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A Polymer Physics Model to Dissect Genome Organization in Healthy and Pathological Phenotypes

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Hi-C Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2301))

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Abstract

Novel technologies revealed a nontrivial spatial organization of the chromosomes within the cell nucleus, which includes different levels of compartmentalization and architectural patterns. Notably, such complex three-dimensional structure plays a crucial role in vital biological functions and its alterations can produce extensive rewiring of genomic regulatory regions, thus leading to gene misexpression and disease. Here, we show that theoretical and computational approaches, based on polymer physics, can be employed to dissect chromatin contacts in three-dimensional space and to predict the effects of pathogenic structural variants on the genome architecture. In particular, we discuss the folding of the human EPHA4 and the murine Pitx1 loci as case studies.

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Author notes

  1. Mattia Conte, Luca Fiorillo, and Simona Bianco contributed equally to this work.

Authors and Affiliations

  1. Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso di Monte Sant’Angelo, Naples, Italy

    Mattia Conte, Luca Fiorillo, Simona Bianco, Andrea M. Chiariello, Andrea Esposito, Francesco Musella, Francesco Flora, Alex Abraham & Mario Nicodemi

  2. Berlin Institute of Health (BIH), MDC-Berlin, Berlin, Germany

    Mario Nicodemi

Authors
  1. Mattia Conte
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  2. Luca Fiorillo
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  3. Simona Bianco
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  4. Andrea M. Chiariello
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  5. Andrea Esposito
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  6. Francesco Musella
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  7. Francesco Flora
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  8. Alex Abraham
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  9. Mario Nicodemi
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Corresponding author

Correspondence to Mario Nicodemi .

Editor information

Editors and Affiliations

  1. Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy

    Silvio Bicciato

  2. IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy

    Francesco Ferrari

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Conte, M. et al. (2022). A Polymer Physics Model to Dissect Genome Organization in Healthy and Pathological Phenotypes. In: Bicciato, S., Ferrari, F. (eds) Hi-C Data Analysis. Methods in Molecular Biology, vol 2301. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1390-0_16

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  • DOI: https://doi.org/10.1007/978-1-0716-1390-0_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1389-4

  • Online ISBN: 978-1-0716-1390-0

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