{
  "abstract": "Epigenetic regulation involves multiple molecular layers, including DNA and RNA modifications, histone post-translational modifications (PTMs), and chromatin accessibility. These processes contribute to cell identity, development, and disease, but their measurement remains technically challenging because sequence context, molecular modification, chromatin state, and transcript structure are often assayed separately. As a representative third-generation sequencing technology, nanopore sequencing is profoundly reshaping the interpretation of the epigenetic code through its distinctive capabilities, including long-read sequencing, direct single-molecule signal detection, and the identification of nucleic acid modifications without bisulfite conversion or PCR in appropriate workflows. This review summarizes applications of nanopore sequencing in epigenomics and epitranscriptomics and evaluates emerging nanopore-based approaches for protein and histone sensing. We focus on what can currently be measured, the experimental and computational requirements for reliable decoding, and the limitations that must be addressed before broader multi-omic and clinical use.",
  "abstract_shown": true,
  "affiliations": [
    "Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China",
    "State Key Laboratory of Genome and Multi-Omics Technologies, BGI Research, Hangzhou 310030, China",
    "Key Laboratory of Spatial Omics of Zhejiang Province, BGI Research, Hangzhou 310030, China"
  ],
  "article_type": "review article",
  "arxiv": null,
  "author_total": 14,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Jiachao Xin",
      "orcid": "0009-0005-8409-7077"
    },
    {
      "affs": [
        0
      ],
      "name": "Jiaxuan Liu",
      "orcid": "0009-0005-8432-2000"
    },
    {
      "affs": [
        0
      ],
      "name": "Yichao Liu"
    },
    {
      "affs": [
        1
      ],
      "name": "Xinru Liu"
    },
    {
      "affs": [
        1
      ],
      "name": "Mengke Ma"
    },
    {
      "affs": [
        1
      ],
      "name": "An Huang"
    },
    {
      "affs": [
        1
      ],
      "name": "Zijie Ye"
    },
    {
      "affs": [
        1
      ],
      "name": "Pengfan Zhang"
    },
    {
      "affs": [
        1
      ],
      "name": "Xue Wang"
    },
    {
      "affs": [
        1
      ],
      "name": "Tao Zeng"
    },
    {
      "affs": [
        1
      ],
      "name": "Xiumei Lin"
    },
    {
      "affs": [
        0
      ],
      "name": "Chengwei Liu",
      "orcid": "0000-0003-2746-2080"
    },
    {
      "affs": [
        1
      ],
      "name": "Liang Lu"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Liang Chen"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/d8vwjfz6k1khg.bib",
  "cited_by": 0,
  "doi": "10.3390/ijms27209175",
  "fulltext_url": "https://europepmc.org/articles/PMC13705466",
  "id": "d8vwjfz6k1khg",
  "issns": [
    "1422-0067"
  ],
  "landing_url": "https://www.mdpi.com/1422-0067/27/20/9175",
  "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": [
    [
      "openalex",
      "2204|Nanopore and Nanochannel Transport Studies"
    ]
  ],
  "openalex": "W7222421162",
  "pdf_url": "https://europepmc.org/articles/PMC13705466?pdf=render",
  "pmcid": "PMC13705466",
  "pmid": "42941945",
  "published": "2026-10-16",
  "publisher": "MDPI AG",
  "ris": "https://research.draconitic.com/paper/d8vwjfz6k1khg.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:57Z",
      "native_id": "10.3390/ijms27209175",
      "source": "crossref",
      "url": "https://www.mdpi.com/1422-0067/27/20/9175"
    },
    {
      "first_seen": "2026-10-30T12:22:12Z",
      "native_id": "MED:42941945",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42941945"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "issn:1422-0067",
      "subfield": "general"
    }
  ],
  "title": "Nanopore Sequencing for Epigenetic Decoding: Applications, Analytical Constraints, and Translational Prospects",
  "title_text": "Nanopore Sequencing for Epigenetic Decoding: Applications, Analytical Constraints, and Translational Prospects",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:22:12Z",
  "url": "https://research.draconitic.com/paper/d8vwjfz6k1khg",
  "venue": "International Journal of Molecular Sciences",
  "versions": []
}