Challenges and guidelines toward 4D nucleome data and model standards

Marc Marti-Renom (1, 2, 3) , Geneviève Almouzni (4, 4) , Wendy Bickmore (5) , Kerstin Bystricky (6) , Giacomo Cavalli (7) , Peter Fraser (8, 9) , Susan M. Gasser (10, 11) , Luca Giorgetti (12) , Edith Heard (13, 13, 14) , Mario Nicodemi (15, 16) , Marcelo Nollmann (17) , Modesto Orozco (18) , Ana Pombo (19, 20, 21) , Maria-Elena Torres-Padilla (22, 23, 24)

1 CRG - Centre for Genomic Regulation - Centre de Regulació Genòmica [Barcelona]
2 UPF - Universitat Pompeu Fabra [Barcelona]
3 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
4 Dynamique du noyau [Institut Curie]
5 Edin. - University of Edinburgh
6 LBME - Laboratoire de biologie moléculaire eucaryote
7 IGH - Institut de génétique humaine
8 The Babraham Institute [Cambridge, UK]
9 FSU - Florida State University [Tallahassee]
10 FMI - Friedrich Miescher Institute for Biomedical Research
11 Unibas - Université de Bâle = University of Basel = Basel Universität
12 Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
13 Génétique et Biologie du Développement
14 Collège de France - Chaire Epigénétique et mémoire cellulaire
15 Dipartimento di Fisica "Ettore Pancini"
16 Berlin Institute of Health, MDC-Berlin, Berlin, Germany
17 CBS - Centre de Biochimie Structurale [Montpellier]
18 Institute for Research in Biomedicine (IRB Barcelona)
19 Berlin Institute of Health, MDC-Berlin, Berlin, Germany.
20 MDC - Max Delbrück Center for Molecular Medicine [Berlin]
21 HU Berlin - Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
22 IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire
23 Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum Munchen, München, Germany
24 Faculty of Biology, Ludwig-Maximilians Universitat, München, Germany.

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.

Domaines: Sciences du Vivant [q-bio]; Génétique

Marc Marti-Renom, Geneviève Almouzni, Wendy Bickmore, Kerstin Bystricky, Giacomo Cavalli, et al.. Challenges and guidelines toward 4D nucleome data and model standards. Nature Genetics, 2018, 50 (10), pp.1352-1358. ⟨10.1038/s41588-018-0236-3⟩. ⟨hal-01980465⟩