{
  "abstract": "Proteins on the cell membrane cluster to respond to extracellular signals; for example, adhesion proteins cluster to enhance extracellular matrix sensing. The maturation of such receptor clusters may require additional adhesome proteins to adapt and reinforce extracellular signal sensing. However, it has been unclear whether the genes encoding these proteins share a spatial organization in the nucleus. Using the adhesome as an example, we show that subsets of genes that code for adhesome proteins exhibit relative spatial clustering and co-regulation in distinct locations within the nucleus. We use Hi-C maps and RNA-seq data from adherent cells to map the correspondence between adhesome gene localization and their expression. Interestingly, we find that the genes encoding several transcription factors, cofactors, and chromatin regulators that regulate these genes are also co-localized with the adhesome gene loci, thereby potentially suggesting a link between the extracellular matrix sensing machinery and gene expression. Additionally, we validate the spatial sub-clustering of adhesome gene loci using MERFISH data and DNA-FISH experiments. Collectively, our results support an association between adhesome gene organization and regulatory state, with a possible role in cellular signal sensing.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America.",
    "Broad Institute of MIT and Harvard, Eric and Wendy Schmidt Center, Cambridge, Massachusetts, United States of America.",
    "Paul Scherrer Institut, Villigen, Switzerland.",
    "Department of Health Science and Technology, ETH Zürich, Zürich, Switzerland.",
    "Massachusetts Institute of Technology, Laboratory for Information and Decision Systems, Cambridge, Massachusetts, United States of America.",
    "Massachusetts Institute of Technology, Institute for Data, Systems, and Society, Cambridge, Massachusetts, United States of America."
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Louis Vincent Cammarata"
    },
    {
      "affs": [
        2
      ],
      "name": "Duhita Sengupta"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Rajshikhar Gupta"
    },
    {
      "affs": [
        1,
        4,
        5
      ],
      "name": "Caroline Uhler",
      "orcid": "0000-0002-7008-0216"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "G V Shivashankar",
      "orcid": "0000-0002-3445-4567"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8n0rcwde3swf1.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0361202",
  "fulltext_url": "https://europepmc.org/articles/PMC13719029",
  "id": "8n0rcwde3swf1",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0361202",
  "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": [
    [
      "heading",
      "Anatomy"
    ],
    [
      "heading",
      "Animal Cells"
    ],
    [
      "heading",
      "Biological Tissue"
    ],
    [
      "heading",
      "Biology and Life Sciences"
    ],
    [
      "heading",
      "Cell Biology"
    ],
    [
      "heading",
      "Cellular Types"
    ],
    [
      "heading",
      "Computer and Information Sciences"
    ],
    [
      "heading",
      "Connective Tissue"
    ],
    [
      "heading",
      "Connective Tissue Cells"
    ],
    [
      "heading",
      "Fibroblasts"
    ],
    [
      "heading",
      "Gene Expression"
    ],
    [
      "heading",
      "Gene Identification and Analysis"
    ],
    [
      "heading",
      "Gene Regulation"
    ],
    [
      "heading",
      "Gene Types"
    ],
    [
      "heading",
      "Genetic Loci"
    ],
    [
      "heading",
      "Genetic Networks"
    ],
    [
      "heading",
      "Genetics"
    ],
    [
      "heading",
      "Genomics"
    ],
    [
      "heading",
      "Locus Control Region"
    ],
    [
      "heading",
      "Medicine and Health Sciences"
    ],
    [
      "heading",
      "Network Analysis"
    ],
    [
      "heading",
      "Regulator Genes"
    ],
    [
      "heading",
      "Research Article"
    ],
    [
      "heading",
      "Transcriptional Control"
    ],
    [
      "plos",
      "/Biology and life sciences/Anatomy/Biological tissue/Connective tissue/Connective tissue cells/Fibroblasts"
    ],
    [
      "plos",
      "/Biology and life sciences/Cell biology/Cellular types/Animal cells/Connective tissue cells/Fibroblasts"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Gene expression/Gene regulation"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Gene expression/Gene regulation/Locus control region"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Gene expression/Gene regulation/Transcriptional control"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Gene identification and analysis/Genetic networks"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Gene types/Regulator genes"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genetic loci"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics"
    ],
    [
      "plos",
      "/Computer and information sciences/Network analysis/Genetic networks"
    ],
    [
      "plos",
      "/Medicine and health sciences/Anatomy/Biological tissue/Connective tissue/Connective tissue cells/Fibroblasts"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://europepmc.org/articles/PMC13719029?pdf=render",
  "pmcid": "PMC13719029",
  "pmid": "42956062",
  "published": "2026-10-29",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/8n0rcwde3swf1.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:17Z",
      "native_id": "10.1371/journal.pone.0361202",
      "source": "plos",
      "url": "https://doi.org/10.1371/journal.pone.0361202"
    },
    {
      "first_seen": "2026-10-31T00:20:39Z",
      "native_id": "MED:42956062",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42956062"
    },
    {
      "first_seen": "2026-11-02T12:22:56Z",
      "native_id": "PMC13719029",
      "source": "pmc",
      "url": "https://doi.org/10.1371/journal.pone.0361202"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "plos:gene expression",
      "subfield": "molecular-biology"
    },
    {
      "field": "biology",
      "origin": "heading:Cell Biology",
      "subfield": "cell-biology"
    },
    {
      "field": "biology",
      "origin": "plos:genetics",
      "subfield": "genetics-genomics"
    },
    {
      "field": "medicine",
      "origin": "plos:anatomy",
      "subfield": "physiology"
    }
  ],
  "title": "Coupling between adhesome assembly and 3D chromatin organization",
  "title_text": "Coupling between adhesome assembly and 3D chromatin organization",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:22:56Z",
  "url": "https://research.draconitic.com/paper/8n0rcwde3swf1",
  "venue": "PLOS One",
  "versions": []
}