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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": "PMID:37845234", "short_attribution": "Calandrelli R et al. (2023)", "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", "status": "current", "@id": "/publications/8334e5bc-68fd-490e-8a63-44fa66066cf5/", "display_title": "Calandrelli R et al. (2023) PMID:37845234", "title": "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D  genome organization in human cells.", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "H3K4me3", "combined": "Target: H3K4me3"}, "experiment_summary": "PLAC-seq against H3K4me3 on HFFc6 (Tier 1)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSWRCYVPJ/", "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": []}