{
  "abstract": "Barrier epithelia are shielded from the external environment by their apical extracellular matrices (aECMs). The molecular complexity of aECMs has challenged understanding of their organization in vivo. To define the molecular architecture of a model aECM we generated a toolkit of 105 fluorescently tagged aECM components using gene editing in C. elegans, focusing on proteins secreted by the epidermis to form the collagen-rich cuticle. We developed efficient pipelines for modular protein tagging and rapid fluorophore swapping. Most tagged collagens were functional and exhibited exquisitely specific patterning across stages, cell types, and matrix substructures. We define multiple reference markers for key substructures including the little-understood cortical layer, as well as the helical crossed fiber arrays that function as a hydrostatic skeleton to maintain organismal shape. We further tagged 30 members of key aECM protein classes including proteases, protease inhibitors, and lipid transporters. Our standardized markers will allow dissection of the mechanistic basis of aECM spatiotemporal patterning in vivo.\n\nBarrier epithelia are protected by apical extracellular matrices (aECMs), but their complex organization remains poorly understood in vivo. This study generates a toolkit of 105 fluorescently tagged aECM components and defines reference markers for key substructures, enabling analysis of spatiotemporal extracellular matrix patterning.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064",
    "Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093"
  ],
  "article_type": "Methods and Resources",
  "arxiv": null,
  "author_total": 13,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "James Matthew Ragle",
      "orcid": "0000-0002-6626-2615"
    },
    {
      "affs": [
        1
      ],
      "name": "Murugesan Pooranachithra",
      "orcid": "0000-0003-3506-7785"
    },
    {
      "affs": [
        0
      ],
      "name": "Guinevere E. Ashley",
      "orcid": "0000-0002-3983-5553"
    },
    {
      "affs": [
        0
      ],
      "name": "Emma Cadena",
      "orcid": "0009-0005-8000-7839"
    },
    {
      "affs": [
        0
      ],
      "name": "Batia Blank"
    },
    {
      "affs": [
        1
      ],
      "name": "Katelyn Kang"
    },
    {
      "affs": [
        1
      ],
      "name": "Cincy Chen"
    },
    {
      "affs": [
        0
      ],
      "name": "Aditree R. Bhowmick",
      "orcid": "0009-0001-6040-8353"
    },
    {
      "affs": [
        0
      ],
      "name": "Soraya Hawk Mercado",
      "orcid": "0009-0000-4227-6134"
    },
    {
      "affs": [
        0
      ],
      "name": "Tabatha E. Wells"
    },
    {
      "affs": [
        0
      ],
      "name": "John C Clancy",
      "orcid": "0000-0003-2867-9740"
    },
    {
      "affs": [
        1
      ],
      "name": "Andrew D. Chisholm",
      "orcid": "0000-0001-5091-0537"
    },
    {
      "affs": [
        0
      ],
      "name": "Jordan D. Ward",
      "orcid": "0000-0001-9870-8936"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2kh451eqn0gz5.bib",
  "cited_by": 22,
  "doi": "10.1371/journal.pbio.3004059",
  "fulltext_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3004059",
  "id": "2kh451eqn0gz5",
  "issns": [
    "1545-7885",
    "1544-9173"
  ],
  "landing_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3004059",
  "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",
      "1307|Cellular Mechanics and Interactions"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Proteins/Collagens"
    ],
    [
      "plos",
      "/Biology and life sciences/Developmental biology/Life cycles/Larvae"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Heredity/Homozygosity"
    ],
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      "plos",
      "/Biology and life sciences/Genetics/Phenotypes"
    ],
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      "plos",
      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Eukaryota/Animals/Invertebrates/Nematoda/Caenorhabditis/Caenorhabditis elegans"
    ],
    [
      "plos",
      "/Biology and life sciences/Physiology/Physiological processes/Molting"
    ],
    [
      "plos",
      "/Biology and life sciences/Zoology/Animals/Invertebrates/Nematoda/Caenorhabditis/Caenorhabditis elegans"
    ],
    [
      "plos",
      "/Research and analysis methods/Animal studies/Experimental organism systems/Animal models/Caenorhabditis elegans"
    ],
    [
      "plos",
      "/Research and analysis methods/Animal studies/Experimental organism systems/Model organisms/Caenorhabditis elegans"
    ],
    [
      "plos",
      "/Research and analysis methods/Model organisms/Caenorhabditis elegans"
    ],
    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
    ]
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  "openalex": "W7221759832",
  "pdf_url": "https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3004059&type=printable",
  "pmcid": "PMC13705611",
  "pmid": "42873825",
  "published": "2026-10-14",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/2kh451eqn0gz5.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:23Z",
      "native_id": "10.1371/journal.pbio.3004059",
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      "url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3004059"
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      "first_seen": "2026-10-30T12:18:46Z",
      "native_id": "MED:42873825",
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      "url": "https://europepmc.org/article/MED/42873825"
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  "subjects": [
    {
      "field": "biology",
      "origin": "plos:genetics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "A systematic fluorescently tagged protein toolkit for dissecting apical extracellular matrix patterning in C. elegans",
  "title_text": "A systematic fluorescently tagged protein toolkit for dissecting apical extracellular matrix patterning in C. elegans",
  "type": "peer-reviewed",
  "updated_at": "2026-11-06T13:20:28Z",
  "url": "https://research.draconitic.com/paper/2kh451eqn0gz5",
  "venue": "PLOS Biology",
  "versions": []
}