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We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.", "authors": ["Akgol Oksuz B", "Yang L", "Abraham S", "Venev SV", "Krietenstein N", "Parsi KM", "Ozadam H", "Oomen ME", "Nand A", "Mao H", "Genga RMJ", "Maehr R", "Rando OJ", "Mirny LA", "Gibcus JH", "Dekker J"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"abstract": "Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. 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We observed pronounced  changes in locus topology between cell types. Subsequent analysis of  single-chromatin fiber traces revealed that these ensemble-average differences  arise through changes in the frequency of commonly sampled topologies. We further  identified two CTCF-bound elements, internal to the SOX9 topologically  associating domain, which promote stripe formation, are positioned near the  domain's 3D geometric center, and bridge enhancer-promoter contacts in a series  of chromatin loops. Ablation of these elements results in diminished SOX9  expression and altered domain-wide contacts. Polymer models with uniform loading  across the domain and frequent cohesin collisions recapitulate this multi-loop,  centrally clustered geometry. Together, we provide mechanistic insights into  architectural stripe formation and gene regulation over ultra-long genomic  ranges.", "display_title": "Chen LF et al. 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