Quantitative Chromosome Conformation Capture (3C-qPCR) -- Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-Seq -- Tough Tissue Hi-C -- Mapping Mammalian 3D Genomes by Micro-C -- Targeted Chromosome Conformation Capture (HiCap) -- Assessment of Higher-Order, Multi-Way Interactions with Tri-C -- Assessing Specific Networks of Chromatin Interactions with HiChIP -- Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-Seq -- The High-Salt Recovered Sequence-Sequencing (HRS-seq) Method: Exploring Genome Association with Nuclear Bodies -- High-Throughput Preparation of Improved Single-Cell Hi-C Libraries Using an Automated Liquid Handling System -- Simultaneous Quantification of Spatial Genome Positioning and Transcriptomics in Single Cells with scDam&T-Seq -- High-Throughput DNA FISH (hiFISH) -- Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells -- CLOuD9: CRISPR-Cas9-Mediated Technique for Reversible Manipulation of Chromatin Architecture -- Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome.

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.