Formation of new chromatin domains determines pathogenicity of genomic duplications
Open accessAbstract
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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The integrity of domain structures is important for the proper regulation of genes.
“Therefore, the integrity of the domain structures is important for the proper regulation of genes8–12.”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [10]
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Self-citationBioelectric signaling as a unique regulator of development and regeneration
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A promoter interaction map for cardiovascular disease genetics
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Developing in 3D: the role of CTCF in cell differentiation
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Gene Regulatory Elements, Major Drivers of Human Disease
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An evolving view of copy number variants
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Developmentally regulated Shh expression is robust to TAD perturbations
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Radiation-induced DNA damage and repair effects on 3D genome organization
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Dosage-sensitive genes in evolution and disease
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The three-dimensional genome: regulating gene expression during pluripotency and development
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Self-citationCTCF shapes chromatin structure and gene expression in health and disease
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Self-citationInterchromosomal interactions: A genomic love story of kissing chromosomes
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Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases
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Self-citationRegulatory functions of the Mediator kinases CDK8 and CDK19
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Chromatin conformation analysis of primary patient tissue using a low input Hi-C method
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The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytesPreprint
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Advances in Chromatin Imaging at Kilobase-Scale Resolution
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Three-dimensional genome rewiring in loci with human accelerated regions
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Principles of Chromosome Architecture Revealed by Hi-C
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Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants
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Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation
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Self-citationConformation of sister chromatids in the replicated human genome
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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
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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
- Venue
- Nature
- Published
- 2016-10
- Volume
- 538
- Issue
- 7624
- Pages
- 265-269
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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 · 2014: 1 · 2012: 1
- 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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