{
  "abstract": "More than twenty years ago, the FANTOM consortium uncovered that mammalian genomes are pervasively transcribed, revealing multitudes of RNAs with unknown functions. A subset of these transcripts has since then been linked to transcriptional control and to chromatin organization via their ability to interact with DNA, suggesting that chromatin-associated RNAs could be key players in genome regulation. Although recent technological advances now enable the mapping of genome-wide RNA-DNA contacts, a lack of analyses integrating these methods with other genomic features and across multiple cellular contexts hinders our comprehensive understanding of the principles underlying RNA-DNA interactions and of their biological importance. As part of the FANTOM6 project, we thus generated RNA-DNA interaction maps in 16 different human cell types, then combined these contacts with multiple layers of other genomic data to investigate how patterns of interaction between RNA and DNA relate to chromatin organization and function. We show that the RNA-DNA interactome is highly dynamic yet reproducibly organized in cell-type specific networks, constituted of a great diversity of interactions that vary in function of their distance, the nature of their sources and the chromatin state of their targets. In particular, we detected numerous regulatory elements that exhibit marked changes in activity when differentially bound by transcripts, implying that thousands of RNA-DNA interactions can play a mechanistic role in gene expression. This regulatory function correlates with RNA-protein interactions and significantly associates with cell type-relevant and disorder-related traits. In addition to providing essential resources for future research in RNA-mediated chromatin regulation, cellular biology and human diseases, our study thus establishes the RNA-DNA interactome as a new genome regulatory layer that defines and maintains cellular identity and behavior.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 131,
  "authors": [
    {
      "name": "Alice Lambolez"
    },
    {
      "name": "Pelin Sahlén"
    },
    {
      "name": "Wenjing Kang"
    },
    {
      "name": "Xufeng Shu"
    },
    {
      "name": "Jessica Severin"
    },
    {
      "name": "Rodrigo Pracana"
    },
    {
      "name": "Ilyes Abdelhamid"
    },
    {
      "name": "Bhavya Dhaka"
    },
    {
      "name": "Christophe Vroland"
    },
    {
      "name": "Valeria Ranzani"
    },
    {
      "name": "Benedetto Polimeni"
    },
    {
      "name": "Masaru Koido"
    },
    {
      "name": "Andrea Vandelli"
    },
    {
      "name": "Maria Mintseva"
    },
    {
      "name": "Marton Rohaly Medved"
    },
    {
      "name": "Kayoko Yasuzawa"
    },
    {
      "name": "Mitsuyoshi Murata"
    },
    {
      "name": "Diane Delobel"
    },
    {
      "name": "Wing Hin Yip"
    },
    {
      "name": "Hiromi Nishiyori-Sueki"
    },
    {
      "name": "Satoshi Takizawa"
    },
    {
      "name": "Tomoe Nobusada"
    },
    {
      "name": "Matthew Brown"
    },
    {
      "name": "Valeria Di Gioia"
    },
    {
      "name": "Yoshimi Inaba"
    },
    {
      "name": "Sachi Kato"
    },
    {
      "name": "Callum Parr"
    },
    {
      "name": "Kentaro Kaji"
    },
    {
      "name": "Tsugumi Kawashima"
    },
    {
      "name": "Tsukasa Kouno"
    },
    {
      "name": "Michihira Tagami"
    },
    {
      "name": "Kokoro Ozaki"
    },
    {
      "name": "Rebecca Vadalà"
    },
    {
      "name": "Federica Marasca"
    },
    {
      "name": "Elisabetta Cozzi"
    },
    {
      "name": "Robert Krautz"
    },
    {
      "name": "Christian Vaagensø"
    },
    {
      "name": "Tomohiro Yamazaki"
    },
    {
      "name": "Xiaoze Li Wang"
    },
    {
      "name": "Quentin Verron"
    },
    {
      "name": "Yuichi Ichikawa"
    },
    {
      "name": "Jen-Chien Chang"
    },
    {
      "name": "Matthew Valentine"
    },
    {
      "name": "Hjörleifur Einarsson"
    },
    {
      "name": "Jonathan Moody"
    },
    {
      "name": "Akira Hasegawa"
    },
    {
      "name": "Ziheng Liao"
    },
    {
      "name": "Kohei Tomizuka"
    },
    {
      "name": "Artemii Zhigulev"
    },
    {
      "name": "Marco Gaviraghi"
    },
    {
      "name": "Zekiye Altan"
    },
    {
      "name": "Stefania Policicchio"
    },
    {
      "name": "Yifan Yu"
    },
    {
      "name": "Claudia Latini"
    },
    {
      "name": "Rossana Piccioni"
    },
    {
      "name": "Chiara Medaglia"
    },
    {
      "name": "Amanda Piveta Schnepper"
    },
    {
      "name": "Laura Carpen"
    },
    {
      "name": "Eugenia Ricciardelli"
    },
    {
      "name": "Matteo Bonfanti"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bbga00g5r6fam.bib",
  "cited_by": 1,
  "doi": "10.64898/2026.08.25.746868",
  "fulltext_url": null,
  "id": "bbga00g5r6fam",
  "issns": [],
  "landing_url": "https://hal.science/hal-05843238v1",
  "language": "en",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "hal",
      "0.sdv"
    ],
    [
      "openalex",
      "1312|Genomics and Chromatin Dynamics"
    ]
  ],
  "openalex": "W7204464823",
  "pdf_url": "https://hal.science/hal-05843238/document",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-26",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/bbga00g5r6fam.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:03Z",
      "native_id": "hal-05843238",
      "source": "hal",
      "url": "https://hal.science/hal-05843238v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Chromatin Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "The human RNA-DNA interactome is cell type-specific and dynamic",
  "title_text": "The human RNA-DNA interactome is cell type-specific and dynamic",
  "type": "preprint",
  "updated_at": "2026-11-04T12:20:48Z",
  "url": "https://research.draconitic.com/paper/bbga00g5r6fam",
  "venue": "HAL",
  "versions": []
}