Capturing Chromosome Conformation: Methods and Protocols

ISBN-13: 9781071606667 / Angielski / Miękka / 2021 / 322 str.

Beatrice Bodega; Chiara Lanzuolo

Spis treści

1. Capturing Chromosome Conformation

            Michel Pucéat

 

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

            Federica Lo Sardo

 

3. 4C-Seq: Interrogating Chromatin Looping with Circular Chromosome Conformation Capture

            Nezih Karasu and Tom Sexton

 

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

            Marco Di Stefano, David Castillo, François Serra, Irene Farabella, Mike N. Goodstadt, and Marc A. Marti-Renom

 

5. Targeted DNase Hi-C

            Zhijun Duan

 

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

            Jérôme D. Robin

 

7. Computational Analysis of Hi-C Data

            Mattia Forcato and Silvio Bicciato

 

8. 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, and Josée Dostie

 

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

            Kim L. de Luca and Jop Kind

 

10. Formaldehyde-Mediated Snapshot of Nuclear Architecture

            Federica Lucini, Andrea Bianchi, and Chiara Lanzuolo

 

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

            Ezio T. Fok, Stephanie Fanucchi, Kerstin Bystricky, and Musa M. Mhlanga

 

12. Preparing Map of Chromosome Territories Distribution Frequency

            Paulina Nastały and Paolo Maiuri

 

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

            Quentin Szabo, Giacomo Cavalli, and Frédéric Bantignies

 

14. 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, and Marina Lusic

 

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

            Tiziana Santini, Julie Martone, and Monica Ballarino

 

16. 3D COMBO chrRNA-DNA-Immuno FISH

            Federica Marasca, Alice Cortesi, and Beatrice Bodega

 

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

            Francesco Gregoretti, Alice Cortesi, Gennaro Oliva, Beatrice Bodega, and Laura Antonelli

Blurb

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.