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Formation of new chromatin domains determines pathogenicity of genomic duplications

Author

Listed:
  • Martin Franke

    (Max Planck Institute for Molecular Genetics, RG Development & Disease
    Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin)

  • Daniel M. Ibrahim

    (Max Planck Institute for Molecular Genetics, RG Development & Disease
    Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin
    Berlin Institute of Health)

  • Guillaume Andrey

    (Max Planck Institute for Molecular Genetics, RG Development & Disease)

  • Wibke Schwarzer

    (Developmental Biology Unit, European Molecular Biology Laboratory)

  • Verena Heinrich

    (Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin
    Max Planck Institute for Molecular Genetics)

  • Robert Schöpflin

    (Max Planck Institute for Molecular Genetics)

  • Katerina Kraft

    (Max Planck Institute for Molecular Genetics, RG Development & Disease
    Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin)

  • Rieke Kempfer

    (Max Planck Institute for Molecular Genetics, RG Development & Disease)

  • Ivana Jerković

    (Max Planck Institute for Molecular Genetics, RG Development & Disease
    Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin)

  • Wing-Lee Chan

    (Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin)

  • Malte Spielmann

    (Max Planck Institute for Molecular Genetics, RG Development & Disease
    Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin)

  • Bernd Timmermann

    (Max Planck Institute for Molecular Genetics, Sequencing Core Facility)

  • Lars Wittler

    (Max Planck Institute for Molecular Genetics)

  • Ingo Kurth

    (Institute of Human Genetics, Jena University Hospital
    Institute of Human Genetics, Uniklinik RWTH Aachen)

  • Paola Cambiaso

    (Bambino Gesù Children's Hospital-IRCCS)

  • Orsetta Zuffardi

    (University of Pavia)

  • Gunnar Houge

    (Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital)

  • Lindsay Lambie

    (National Health Laboratory Service, University of the Witwatersrand)

  • Francesco Brancati

    (Health and Environmental Sciences, University of L’Aquila
    Istituto Dermopatico dell’Immacolata (IDI) IRCCS)

  • Ana Pombo

    (Berlin Institute of Health
    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine)

  • Martin Vingron

    (Max Planck Institute for Molecular Genetics)

  • Francois Spitz

    (Developmental Biology Unit, European Molecular Biology Laboratory)

  • Stefan Mundlos

    (Max Planck Institute for Molecular Genetics, RG Development & Disease
    Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin
    Berlin Institute of Health
    Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin)

Abstract

Genomic duplications in the SOX9 region are associated with human disease phenotypes; a study using human cells and mouse models reveals that the duplications can cause the formation of new higher-order chromatin structures called topologically associated domains (TADs) thereby resulting in changes in gene expression.

Suggested Citation

  • Martin Franke & Daniel M. Ibrahim & Guillaume Andrey & Wibke Schwarzer & Verena Heinrich & Robert Schöpflin & Katerina Kraft & Rieke Kempfer & Ivana Jerković & Wing-Lee Chan & Malte Spielmann & Bernd , 2016. "Formation of new chromatin domains determines pathogenicity of genomic duplications," Nature, Nature, vol. 538(7624), pages 265-269, October.
    • Handle: RePEc:nat:nature:v:538:y:2016:i:7624:d:10.1038_nature19800
    DOI: 10.1038/nature19800
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    Cited by:

    1. Jie Zhang & Gongcheng Hu & Yuli Lu & Huawei Ren & Yin Huang & Yulin Wen & Binrui Ji & Diyang Wang & Haidong Wang & Huisheng Liu & Ning Ma & Lingling Zhang & Guangjin Pan & Yibo Qu & Hua Wang & Wei Zha, 2024. "CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Samuel Abassah-Oppong & Matteo Zoia & Brandon J. Mannion & Raquel Rouco & Virginie Tissières & Cailyn H. Spurrell & Virginia Roland & Fabrice Darbellay & Anja Itum & Julie Gamart & Tabitha A. Festa-Da, 2024. "A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    3. Beatriz del Blanco & Sergio Niñerola & Ana M. Martín-González & Juan Paraíso-Luna & Minji Kim & Rafael Muñoz-Viana & Carina Racovac & Jose V. Sanchez-Mut & Yijun Ruan & Ángel Barco, 2024. "Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    4. Uirá Souto Melo & Jerome Jatzlau & Cesar A. Prada-Medina & Elisabetta Flex & Sunhild Hartmann & Salaheddine Ali & Robert Schöpflin & Laura Bernardini & Andrea Ciolfi & M-Hossein Moeinzadeh & Marius-Ko, 2023. "Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    5. Robert Schöpflin & Uirá Souto Melo & Hossein Moeinzadeh & David Heller & Verena Laupert & Jakob Hertzberg & Manuel Holtgrewe & Nico Alavi & Marius-Konstantin Klever & Julius Jungnitsch & Emel Comak & , 2022. "Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Surya K Ghosh & Daniel Jost, 2018. "How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes," PLOS Computational Biology, Public Library of Science, vol. 14(5), pages 1-26, May.
    7. Sabina Moser Tralamazza & Emile Gluck-Thaler & Alice Feurtey & Daniel Croll, 2024. "Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    8. Vinícius G. Contessoto & Olga Dudchenko & Erez Lieberman Aiden & Peter G. Wolynes & José N. Onuchic & Michele Pierro, 2023. "Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    9. Andrea Wilderman & Eva D’haene & Machteld Baetens & Tara N. Yankee & Emma Wentworth Winchester & Nicole Glidden & Ellen Roets & Jo Dorpe & Sandra Janssens & Danny E. Miller & Miranda Galey & Kari M. B, 2024. "A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    10. Giulia Cova & Juliane Glaser & Robert Schöpflin & Cesar Augusto Prada-Medina & Salaheddine Ali & Martin Franke & Rita Falcone & Miriam Federer & Emanuela Ponzi & Romina Ficarella & Francesca Novara & , 2023. "Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    11. Jia-Yong Zhong & Longjian Niu & Zhuo-Bin Lin & Xin Bai & Ying Chen & Feng Luo & Chunhui Hou & Chuan-Le Xiao, 2023. "High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    12. Ting Xie & Adi Danieli-Mackay & Mariachiara Buccarelli & Mariano Barbieri & Ioanna Papadionysiou & Q. Giorgio D’Alessandris & Claudia Robens & Nadine Übelmesser & Omkar Suhas Vinchure & Liverana Laure, 2024. "Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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