Ana Pombo
  3. Gene Regulation and Chromatin Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK

    • Robert A. Beagrie
    •  & Niall Dillon
  4. Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy

    • Antonio Scialdone
    •  & Mario Nicodemi
  5. Berlin Institute of Health (BIH), Berlin 10117, Germany

    • Mariano Barbieri
    •  & Ana Pombo
  6. Department of Biochemistry and Goodman Cancer Research Centre, McGill University, 3655 Promenade Sir-William-Osler, Montréal, Québec H3G 1Y6, Canada

    • James Fraser
    •  & Josée Dostie
  7. Genomics Laboratory, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK

    • Laurence Game
  8. Hutchison/MRC Research Centre and Department of Pathology, University of Cambridge, Cambridge CB2 0XZ, UK

    • Paul A. W. Edwards
  9. Institute for Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany

    • Ana Pombo

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Contributions

A.P. and P.A.W.E. devised the GAM concept. A.P., R.A.B., M.C., L.M.L. and M.R.B. optimized the GAM experimental protocol. R.A.B. produced the GAM datasets, and with L.G. developed the sequencing strategy. M.C. produced the control WGA-amplified DNA dataset. D.C.A.K. and S.Q.X. performed the FISH experiments. A.P. and N.D. supervised the experiments. R.A.B., M.S. and I.d.S. performed the bioinformatics analyses. M.N. conceived the SLICE model concept. M.N., A.S., A.P. and R.A.B. developed the SLICE model and A.S. implemented full calculations. M.B. performed the polymer modelling analysis. A.P. and M.N. supervised computational analyses. A.P. and R.A.B. developed the radial position and compaction analyses. J.F. processed the Hi-C data, supervised by J.D. R.A.B., A.P., A.S., M.N. and M.S. wrote the paper, all authors revised the manuscript. The authors consider D.C.A.K, M.C. and S.Q.X to have contributed equally to this work.

Competing interests

A related patent has been filed on behalf of A.P., P.A.W.E., M.N., A.S. and R.A.B. by the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin. The other authors declare no competing financial interests.

Corresponding authors

Correspondence to Mario Nicodemi or Ana Pombo.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Notes 1-3.

Excel files

  1. 1.

    Supplementary Table 1

    Details of sequencing datasets generated for this study (NPs, negative and positive control), including experimental batch, sequencing depth, and all metrics used to judge the quality of each NP.

  2. 2.

    Supplementary Table 2

    This table contains a list of TADs forming the top 2% most interacting TAD triplets, including their transcriptional/se class.

  3. 3.

    Supplementary Table 3

    Details of published genome-wide datasets used in this study, including accession numbers.

  4. 4.

    Supplementary Table 4

    Details of FISH probes used for validating long-range interactions.

  5. 5.

    Supplementary Table 5

    Measurements of distances between the edges of two FISH probe signals.

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DOI

https://doi.org/10.1038/nature21411

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