{
  "abstract": "Transcription factors (TFs) form dynamic, high-concentration clusters, condensates, or hubs, proposed to increase TF binding frequency at target enhancers. However, how enhancer sequence shapes hub properties remains unclear. We developed a live imaging-based framework to quantify the spatiotemporal relationship between TF hubs and actively transcribed genes in live Drosophila embryos. Examining hubs formed by the TF Dorsal across enhancers with defined binding site composition, we find that hub enrichment and persistence scale with the number of Dorsal binding motifs. However, these hub properties do not predict transcriptional bursts for a given enhancer. Combining quantitative imaging with computational modeling, we show that Dorsal hub formation can be explained by TF-DNA binding kinetics alone. These findings support a model in which TF hubs emerge from enhancer-encoded TF-DNA interactions rather than higher-order regulatory assemblies.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.",
    "Developmental, Stem Cell, and Regenerative Biology Graduate Group, Perelman School of Medicine, Philadelphia, PA 19104, USA.",
    "Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA.",
    "Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.",
    "Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.",
    "Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA.",
    "Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.",
    "Department of Physics, University of California, Berkeley, CA 94720, USA.",
    "Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA 94720, USA.",
    "Chan Zuckerberg Biohub–San Francisco, San Francisco, CA 94158, USA.",
    "Howard Hughes Medical Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA.",
    "Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Samantha Fallacaro",
      "orcid": "0000-0001-7749-0034"
    },
    {
      "affs": [
        0,
        2,
        3
      ],
      "name": "Manya Kapoor",
      "orcid": "0000-0002-0352-5131"
    },
    {
      "affs": [
        0,
        2,
        4
      ],
      "name": "Lillian Encarnation",
      "orcid": "0009-0008-6790-0712"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Apratim Mukherjee",
      "orcid": "0000-0002-1762-3277"
    },
    {
      "affs": [
        5
      ],
      "name": "Meghan A. Turner",
      "orcid": "0000-0003-2451-5036"
    },
    {
      "affs": [
        5,
        6,
        7,
        8,
        9
      ],
      "name": "Hernan G. Garcia",
      "orcid": "0000-0002-5212-3649"
    },
    {
      "affs": [
        0,
        2,
        10,
        11
      ],
      "name": "Mustafa Mir",
      "orcid": "0000-0001-8280-2821"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/968hme8c0qpyy.bib",
  "cited_by": 6,
  "doi": "10.1126/sciadv.aeh1086",
  "fulltext_url": "https://europepmc.org/articles/PMC13651869",
  "id": "968hme8c0qpyy",
  "issns": [
    "2375-2548"
  ],
  "landing_url": "https://www.science.org/doi/10.1126/sciadv.aeh1086",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Chromatin Dynamics"
    ]
  ],
  "openalex": "W7221159231",
  "pdf_url": "https://europepmc.org/articles/PMC13651869?pdf=render",
  "pmcid": "PMC13651869",
  "pmid": "42853937",
  "published": "2026-10-09",
  "publisher": "American Association for the Advancement of Science (AAAS)",
  "ris": "https://research.draconitic.com/paper/968hme8c0qpyy.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:41Z",
      "native_id": "10.1126/sciadv.aeh1086",
      "source": "crossref",
      "url": "https://www.science.org/doi/10.1126/sciadv.aeh1086"
    },
    {
      "first_seen": "2026-10-30T12:18:12Z",
      "native_id": "MED:42853937",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42853937"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Chromatin Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Enhancer binding kinetics explain transcription factor hub formation",
  "title_text": "Enhancer binding kinetics explain transcription factor hub formation",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:12Z",
  "url": "https://research.draconitic.com/paper/968hme8c0qpyy",
  "venue": "Science Advances",
  "versions": []
}