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Spatial Genome Organization

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Tom Sexton

    1. Institut de génétique et de biologie moléculaire et cellulaire (IGBMC), Illkirch, France

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  • 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 2532)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xi
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  2. Sailing the ‘3Cs’: Chromosome Conformation Capture and Its Variants

    1. Front Matter

      Pages 1-1
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    2. Quantitative Chromosome Conformation Capture (3C-qPCR)

      • Cosette Rebouissou, Séphora Sallis, Thierry Forné
      Pages 3-13

    3. Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq

      • Mélanie Miranda, Daan Noordermeer, Benoit Moindrot
      Pages 15-33

    4. Tough Tissue Hi-C

      • Stefan Grob
      Pages 35-50

    5. Mapping Mammalian 3D Genomes by Micro-C

      • Elena Slobodyanyuk, Claudia Cattoglio, Tsung-Han S. Hsieh
      Pages 51-71

  3. Targeted Hi-C Approaches

    1. Front Matter

      Pages 73-73
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    2. Targeted Chromosome Conformation Capture (HiCap)

      • Artemy Zhigulev, Pelin Sahlén
      Pages 75-94

    3. Assessment of Multiway Interactions with Tri-C

      • A. Marieke Oudelaar, Damien J. Downes, Jim R. Hughes
      Pages 95-112

    4. Assessing Specific Networks of Chromatin Interactions with HiChIP

      • Dafne Campigli Di Giammartino, Alexander Polyzos, Effie Apostolou
      Pages 113-141

  4. Sequencing-Based Approaches to Assess Nuclear Environment

    1. Front Matter

      Pages 143-143
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    2. Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq

      • Liguo Zhang, Yu Chen, Andrew S. Belmont
      Pages 145-186

    3. The High-Salt Recovered Sequence-Sequencing (HRS-seq) Method: Exploring Genome Association with Nuclear Bodies

      • Cosette Rebouissou, Marie-Odile Baudement, Thierry Forné
      Pages 187-197

  6. Visualizing Spatial Genome Organization

    1. Front Matter

      Pages 243-243
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    2. High-Throughput DNA FISH (hiFISH)

      • Elizabeth Finn, Tom Misteli, Gianluca Pegoraro
      Pages 245-274

    3. Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells

      • Thomas Sabaté, Christophe Zimmer, Edouard Bertrand
      Pages 275-290

  7. Functionally Dissecting Chromatin Architecture

    1. Front Matter

      Pages 291-291
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Keywords

About this book

This detailed volume explores a variety of cutting-edge techniques used to interrogate spatial genome organization. Beginning with a section covering the vital chromosome conformation capture (3C) technique, this collection continues with chapters on targeted Hi-C approaches, sequencing-based approaches to assess nuclear environment, as well as single-cell technologies to better characterize the heterogeneity and dynamics of nuclear architectures and approaches to visualize them by microscopy. Finally, in order to be able to ask functional questions about the role of spatial chromatin organization in genomic control, the last section provides methods for acute manipulations of chromatin architecture. 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, Spatial Genome Organization: Methods and Protocols is an ideal resource for researchers searching for the best techniques to address their own specific research questions.

Editors and Affiliations

  • Institut de génétique et de biologie moléculaire et cellulaire (IGBMC), Illkirch, France

    Tom Sexton

Bibliographic Information

  • Book Title: Spatial Genome Organization

  • Book Subtitle: Methods and Protocols

  • Editors: Tom Sexton

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2497-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2496-8Published: 23 July 2022

  • Softcover ISBN: 978-1-0716-2499-9Published: 23 July 2023

  • eBook ISBN: 978-1-0716-2497-5Published: 22 July 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 333

  • Number of Illustrations: 7 b/w illustrations, 45 illustrations in colour

  • Topics: Biological Techniques, Genetics and Genomics

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