{
  "abstract": "RNA structures that form inside living cells govern processes ranging from translation to RNA decay, many of which are controlled by RNA-binding proteins (RBPs). Because RBP specificity can depend on both RNA sequence and folding, traditional pulldown-based methods often obscure the structural context of bound RNAs. Here, a quantitative framework based on dimethyl sulfate mutational profiling and sequencing was established to directly measure RNA structure and RBP binding in human cells at single-nucleotide resolution. Applied to a 1600-member MS2 hairpin library, this approach revealed that RNA folding is the strongest determinant of MS2 coat protein (MCP) recognition in the MS2–MCP system, requiring formation of a stable hairpin and a consensus loop sequence, with stem length or GC content contributing primarily through their effect on hairpin folding. An in-cell occupancy model was derived to quantify fractional binding from structural readouts. Complementary systems using degron-tuned MCP and a downregulatory MCP fusion demonstrated binding behavior under subsaturating protein concentrations and showed that inferred occupancy quantitatively predicts RNA degradation efficiency. Together, these results establish a quantitative strategy for measuring RBP–RNA specificity and affinity directly in cells, using the MS2–MCP system to link RNA structure, protein occupancy, and regulatory outcome.",
  "abstract_shown": true,
  "affiliations": [
    "Biophysics Program, Stanford University School of Medicine , Stanford, CA 94305 ,",
    "Department of Chemistry, Texas A&M University, College Station , TX 77843 ,",
    "Department of Bioengineering, Stanford University , Stanford, CA 94305 ,"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Abby R Thurm"
    },
    {
      "affs": [
        1
      ],
      "name": "Tanya H Nguyen"
    },
    {
      "affs": [
        1
      ],
      "name": "Jesus Damian Torres Campos"
    },
    {
      "affs": [
        1
      ],
      "name": "Matthew Mansfield"
    },
    {
      "affs": [
        2
      ],
      "name": "Lacramioara Bintu"
    },
    {
      "affs": [
        1
      ],
      "name": "Lauren D Hagler",
      "orcid": "0000-0002-2057-3629"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fb977c14tq4d1.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag1019",
  "fulltext_url": "https://europepmc.org/articles/PMC13720505",
  "id": "fb977c14tq4d1",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/article/doi/10.1093/nar/gkag1019/9005089",
  "language": "eng",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI00010"
    ],
    [
      "heading",
      "Methods"
    ],
    [
      "heading",
      "Narese/42"
    ],
    [
      "heading",
      "Narese/43"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://academic.oup.com/nar/article-pdf/54/20/gkag1019/72614322/gkag1019.pdf",
  "pmcid": "PMC13720505",
  "pmid": "42960510",
  "published": "2026-10-01",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/fb977c14tq4d1.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:50Z",
      "native_id": "10.1093/nar/gkag1019",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/article/doi/10.1093/nar/gkag1019/9005089"
    },
    {
      "first_seen": "2026-11-01T00:20:52Z",
      "native_id": "MED:42960510",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42960510"
    },
    {
      "first_seen": "2026-11-03T12:21:22Z",
      "native_id": "PMC13720505",
      "source": "pmc",
      "url": "https://doi.org/10.1093/nar/gkag1019"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "issn:0305-1048",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells",
  "title_text": "Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells",
  "type": "peer-reviewed",
  "updated_at": "2026-11-03T12:21:22Z",
  "url": "https://research.draconitic.com/paper/fb977c14tq4d1",
  "venue": "Nucleic Acids Research",
  "versions": []
}