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Peer-reviewedCC BYScience

Human body single-cell atlas of three-dimensional genome organization and DNA methylation

  • Jingtian Zhou1,2,3
  • Yue Wu4,3
  • Hanqing Liu3,5
  • Wei Tian3
  • Rosa Castanon3
  • Anna Bartlett3
  • Zuolong Zhang6
  • Guocong Yao7
  • Difang Shi3
  • Ben Clock8
  • Samantha Marcotte8
  • Joseph R. Nery3
17 more authors
  • Michelle Liem9
  • Naomi Claffey9
  • Lara Boggeman9
  • Cesar Barragan3
  • Rafael Arrojo e Drigo10,11,12
  • Annika K K Weimer13,14
  • Minyi Shi13
  • Johnathan Cooper‐Knock15
  • Sai Zhang16,17
  • Michael P. Snyder13
  • Sebastian Preißl18,19,20,21
  • Bing Ren18,22
  • Carolyn O’Connor9
  • Shengbo Chen23
  • Chongyuan Luo24
  • Jesse R. Dixon8
  • Joseph R. Ecker3,25
25 affiliations
  1. 1Arc Institute, Palo Alto, CA, USA
  2. 2Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
  3. 3Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
  4. 4Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
  5. 5Society of Fellows, Harvard University, Cambridge, MA, USA
  6. 6School of Software, Henan University, Kaifeng, Henan, China
  7. 7School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China
  8. 8Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
  9. 9Flow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA
  10. 10Center for Computational Systems Biology, Vanderbilt University, Nashville, TN, USA
  11. 11Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
  12. 12Diabetes Research and Training Center (DRTC), Vanderbilt University Medical Center, Nashville, TN, USA
  13. 13Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
  14. 14Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
  15. 15Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
  16. 16Department of Biomedical Informatics & Data Science, Yale School of Medicine, New Haven, CT, USA
  17. 17Department of Epidemiology, University of Florida, Gainesville, FL, USA
  18. 18Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
  19. 19Department of Pharmacology and Toxicology, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
  20. 20Field of Excellence BioHealth, University of Graz, Graz, Austria
  21. 21Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
  22. 22Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
  23. 23School of Software, Nanchang University, Nanchang, Jiangxi, China
  24. 24Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
  25. 25Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
Open at sourceDOICite

Abstract

Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multiomic profiling of three-dimensional (3D) genome structure and DNA methylation for 86,689 single nuclei across 16 tissues, identifying 35 major and 206 cell subtypes. We revealed extensive changes in CG and non-CG methylation across cell types and characterized 3D chromatin structure at an unprecedented cellular resolution. Extensive discrepancies exist between cell types delineated by DNA methylation and genome structure, which indicates that the role of distinct epigenomic features in maintaining cell identity may vary by lineage. This study expands our understanding of the diversity of DNA methylation and chromatin structure and offers a reference for exploring gene regulation in human health and disease.

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Cite

BibTeXRIS
BibTeX
@article{zhou2026human,
  title = {{Human body single-cell atlas of three-dimensional genome organization and DNA methylation}},
  author = {Jingtian Zhou and Yue Wu and Hanqing Liu and Wei Tian and Rosa Castanon and Anna Bartlett and Zuolong Zhang and Guocong Yao and Difang Shi and Ben Clock and Samantha Marcotte and Joseph R. Nery and Michelle Liem and Naomi Claffey and Lara Boggeman and Cesar Barragan and Rafael Arrojo e Drigo and Annika K K Weimer and Minyi Shi and Johnathan Cooper‐Knock and Sai Zhang and Michael P. Snyder and Sebastian Preißl and Bing Ren and Carolyn O’Connor and Shengbo Chen and Chongyuan Luo and Jesse R. Dixon and Joseph R. Ecker},
  journal = {Science},
  year = {2026},
  month = jul,
  doi = {10.1126/science.adx0673},
  url = {https://doi.org/10.1126/science.adx0673},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Human body single-cell atlas of three-dimensional genome organization and DNA methylation
AU  - Jingtian Zhou
AU  - Yue Wu
AU  - Hanqing Liu
AU  - Wei Tian
AU  - Rosa Castanon
AU  - Anna Bartlett
AU  - Zuolong Zhang
AU  - Guocong Yao
AU  - Difang Shi
AU  - Ben Clock
AU  - Samantha Marcotte
AU  - Joseph R. Nery
AU  - Michelle Liem
AU  - Naomi Claffey
AU  - Lara Boggeman
AU  - Cesar Barragan
AU  - Rafael Arrojo e Drigo
AU  - Annika K K Weimer
AU  - Minyi Shi
AU  - Johnathan Cooper‐Knock
AU  - Sai Zhang
AU  - Michael P. Snyder
AU  - Sebastian Preißl
AU  - Bing Ren
AU  - Carolyn O’Connor
AU  - Shengbo Chen
AU  - Chongyuan Luo
AU  - Jesse R. Dixon
AU  - Joseph R. Ecker
PY  - 2026
DA  - 2026/07/23
JO  - Science
DO  - 10.1126/science.adx0673
UR  - https://doi.org/10.1126/science.adx0673
AB  - Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multiomic profiling of three-dimensional (3D) genome structure and DNA methylation for 86,689 single nuclei across 16 tissues, identifying 35 major and 206 cell subtypes. We revealed extensive changes in CG and non-CG methylation across cell types and characterized 3D chromatin structure at an unprecedented cellular resolution. Extensive discrepancies exist between cell types delineated by DNA methylation and genome structure, which indicates that the role of distinct epigenomic features in maintaining cell identity may vary by lineage. This study expands our understanding of the diversity of DNA methylation and chromatin structure and offers a reference for exploring gene regulation in human health and disease.
SN  - 0036-8075
SN  - 0193-4511
SN  - 1095-9203
ER  -