Capturing Chromosome Conformation

1. Front Matter

   Pages i-xi

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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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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.

• 3D genome organization
• Tridimensional chromatin conformation
• Chromosome conformation capture
• Nuclear compartmentalization
• Imaging visualization
• Next generation sequencing

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

  Beatrice Bodega

• Istituto Nazionale di Genetica Molecolare, Milan, Italy

  Chiara Lanzuolo

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