Titlebook: Computational Methods for 3D Genome Analysis; Ryuichiro Nakato Book 2025 The Editor(s) (if applicable) and The Author(s), under exclusive

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Structural Maintenance of Chromosomes Complexesnd prokaryotic SMC complexes. Thereafter, the current model for how SMC complexes perform in vitro DNA loop extrusion is presented. Lastly, chromosome loop formation by SMC complexes is introduced, and how the DNA loop extrusion mechanism contributes to chromosome looping by SMC complexes in cells is discussed.

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Methods for Genome-Wide Chromatin Interaction Analysisomatin structures such as a loop structure, a domain structure called topologically associating domains (TADs), and compartments. In this chapter, I introduce chromatin interaction techniques using NGS and outline the principles and features of each method.

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Micro-C Analysis Workflow Using Pairtools and Juicerave been developed to comprehensively reveal 3D chromosome structures. Micro-C is one such method that can detect the structures at nucleosome resolution. In this chapter, I provide a basic method for Micro-C analysis. I present and discuss a series of data analyses ranging from mapping to basic downstream analyses, including loop detection.

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HOMER for Analysis of Hi-C Data and Assessment of Composite Structure of the X Chromosomet and interaction matrix format for visualization with Juicebox. The method is demonstrated for the mouse composite X chromosome in which reads from the active and inactive X chromosomes are combined after mock DMSO treatment or targeted degradation of cohesin.

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Acquisition and Analysis Methods for Hi-C Data from Medaka Early Embryosd comparing structures effectively depending on the characteristics of the genome or cell type. Here, we describe a method for acquiring Hi-C data from medaka early embryos and quantifying the structural changes during the developmental process.

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Erstversorgung durch den Krankenhausarztomatin structures such as a loop structure, a domain structure called topologically associating domains (TADs), and compartments. In this chapter, I introduce chromatin interaction techniques using NGS and outline the principles and features of each method.