Single-molecule chromatin profiling reveals cell type-specific A/B compartment alteration and multi-enhancer transcriptional coordination

Luo-Ran Liu; Jia-Yong Zhong; Xin Bai; Chen-Liang Ye; Chunhui Hou; Junjun Ding; Wei Chi; Chuan-Le Xiao; Longjian Niu

doi:10.1016/j.jgg.2025.09.011

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Single-molecule chromatin profiling reveals cell type-specific A/B compartment alteration and multi-enhancer transcriptional coordination

doi: 10.1016/j.jgg.2025.09.011

a. State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, Guangdong 510060, China;
b. Shenzhen Eye Hospital, Shenzhen Eye Medical Center, Southern Medical University, Shenzhen 518040, China;
c. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China;
d. Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China

Funds:

We thank all those who generated and freely released the data analyzed in our present study. This work was supported by grants from Key Project Fund of National Natural Science Foundation (No. 82230031), the Regional Innovation and Development Joint Fund of the National Natural Science Foundation of China (No. U24A200954), the Key Special Project of ‘Cutting-Edge Biotechnology’ in the National Key Research and Development Program of China (No. 2024YFC3406200), Sanming Project of Medicine in Shenzhen (No. SZSM202411007), Guangdong Basic and Applied Basic Research Foundation Regional Joint Fund Key Program (No. 2023B1515120051), and Shenzhen Bay Laboratory Basic Research (No. SZBK2021080601009) to Chi Wei, and the Youth Fund of the National Natural Science Foundation of China (No. 32300515) to Niu Longjian.

Received Date: 2025-05-23
Accepted Date: 2025-09-30
Rev Recd Date: 2025-09-30

Available Online: 2025-10-10

Abstract

Abstract

In eukaryotic organisms, the three-dimensional organization and epigenomic landscape of chromatin are fundamental to the regulation of gene expression. Previous studies have provided significant insights into CpG methylation, chromatin accessibility, and the dynamics of 3D architecture. However, a systematic delineation of how these epigenomic features regulate transcriptional activity remains limited. In this study, we develop nanoCAM-seq, a single-molecule sequencing technique designed to simultaneously profile higher-order chromatin interactions, chromatin accessibility, and endogenous CpG methylation. This approach provides an integrative view of chromatin features associated with cis-regulatory elements and reveals their coordinated dynamics during transitions of A/B compartments. Single-molecule analyses using nanoCAM-seq further reveal that promoters characterized by low CpG methylation and high chromatin accessibility more frequently interact with multiple enhancers. Collectively, our findings establish nanoCAM-seq as a powerful approach for resolving the coordinated dynamics of chromatin architecture and epigenetic modifications, offering critical insights into the regulatory mechanisms underlying gene expression.
- 3D genome,
- DNA methylation,
- Gene regulation,
- Chromatin accessibility,
- Epigenetics

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