Spatial Genome Organization: Methods and Protocols

ISBN-13: 9781071624968 / Angielski / Twarda / 2022

Sexton, Tom

Opis

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.

Spis treści

Part I: Sailing the ‘3Cs’: Chromosome Conformation Capture and Its Variants

 

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

            Cosette Rebouissou, Séphora Sallis, and Thierry Forné

 

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

            Mélanie Miranda, Daan Noordermeer, and Benoit Moindrot

 

3. Tough Tissue Hi-C

            Stefan Grob

 

4. Mapping Mammalian 3D Genomes by Micro-C

            Elena Slobodyanyuk, Claudia Cattoglio, and Tsung-Han S. Hsieh

 

Part II: Targeted Hi-C Approaches

 

5. Targeted Chromosome Conformation Capture (HiCap)

            Artemy Zhigulev and Pelin Sahlén

 

6. Assessment of Higher-Order, Multi-Way Interactions with Tri-C

            A. Marieke Oudelaar, Damien J. Downes, and Jim R. Hughes

 

7. Assessing Specific Networks of Chromatin Interactions with HiChIP

            Dafne Campigli Di Giammartino, Alexander Polyzos, and Effie Apostolou

 

Part III: Sequencing-Based Approaches to Assess Nuclear Environment

 

8. Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-Seq

            Liguo Zhang, Yu Chen, and Andrew S. Belmont

 

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

            Cosette Rebouissou, Marie-Odile Baudement, and Thierry Forné

 

Part IV: Single-Cell Approaches

 

10. High-Throughput Preparation of Improved Single-Cell Hi-C Libraries Using an Automated Liquid Handling System

            Wing Leung and Takashi Nagano

 

11. Simultaneous Quantification of Spatial Genome Positioning and Transcriptomics in Single Cells with scDam&T-Seq

            Silke J.A. Lochs and Jop Kind

 

Part V: Visualizing Spatial Genome Organization

 

12. High-Throughput DNA FISH (hiFISH)

            Elizabeth Finn, Tom Misteli, and Gianluca Pegoraro

 

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

            Thomas Sabate, Christophe Zimmer, and Edouard Bertrand

 

Part VI: Functionally Dissecting Chromatin Architecture

 

14. CLOuD9: CRISPR-Cas9-Mediated Technique for Reversible Manipulation of Chromatin Architecture

            Wei Qiang Seow, Poonam Agarwal, and Kevin C. Wang

 

15. Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome

            Michela Maresca, Ning Qing Liu, and Elzo de Wit