Spatial genome organization : methods and protocols / edited by Tom Sexton -- New York, NY : Humana Press, [2022] . – (58.17/M592/v.2532)

Contents

Preface
Contributors
PART I  SAILING THE '3Cs': CHROMOSOME CONFORMATION CAPTURE AND ITS VARIANTS
1  Quantitative Chromosome Conformation Capture (3C-qPCR)
2  Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq
3  Tough Tissue Hi-C
4  Mapping Mammalian 3D Genomes by Micro-C
PART II  TARGETED HI-C APPROACHES
5  Targeted Chromosome Conformation Capture (HiCap)
6  Assessment of Multiway Interactions with Tri-C
7  Assessing Specific Networks of Chromatin Interactions with HiChIP
PART III  SEQUENCING-BASED APPROACHES TO ASSESS NUCLEAR ENVIRONMENT
8  Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq
9  The High-Salt Recovered Sequence-Sequencing (HRS-seq) Method: Exploring Genome Association with Nuclear Bodies
PART IV SINGLE-CELL APPROACHES
10  High-Throughput Preparation of Improved Single-Cell Hi-C Libraries Using an Automated Liquid Handling System
11  Simultaneous Quantification of Spatial Genome Positioning and Transcriptomics in Single Cells with scDam&T-Seq
PART V  VISUALIZING SPATIAL GENOME ORGANIZATION
12  High-Throughput DNA FISH (hiFISH)
13  Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells
PART VI  FUNCTIONALLY DISSECTING CHROMATIN ARCHITECTURE
14  CLOuD9: CRISPR-Cas9-Mediated Technique for Reversible Manipulation of Chromatin Architecture
15  Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome
Index