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Capturing Chromosome Conformation

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Beatrice Bodega

    1. Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy

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  2. Chiara Lanzuolo

    1. Istituto Nazionale di Genetica Molecolare, Milan, Italy

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2157)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Capturing Chromosome Conformation

    • Michel Pucéat
    Pages 1-7

  3. The Chromosome Conformation Capture (3C) in Drosophila melanogaster

    • Federica Lo Sardo
    Pages 9-17

  4. 4C-Seq: Interrogating Chromatin Looping with Circular Chromosome Conformation Capture

    • Nezih Karasu, Tom Sexton
    Pages 19-34

  5. Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments

    • Marco Di Stefano, David Castillo, François Serra, Irene Farabella, Mike N. Goodstadt, Marc A. Marti-Renom
    Pages 35-63

  6. Targeted DNase Hi-C

    • Zhijun Duan
    Pages 65-83

  7. C-HiC: A High-Resolution Method for Unbiased Chromatin Conformation Capture Targeting Small Locus

    • Jérôme D. Robin
    Pages 85-102

  8. Computational Analysis of Hi-C Data

    • Mattia Forcato, Silvio Bicciato
    Pages 103-125

  9. Profiling Chromatin Landscape at High Resolution and Throughput with 2C-ChIP

    • Xue Qing David Wang, Christopher J. F. Cameron, Dana Segal, Denis Paquette, Mathieu Blanchette, Josée Dostie
    Pages 127-157

  10. Single-Cell DamID to Capture Contacts Between DNA and the Nuclear Lamina in Individual Mammalian Cells

    • Kim L. de Luca, Jop Kind
    Pages 159-172

  11. Formaldehyde-Mediated Snapshot of Nuclear Architecture

    • Federica Lucini, Andrea Bianchi, Chiara Lanzuolo
    Pages 173-195

  12. Visualization of Chromatin Dynamics by Live Cell Microscopy Using CRISPR/Cas9 Gene Editing and ANCHOR Labeling

    • Ezio T. Fok, Stephanie Fanucchi, Kerstin Bystricky, Musa M. Mhlanga
    Pages 197-212

  13. Preparing Map of Chromosome Territory Distribution Frequency

    • Paulina Nastały, Paolo Maiuri
    Pages 213-219

  14. Higher-Order Chromatin Organization Using 3D DNA Fluorescent In Situ Hybridization

    • Quentin Szabo, Giacomo Cavalli, Frédéric Bantignies
    Pages 221-237

  15. 3D Immuno-DNA Fluorescence In Situ Hybridization (FISH) for Detection of HIV-1 and Cellular Genes in Primary CD4+ T Cells

    • Bojana Lucic, Julia Wegner, Mia Stanic, Katharina Laurence Jost, Marina Lusic
    Pages 239-249

  16. Visualization of Nuclear and Cytoplasmic Long Noncoding RNAs at Single-Cell Level by RNA-FISH

    • Tiziana Santini, Julie Martone, Monica Ballarino
    Pages 251-280

  17. 3D COMBO chrRNA–DNA–ImmunoFISH

    • Federica Marasca, Alice Cortesi, Beatrice Bodega
    Pages 281-297

  18. An Algorithm for the Analysis of the 3D Spatial Organization of the Genome

    • Francesco Gregoretti, Alice Cortesi, Gennaro Oliva, Beatrice Bodega, Laura Antonelli
    Pages 299-320

  19. Back Matter

    Pages 321-322
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Keywords

About this book

This detailed book collects methods based on the evolution of the chromosome conformation capture (3C) technique and other complementary approaches to dissect chromatin conformation with an emphasis on dissection of nuclear compartmentalization and visualization in imaging. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Capturing Chromosome Conformation: Methods and Protocols serves as an ideal guide for researchers working to further understand 3D genome organization.

Editors and Affiliations

  • Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy

    Beatrice Bodega

  • Istituto Nazionale di Genetica Molecolare, Milan, Italy

    Chiara Lanzuolo

Bibliographic Information

  • Book Title: Capturing Chromosome Conformation

  • Book Subtitle: Methods and Protocols

  • Editors: Beatrice Bodega, Chiara Lanzuolo

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0664-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-0663-6Published: 21 August 2020

  • Softcover ISBN: 978-1-0716-0666-7Published: 21 August 2021

  • eBook ISBN: 978-1-0716-0664-3Published: 20 August 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 322

  • Number of Illustrations: 12 b/w illustrations, 54 illustrations in colour

  • Topics: Biological Techniques, Cell Biology, Genetics and Genomics

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