{
  "abstract": "We introduce RAD-seq (RNA Accessibility via Deamination sequencing), a simple and scalable method that quantifies RNA accessibility by protein binding in vivo. RAD-seq uses TadA8.20-mediated adenosine deamination to report the local exposure of each adenosine to its molecular environment, integrating the combined effects of base pairing, RNA folding, and RNA-binding protein (RBP) occupancy in a single experiment. RAD-seq profiles recapitulate known structural signatures, reveal high-resolution RBP footprints, report on the influence of RNA modifications, and capture dynamic remodeling of RNA accessibility during oxidative and heat-shock stress. By integrating RAD-seq with RNA Bind-n-Seq motifs, we detected local enrichment of the RNA N6-methyladenosine (m6A) methyltransferase recruiter TRA2A following knockdown of the exon junction anchor protein EIF4A3, revealing a potential mechanism that links RNA accessibility to enhanced TRA2A recruitment and m6A deposition. Extending this framework, we introduce an unsupervised statistical model that combines RAD-seq with motif priors to infer binding landscapes for multiple RBPs, reproducing the information from numerous CLIP-seq datasets from a single RAD-seq experiment. These results indicate RAD-seq as a generalizable approach for joint profiling of RNA structure and protein occupancy, defining enzymatic RNA accessibility as a new dimension to investigate regulatory elements on RNA.",
  "abstract_shown": true,
  "affiliations": [
    "Univ. Chicago"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "name": "Y. Li"
    },
    {
      "name": "C. Ye"
    },
    {
      "name": "R. Ge"
    },
    {
      "name": "C.-W. Ju"
    },
    {
      "name": "Y. Xiao"
    },
    {
      "name": "W. Tang"
    },
    {
      "name": "M. Chen"
    },
    {
      "affs": [
        0
      ],
      "name": "C. He"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1ts5e9dxg59za.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.11.02.763788",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1.full",
  "id": "1ts5e9dxg59za",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "biochemistry"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-02",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/1ts5e9dxg59za.ris",
  "sources": [
    {
      "first_seen": "2026-11-04T12:21:04Z",
      "native_id": "10.64898/2026.11.02.763788",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:biochemistry",
      "subfield": "general"
    }
  ],
  "title": "RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure",
  "title_text": "RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure",
  "type": "preprint",
  "updated_at": "2026-11-05T00:21:17Z",
  "url": "https://research.draconitic.com/paper/1ts5e9dxg59za",
  "venue": "bioRxiv",
  "versions": []
}