High-throughput droplet-based enzymatic DNA methylome profiling enables single-cell resolution of epigenetic heterogeneity
9 affiliations
- 1China National Center for Bioinformation, Beijing 100101, China.
- 2Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
- 3University of Chinese Academy of Sciences, Beijing 100049, China.
- 4Department of Pharmacy, Peking University First Hospital, Beijing 100034, China.
- 5School of Medicine, Nankai University, Tianjin 30071, China.
- 6Department of Urology, Chinese PLA General Hospital, Beijing 100039, China.
- 7SeekGene BioSciences Co. Ltd., Beijing 102206, China.
- 8Department of Urology, Peking University First Hospital, Institution of Urology, Peking University, Beijing 100034, China.
- 9Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China.
Abstract
DNA methylation is a fundamental epigenetic modification that regulates gene expression, cellular identity, and disease-associated regulatory programs. However, high-throughput single-cell DNA methylation technologies have been limited by DNA degradation, low CpG recovery, and the poor scalability of bisulfite-based methods. Here, we present scEM-seq, a droplet-based single-cell enzymatic methylome sequencing method that integrates barcode ligation within a single emulsification step, followed by postemulsion cytosine-to-uracil conversion. This design substantially reduces DNA loss and enables robust profiling of tens of thousands of single cells per experiment. scEM-seq generates high-quality single-cell methylomes with moderately improved CpG coverage and balanced read utilization compared with other droplet-based microfluidic methods. Applied to peripheral blood mononuclear cells, scEM-seq accurately resolves major immune lineages, and in prostate cancer tissues, it reveals diverse malignant cell states and patient-specific epigenetic and copy number architectures. scEM-seq enables scalable single-cell dissection of epigenetic heterogeneity across diverse biological and disease contexts, broadening the scope of DNA methylation-based studies into cellular regulation and disease.
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BibTeX
@article{li2026highthroughput,
title = {{High-throughput droplet-based enzymatic DNA methylome profiling enables single-cell resolution of epigenetic heterogeneity}},
author = {Gaojie Li and Yang Yang and Zhuoran Li and Qi Wang and Ying Wang and Bin Guo and Kunmeng Yang and Ming Tan and Jinwei Li and Jiacheng Sun and Guangxin Zhang and Shengwei Xiong and Mei Zhang and Zhihua Zhang and Yingying Xie and Yue Shi and Xin Ma and Weimin Ci},
journal = {Science Advances},
year = {2026},
month = oct,
doi = {10.1126/sciadv.aef2844},
url = {https://www.science.org/doi/10.1126/sciadv.aef2844},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - High-throughput droplet-based enzymatic DNA methylome profiling enables single-cell resolution of epigenetic heterogeneity
AU - Gaojie Li
AU - Yang Yang
AU - Zhuoran Li
AU - Qi Wang
AU - Ying Wang
AU - Bin Guo
AU - Kunmeng Yang
AU - Ming Tan
AU - Jinwei Li
AU - Jiacheng Sun
AU - Guangxin Zhang
AU - Shengwei Xiong
AU - Mei Zhang
AU - Zhihua Zhang
AU - Yingying Xie
AU - Yue Shi
AU - Xin Ma
AU - Weimin Ci
PY - 2026
DA - 2026/10/23
JO - Science Advances
DO - 10.1126/sciadv.aef2844
UR - https://www.science.org/doi/10.1126/sciadv.aef2844
AB - DNA methylation is a fundamental epigenetic modification that regulates gene expression, cellular identity, and disease-associated regulatory programs. However, high-throughput single-cell DNA methylation technologies have been limited by DNA degradation, low CpG recovery, and the poor scalability of bisulfite-based methods. Here, we present scEM-seq, a droplet-based single-cell enzymatic methylome sequencing method that integrates barcode ligation within a single emulsification step, followed by postemulsion cytosine-to-uracil conversion. This design substantially reduces DNA loss and enables robust profiling of tens of thousands of single cells per experiment. scEM-seq generates high-quality single-cell methylomes with moderately improved CpG coverage and balanced read utilization compared with other droplet-based microfluidic methods. Applied to peripheral blood mononuclear cells, scEM-seq accurately resolves major immune lineages, and in prostate cancer tissues, it reveals diverse malignant cell states and patient-specific epigenetic and copy number architectures. scEM-seq enables scalable single-cell dissection of epigenetic heterogeneity across diverse biological and disease contexts, broadening the scope of DNA methylation-based studies into cellular regulation and disease.
SN - 2375-2548
ER -