![]() ![]() 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Ke Y, Xu Y, Chen X et al (2017) 3D chromatin structures of mature gametes and structural reprogramming during mammalian resource. ĭu Z, Zheng H, Huang B et al (2017) Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nagano T, Lubling Y, Stevens TJ et al (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Hughes JR, Roberts N, McGowan S et al (2014) Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. ĭryden NH, Broome LR, Dudbridge F et al (2014) Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Hsieh THS, Weiner A, Lajoie B et al (2015) Mapping nucleosome resolution chromosome folding in yeast by micro-C. Ma W, Ay F, Lee C et al (2015) Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Kalhor R, Tjong H, Jayathilaka N et al (2012) Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nagano T, Várnai C, Schoenfelder S et al (2015) Comparison of Hi-C results using in-solution versus in-nucleus ligation. ĭarrow EM, Huntley MH, Dudchenko O et al (2016) Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Giorgetti L, Lajoie BR, Carter AC et al (2016) Structural organization of the inactive X chromosome in the mouse. Minajigi A, Froberg JE, Wei C et al (2015) A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. ĭeng X, Ma W, Ramani V et al (2015) Bipartite structure of the inactive mouse X chromosome. Rao SSP, Huntley MH, Durand NC et al (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Nora EP, Lajoie BR, Schulz EG et al (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. ĭixon JR, Selvaraj S, Yue F et al (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Ĭremer T, Kreth G, Koester H et al (2000) Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture. Lieberman-Aiden E, van Berkum NL, Williams L et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Zhao Z, Tavoosidana G, Sjölinder M et al (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Simonis M, Klous P, Splinter E et al (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). ĭixon JR, Gorkin DU, Ren B (2016) Chromatin domains: the unit of chromosome organization. ĭenker A, De Laat W (2016) The second decade of 3C technologies: detailed insights into nuclear organization. ĭe Wit E, de Laat W (2012) A decade of 3C technologies-insights into nuclear organization. ĭekker J, Marti-Renom MA, Mirny LA (2013) Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Key wordsĭekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. In this chapter, we provide a detailed description on how to calculate A/B compartment profiles from processed Hi-C data on the autosomes and the active/inactive X chromosomes. On the other hand, genomics data repository sites sometimes contain processed Hi-C data sets, allowing researchers to perform further analysis without the need for high-spec workstations and servers. This presents a significant hurdle for those who wish to implement Hi-C technology into their laboratory. Despite its powerfulness, Hi-C data analysis is much more involved compared to conventional NGS applications such as RNA-seq or ChIP-seq and requires many more steps. Hi-C has identified new levels of chromosome organization such as A/B compartments, topologically associating domains (TADs) as well as large megadomains on the inactive X chromosome, while allowing the identification of chromatin loops at the genome scale. Recent advances in next-generation sequencing (NGS) and chromosome conformation capture (3C) analysis have led to the development of Hi-C, a genome-wide version of the 3C method. ![]()
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