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(2021)", "date_published": "2021-09", "title": "Systematic evaluation of chromosome conformation capture assays.", "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. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a  systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. 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"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "8334e5bc-68fd-490e-8a63-44fa66066cf5", "@id": "/publications/8334e5bc-68fd-490e-8a63-44fa66066cf5/", "ID": "PMID:37845234", "display_title": "Calandrelli R et al. (2023) PMID:37845234", "journal": "Nature communications", "@type": ["Publication", "Item"], "short_attribution": "Calandrelli R et al. (2023)", "date_published": "2023-10-16", "title": "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D  genome organization in human cells.", "abstract": "The interphase genome is dynamically organized in the nucleus and decorated with  chromatin-associated RNA (caRNA). It remains unclear whether the genome  architecture modulates the spatial distribution of caRNA and vice versa. Here, we  generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human  cells. These maps reveal the chromosomal domains demarcated by locally  transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the  spreading of caRNA is constrained by the boundaries of topologically associating  domains (TADs), demonstrating the role of the 3D genome structure in modulating  the spatial distribution of RNA. Conversely, stopping transcription or acute  depletion of RNA induces thousands of chromatin loops genome-wide. Activation or  suppression of the transcription of specific genes suppresses or creates  chromatin loops straddling these genes. Deletion of a specific caRNA-producing  genomic sequence promotes chromatin loops that straddle the interchromosomal  target sequences of this caRNA. These data suggest a feedback loop where the 3D  genome modulates the spatial distribution of RNA, which in turn affects the  dynamic 3D genome organization.", "authors": ["Calandrelli R", "Wen X", "Charles Richard JL", "Luo Z", "Nguyen TC", "Chen CJ", "Qi Z", "Xue S", "Chen W", "Yan Z", "Wu W", "Zaleta-Rivera K", "Hu R", "Yu M", "Wang Y", "Li W", "Ma J", "Ren B", "Zhong S"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "DpnII", "combined": "Enzyme: DpnII"}, "experiment_summary": "in situ Hi-C on HFFc6 (Tier 1) with DpnII", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS31QX9F6/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "warning": null, "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "@id": "/badges/gold-biosample/", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "description": "Gold biosample"}}}]}, "validation-errors": []}