{
  "abstract": "Human kidney development remains incompletely characterized at the level of chromatin accessibility. Here, we investigate chromatin accessibility dynamics (CAD) during the differentiation of human embryonic stem cells (hESCs) into kidney organoids (E-iKOs). Time-course ATAC-seq reveals progressive remodeling of pluripotency-associated chromatin landscapes toward an intermediate mesoderm state, followed by metanephric mesenchyme specification and early nephron epithelialization. These transitions are accompanied by increased accessibility at genomic regions enriched for binding motifs of transcription factors, including SIX, HOX, LHX, PAX, EBF, RFX, WT1, HNF1B, and TEAD. Functional analyses demonstrate that HNF1β is required for tubular differentiation, as HNF1β deficiency results in severe defects in tubule formation while podocytes remain detectable. Integrative analysis of chromatin accessibility and time-course transcriptomics further identifies the histone H3K79 methyltransferase DOT1L as a regulator required for nephron progenitor induction and epithelial differentiation. DOT1L deficiency is associated with widespread alterations in chromatin accessibility and gene expression, particularly at regions enriched for SIX, HOX, PAX, EBF, WT1, HNF1B, and TEAD motifs, accompanied by impaired mesenchymal-to-epithelial transition. Together, this study provides a valuable resource describing chromatin accessibility dynamics during human kidney organoid differentiation and a foundation for future studies of human nephrogenesis in vitro.",
  "abstract_shown": true,
  "affiliations": [
    "Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institute, Department of nephrology,, The Fifth Affiliated Hospital of Guangzhou Medical University；Guangzhou National Laboratory, Guangzhou, Guangdong, China.",
    "Department of Nephropathy, The First Affiliated Hospital of Zhengzhou University, No. 1 East Jianshe Road, Zhengzhou, Henan, China.",
    "School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China.",
    "Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. peiduanqing@westlake.edu.cn.",
    "Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institute, Department of nephrology,, The Fifth Affiliated Hospital of Guangzhou Medical University；Guangzhou National Laboratory, Guangzhou, Guangdong, China. cao_shangtao@gzlab.ac.cn."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 19,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Huan Chen"
    },
    {
      "affs": [
        1
      ],
      "name": "Yapei Yuan"
    },
    {
      "affs": [
        0
      ],
      "name": "Baomei Cai"
    },
    {
      "affs": [
        0
      ],
      "name": "Sihua Ou"
    },
    {
      "affs": [
        0
      ],
      "name": "Ruifang Zhang"
    },
    {
      "affs": [
        0
      ],
      "name": "Yiyi Cheng"
    },
    {
      "affs": [
        0
      ],
      "name": "Chunhua Zhou"
    },
    {
      "affs": [
        0
      ],
      "name": "Yudong Fu"
    },
    {
      "affs": [
        0
      ],
      "name": "Sihao Chen"
    },
    {
      "affs": [
        0
      ],
      "name": "Yingxiu Chen"
    },
    {
      "affs": [
        0
      ],
      "name": "Ziyu Feng"
    },
    {
      "affs": [
        2
      ],
      "name": "Yunjing Du"
    },
    {
      "affs": [
        0
      ],
      "name": "Wei He"
    },
    {
      "affs": [
        0
      ],
      "name": "Shengyong Yu"
    },
    {
      "affs": [
        0
      ],
      "name": "Mengjie Pan"
    },
    {
      "affs": [
        0
      ],
      "name": "Yuehong Yan"
    },
    {
      "affs": [
        0
      ],
      "name": "Dajiang Qin"
    },
    {
      "affs": [
        3
      ],
      "name": "Duanqing Pei"
    },
    {
      "affs": [
        4
      ],
      "name": "Shangtao Cao",
      "orcid": "0000-0003-1379-0008"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/cgn8p1rbe4kdh.bib",
  "cited_by": 0,
  "doi": "10.1186/s13578-026-01628-6",
  "fulltext_url": "https://europepmc.org/articles/PMC13721210",
  "id": "cgn8p1rbe4kdh",
  "issns": [
    "2045-3701"
  ],
  "landing_url": "https://europepmc.org/article/MED/42958463",
  "language": "eng",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Research"
    ],
    [
      "openalex",
      "1312|Renal and related cancers"
    ]
  ],
  "openalex": "W7172454302",
  "pdf_url": "https://europepmc.org/articles/PMC13721210?pdf=render",
  "pmcid": "PMC13721210",
  "pmid": "42958463",
  "published": "2026-08-04",
  "publisher": "BMC",
  "ris": "https://research.draconitic.com/paper/cgn8p1rbe4kdh.ris",
  "sources": [
    {
      "first_seen": "2026-11-01T00:20:47Z",
      "native_id": "MED:42958463",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42958463"
    },
    {
      "first_seen": "2026-11-03T12:21:56Z",
      "native_id": "PMC13721210",
      "source": "pmc",
      "url": "https://doi.org/10.1186/s13578-026-01628-6"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Renal and related cancers",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Chromatin accessibility dynamics during kidney organoid induction from human embryonic stem cells.",
  "title_text": "Chromatin accessibility dynamics during kidney organoid induction from human embryonic stem cells.",
  "type": "peer-reviewed",
  "updated_at": "2026-11-03T12:21:56Z",
  "url": "https://research.draconitic.com/paper/cgn8p1rbe4kdh",
  "venue": "Cell & bioscience",
  "versions": []
}