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While our genome has historically been viewed as a linear sequence of bases, it has progressively become clear that this is an inadequate way to represent our genetic information. Notably, research over the last 30 years has begun to shed light on the fact that the higher-order, 3-dimensional organization of our genome plays a critical role in the interpretation of the genetic information encoded in our genome. The structure of our genome in the nucleus has been clearly demonstrated to play influential roles in diverse nuclear processes including DNA replication and gene expression. Despite this, our understanding of the structure of our genome within the nucleus remains incomplete. The reasons for this include limitations in the resolution and throughput of existing tools in chromatin topology mapping, a scarcity of the analytical tools for studying genome structure datasets, and the difficulty to relate the nuclear structure to function. Due to recent advancements in molecular methods based on high-throughput DNA sequencing, single cell analytical approaches, and high-resolution microscopy, the time for breaking through these previous limitations has come. We will establish a highly collaborative, innovative team in order to develop the tools necessary to transform our understanding of chromatin architecture and function in mammalian cells. We will begin by developing datasets that establish gold standards for the study of nuclear structure and function using genetic, biochemical and imaging approaches. We will optimize current existing technologies for mapping genome wide chromatin interactions, while also developing novel, complementary approaches for studying chromatin structure. We will also develop innovative analytical methods to interpret the chromatin structural data, unraveling principles of structural- and temporal- chromatin organization. Our highly collaborative team will draw on the diverse experiences of its members to provide a synergistic environment to push the limits of our understanding of nuclear structure. 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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.", "@id": "/publications/8334e5bc-68fd-490e-8a63-44fa66066cf5/", "status": "current", "title": "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D  genome organization in human cells.", "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"], "journal": "Nature communications", "date_published": "2023-10-16", "short_attribution": "Calandrelli R et al. (2023)", "ID": "PMID:37845234", "@type": ["Publication", "Item"], "uuid": "8334e5bc-68fd-490e-8a63-44fa66066cf5", "display_title": "Calandrelli R et al. (2023) PMID:37845234", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "H3K4me3", "combined": "Target: H3K4me3"}, "experiment_summary": "PLAC-seq against H3K4me3 on H1-hESC (Tier 1)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSW82ND6G/", "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": []}