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Nat Genet. 2018 Oct;50(10):1352-1358. doi: 10.1038/s41588-018-0236-3. Epub 2018 Sep 27.

Challenges and guidelines toward 4D nucleome data and model standards.

Author information

1
Gene Regulation, Stem Cells and Cancer Program, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. martirenom@cnag.crg.eu.
2
Universitat Pompeu Fabra (UPF), Barcelona, Spain. martirenom@cnag.crg.eu.
3
ICREA, Barcelona, Spain. martirenom@cnag.crg.eu.
4
Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.
5
MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, UK.
6
Laboratoire de Biologie Molécualire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France.
7
Institute of Human Genetics, UMR 9002 of the CNRS and the University of Montpellier, Montpellier, France.
8
Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK.
9
Department of Biological Science, Florida State University, Tallahassee, Florida, USA.
10
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
11
University of Basel, Basel, Switzerland.
12
Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.
13
Dipartimento di Fisica "E. Pancini", Università di Napoli "Federico II", INFN Sezione di Napoli, Naples, Italy.
14
Berlin Institute of Health, MDC-Berlin, Berlin, Germany.
15
Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Universite de Montpellier, Montpellier, France.
16
Institute for Research in Biomedicine Barcelona (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
17
Departament de Bioquimica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain.
18
Epigenetic Regulation and Chromatin Architecture, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
19
Institute for Biology, Humboldt-Universitat zu Berlin, Berlin, Germany.
20
Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum Munchen, München, Germany.
21
Faculty of Biology, Ludwig-Maximilians Universitat, München, Germany.

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.

PMID:
30262815
DOI:
10.1038/s41588-018-0236-3
[Indexed for MEDLINE]

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