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Challenges and guidelines toward 4D nucleome data and model standards

Nature Genetics volume 50, pages 1352–1358 (2018)Cite this article

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Abstract

Due to recent advances in experimental and theoretical approaches, the dynamic three-dimensional organization (3D) of the nucleus has become a very active area of research in life sciences. We now understand that the linear genome is folded in ways that may modulate how genes are expressed during the basic functioning of cells. Importantly, it is now possible to build 3D models of how the genome folds within the nucleus and changes over time (4D). Because genome folding influences its function, this opens exciting new possibilities to broaden our understanding of the mechanisms that determine cell fate. However, the rapid evolution of methods and the increasing complexity of data can result in ambiguity and reproducibility challenges, which may hamper the progress of this field. Here, we describe such challenges ahead and provide guidelines to think about strategies for shared standardized validation of experimental 4D nucleome data sets and models.

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Fig. 1: Toward FAIR data, unified standards and RICH visualizations in 4D nucleome research.

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Acknowledgements

We thank the community of researchers around the EU 4DNucleome Initiative for their continuous support.

Author information

Authors and Affiliations

  1. Gene Regulation, Stem Cells and Cancer Program, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

    Marc A. Marti-Renom

  2. Universitat Pompeu Fabra (UPF), Barcelona, Spain

    Marc A. Marti-Renom

  3. ICREA, Barcelona, Spain

    Marc A. Marti-Renom

  4. Institut Curie, PSL Research University, CNRS UMR3664, Paris, France

    Genevieve Almouzni

  5. MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, UK

    Wendy A. Bickmore

  6. Laboratoire de Biologie Molécualire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France

    Kerstin Bystricky

  7. Institute of Human Genetics, UMR 9002 of the CNRS and the University of Montpellier, Montpellier, France

    Giacomo Cavalli

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

    Peter Fraser

  9. Department of Biological Science, Florida State University, Tallahassee, Florida, USA

    Peter Fraser

  10. Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

    Susan M. Gasser & Luca Giorgetti

  11. University of Basel, Basel, Switzerland

    Susan M. Gasser

  12. Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France

    Edith Heard

  13. Dipartimento di Fisica “E. Pancini”, Università di Napoli “Federico II”, INFN Sezione di Napoli, Naples, Italy

    Mario Nicodemi

  14. Berlin Institute of Health, MDC-Berlin, Berlin, Germany

    Mario Nicodemi & Ana Pombo

  15. Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Universite de Montpellier, Montpellier, France

    Marcelo Nollmann

  16. Institute for Research in Biomedicine Barcelona (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

    Modesto Orozco

  17. Departament de Bioquimica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain

    Modesto Orozco

  18. Epigenetic Regulation and Chromatin Architecture, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany

    Ana Pombo

  19. Institute for Biology, Humboldt-Universitat zu Berlin, Berlin, Germany

    Ana Pombo

  20. Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum Munchen, München, Germany

    Maria-Elena Torres-Padilla

  21. Faculty of Biology, Ludwig-Maximilians Universitat, München, Germany

    Maria-Elena Torres-Padilla

Authors
  1. Marc A. Marti-Renom
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  2. Genevieve Almouzni
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  3. Wendy A. Bickmore
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  4. Kerstin Bystricky
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  5. Giacomo Cavalli
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  6. Peter Fraser
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  7. Susan M. Gasser
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  8. Luca Giorgetti
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  9. Edith Heard
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  10. Mario Nicodemi
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  11. Marcelo Nollmann
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  12. Modesto Orozco
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  13. Ana Pombo
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  14. Maria-Elena Torres-Padilla
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Contributions

All authors wrote and approved the manuscript.

Corresponding author

Correspondence to Marc A. Marti-Renom.

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Marti-Renom, M.A., Almouzni, G., Bickmore, W.A. et al. Challenges and guidelines toward 4D nucleome data and model standards. Nat Genet 50, 1352–1358 (2018). https://doi.org/10.1038/s41588-018-0236-3

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  • DOI: https://doi.org/10.1038/s41588-018-0236-3

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