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Peer-reviewedCC BY 4.0International Journal of Molecular Sciences

Nanopore Sequencing for Epigenetic Decoding: Applications, Analytical Constraints, and Translational Prospects

  • Jiachao Xin1
  • Jiaxuan Liu1
  • Yichao Liu1
  • Xinru Liu2
  • Mengke Ma2
  • An Huang2
  • Zijie Ye2
  • Pengfan Zhang2
  • Xue Wang2
  • Tao Zeng2
  • Xiumei Lin2
  • Chengwei Liu1
2 more authors
  • Liang Lu2
  • Liang Chen2,3
  1. 1Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
  2. 2State Key Laboratory of Genome and Multi-Omics Technologies, BGI Research, Hangzhou 310030, China
  3. 3Key Laboratory of Spatial Omics of Zhejiang Province, BGI Research, Hangzhou 310030, China
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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.

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Cite

BibTeXRIS
BibTeX
@article{xin2026nanopore,
  title = {{Nanopore Sequencing for Epigenetic Decoding: Applications, Analytical Constraints, and Translational Prospects}},
  author = {Jiachao Xin and Jiaxuan Liu and Yichao Liu and Xinru Liu and Mengke Ma and An Huang and Zijie Ye and Pengfan Zhang and Xue Wang and Tao Zeng and Xiumei Lin and Chengwei Liu and Liang Lu and Liang Chen},
  journal = {International Journal of Molecular Sciences},
  year = {2026},
  month = oct,
  doi = {10.3390/ijms27209175},
  url = {https://www.mdpi.com/1422-0067/27/20/9175},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Nanopore Sequencing for Epigenetic Decoding: Applications, Analytical Constraints, and Translational Prospects
AU  - Jiachao Xin
AU  - Jiaxuan Liu
AU  - Yichao Liu
AU  - Xinru Liu
AU  - Mengke Ma
AU  - An Huang
AU  - Zijie Ye
AU  - Pengfan Zhang
AU  - Xue Wang
AU  - Tao Zeng
AU  - Xiumei Lin
AU  - Chengwei Liu
AU  - Liang Lu
AU  - Liang Chen
PY  - 2026
DA  - 2026/10/16
JO  - International Journal of Molecular Sciences
DO  - 10.3390/ijms27209175
UR  - https://www.mdpi.com/1422-0067/27/20/9175
AB  - 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.
SN  - 1422-0067
ER  -