Cited by 703Genomics and Chromatin DynamicsGenomic variations and chromosomal abnormalitiesGenetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities

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Formation of new chromatin domains determines pathogenicity of genomic duplications

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Franke, Martin, Ibrahim, Daniel M., Andrey, Guillaume, Schwarzer, Wibke, Heinrich, Verena, Schöpflin, Robert, Kraft, Katerina, Kempfer, Rieke, Jerković, Ivana, Chan, Wing-Lee, Spielmann, Malte, Timmermann, Bernd, Wittler, Lars, Kurth, Ingo, Cambiaso, Paola, Zuffardi, Orsetta, Houge, Gunnar, Lambie, Lindsay, Brancati, Francesco, Pombo, Ana, Vingron, Martin, Spitz, Francois, Mundlos, Stefan·2016·Nature

DOI 10.1038/nature19800

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Abstract

Chromosome conformation capture methods have identified subchromosomal structures of higher-order chromatin interactions called topologically associated domains (TADs) that are separated from each other by boundary regions. By subdividing the genome into discrete regulatory units, TADs restrict the contacts that enhancers establish with their target genes. However, the mechanisms that underlie partitioning of the genome into TADs remain poorly understood. Here we show by chromosome conformation capture (capture Hi-C and 4C-seq methods) that genomic duplications in patient cells and genetically modified mice can result in the formation of new chromatin domains (neo-TADs) and that this process determines their molecular pathology. Duplications of non-coding DNA within the mouse Sox9 TAD (intra-TAD) that cause female to male sex reversal in humans, showed increased contact of the duplicated regions within the TAD, but no change in the overall TAD structure. In contrast, overlapping duplications that extended over the next boundary into the neighbouring TAD (inter-TAD), resulted in the formation of a new chromatin domain (neo-TAD) that was isolated from the rest of the genome. As a consequence of this insulation, inter-TAD duplications had no phenotypic effect. However, incorporation of the next flanking gene, Kcnj2, in the neo-TAD resulted in ectopic contacts of Kcnj2 with the duplicated part of the Sox9 regulatory region, consecutive misexpression of Kcnj2, and a limb malformation phenotype. Our findings provide evidence that TADs are genomic regulatory units with a high degree of internal stability that can be sculptured by structural genomic variations. This process is important for the interpretation of copy number variations, as these variations are routinely detected in diagnostic tests for genetic disease and cancer. This finding also has relevance in an evolutionary setting because copy-number differences are thought to have a crucial role in the evolution of genome complexity.

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Additional file 10 of Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Additional file 2 of Common DNA sequence variation influences 3-dimensional conformation of the human genome
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Additional file 3 of Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Additional file 7 of Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Additional file 4 of Common DNA sequence variation influences 3-dimensional conformation of the human genome
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Additional file 6 of Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Additional file 3 of Common DNA sequence variation influences 3-dimensional conformation of the human genome
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Additional file 8 of Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Additional file 12 of Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Additional file 7 of Common DNA sequence variation influences 3-dimensional conformation of the human genome
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Additional file 5 of Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Additional file 2 of Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Additional file 9 of Common DNA sequence variation influences 3-dimensional conformation of the human genome
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Additional file 4 of Co-localization of clusters of TCR-regulated genes with TAD rearrangements
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Additional file 3 of Co-localization of clusters of TCR-regulated genes with TAD rearrangements
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Additional file 1 of Common DNA sequence variation influences 3-dimensional conformation of the human genome
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Additional file 2 of TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
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Authors: Franke, M., Ibrahim, D. M., Andrey, G., Schwarzer, W., Heinrich, V., Schöpflin, R., Kraft, K., Kempfer, R., Jerković, I., Chan, W.-L., Spielmann, M., Timmermann, B., Wittler, L., Kurth, I., Cambiaso, P., Zuffardi, O., Houge, G., Lambie, L., Brancati, F., Pombo, A., Vingron, M., Spitz, F., & Mundlos, S.
Affiliations: Max Planck Institute for Molecular Genetics (DE)
Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
European Molecular Biology Laboratory (DE)
Charité – Universitätsmedizin Berlin (DE)
Universitätsklinikum Aachen (DE)
Bambino Gesù Children's Hospital (IT)
University of Pavia (IT)
Haukeland University Hospital (NO)
National Health Laboratory Service (ZA)
University of L'Aquila (IT)
Max Delbrück Center (DE)
Berlin-Brandenburger Centrum für Regenerative Therapien (DE)
Corresponding author: Mundlos, Stefan
ORCID: Franke, Martin
Ibrahim, Daniel M.
Andrey, Guillaume
Schwarzer, Wibke
Heinrich, Verena
Kraft, Katerina
Kempfer, Rieke
Jerković, Ivana
Spielmann, Malte
Wittler, Lars
Kurth, Ingo
Zuffardi, Orsetta
Houge, Gunnar
Brancati, Francesco
Pombo, Ana
Vingron, Martin
Mundlos, Stefan
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2016-10
Volume: 538
Issue: 7624
Pages: 265-269
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature19800
OpenAlex: W2528263447
Cited by: 673
References: 38
Citations by year: 2026: 36 · 2025: 38 · 2024: 45 · 2023: 58 · 2022: 87 · 2021: 78 · 2020: 89 · 2019: 91 · 2018: 76 · 2017: 59 · 2016: 12
FWCI: 41.42
Type: journal article
Language: en
Open access: green
hdl.handle.net
Licence: other-oa
www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
Archive ouverte UNIGE (University of Geneva) (publishedVersion)
Max Planck Digital Library (submittedVersion, other-oa)
RePEc: Research Papers in Economics (submittedVersion)
MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
RWTH Publications (RWTH Aachen) (submittedVersion)
MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Archivio Istituzionale della Ricerca - Università degli Studi dell Aquila (submittedVersion)
Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
Funders: Max-Planck-Förderstiftung
Deutsche Forschungsgemeinschaft
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
Keywords: genomic duplication, topologically associating domains, SOX9, KCNJ2, structural variants, enhancer-promoter interactions, gene misexpression, limb malformations, sex reversal, chromatin insulation, gene dosage, higher-order chromatin structure, mouse models of human disease, 4C-seq, Hi-C
MeSH terms: Animals, Disease, DNA, Female, Fibroblasts, Fingers, Foot Deformities, Congenital, Hand Deformities, Congenital, Male, Phenotype, Gene Expression, Facies, Gene Duplication, Genomics, Chromatin Assembly and Disassembly, Mice, SOX9 Transcription Factor, DNA Copy Number Variations

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