欢迎来到OAJRC平台！

期刊栏目

投稿

审稿

期刊目次

加入编委

期刊订阅

添加您的邮件地址以接收即将发行期刊数据：

当前位置：国际医学与数据杂志 > 2025年 9卷 (2)期

Open Access Article

International Journal of Medicine and Data. 2025; 9: (2) ; 20-26 ; DOI: 10.12208/j.ijmd.20250022.

Progress of single-cell epigenetic imaging methods
单细胞表观遗传成像方法研究进展

作者： 王梦灵, 郝翟, 张左玲, 王琛, 宋沁馨, 邹秉杰 *

中国药科大学江苏南京

*通讯作者：邹秉杰,单位：中国药科大学江苏南京；

发布时间: 2025-05-23 总浏览量: 135

PDF 全文下载引用本文

摘要

表观遗传修饰在调控基因表达、细胞命运决定及疾病发生中扮演关键角色，其时空动态特性与细胞异质性密切相关，需要利用合适的分析技术进行精准解析。对此，传统均质样本分析方法难以捕捉单细胞层面的表观调控差异，而单细胞表观遗传成像技术在细胞异质性分析方面已展示出良好的应用，并随着该领域技术发展，其在空间分辨率与动态监测方面也已取得突破。本文对近几年开发的基于光学显微技术的免疫荧光成像、基于核酸扩增的原位标记荧光成像、基于基因编码的荧光蛋白成像等单细胞表观遗传成像方法进行了系统总结，并对它们的成像原理作简要说明。文章重点关注了这些方法的检测通量性能、成像分辨率以及信号放大性能，并概述了它们在实际科研和临床工作中的应用，以期为新的单细胞表观遗传成像方法的开发提供参考，同时推动相关技术向疾病机制解析、表观药物筛选等生物医学与精准医疗的转化应用。

关键词： 单细胞成像；表观遗传；免疫荧光；荧光成像；荧光蛋白；进展

Abstract

Pigenetic modifications play a crucial role in regulating gene expression, cell fate determination, and disease occurrence. Their spatiotemporal dynamic characteristics are closely related to cellular heterogeneity, which requires the use of appropriate analytical techniques for precise interpretation. Traditional homogeneous sample analysis methods are difficult to capture epigenetic regulatory differences at the single-cell level, while single-cell epigenetic imaging techniques have shown good applications in the analysis of cellular heterogeneity. With the development of this field, they have also achieved breakthroughs in spatial resolution and dynamic monitoring. This article systematically summarizes the single-cell epigenetic imaging methods developed in recent years based on optical microscopy technology, such as immunofluorescence imaging, in situ labeling fluorescence imaging based on nucleic acid amplification, and fluorescent protein imaging based on gene encoding. It briefly explains their imaging principles and focuses on the detection throughput performance, imaging resolution, and signal amplification performance of these methods. It also provides an overview of their applications in actual scientific research and clinical work, with the aim of providing references for the development of new single-cell epigenetic imaging methods and promoting the transformation and application of related technologies in the fields of disease mechanism analysis and epigenetic drug screening in biomedicine and precision medicine.

Key words： Single-cell imaging; Epigenetics; Immunofluorescence; Fluorescence imaging; Fluorescent protein; Progress

参考文献 References

[1] Nowell P C. The clonal evolution of tumor cell populations [J]. Science, 1976, 194(4260): 23-8.

[2] Turajlic S, Sottoriva A, Graham T, et al. Resolving genetic heterogeneity in cancer [J]. Nat Rev Genet, 2019, 20(7): 404-16.

[3] Waddington C H. The epigenotype. 1942 [J]. Int J Epidemiol, 2012, 41(1): 10-3.

[4] Lister R, Pelizzola M, Dowen R H, et al. Human DNA methylomes at base resolution show widespread epigenomic differences [J]. Nature, 2009, 462(7271): 315-22.

[5] Buenrostro J D, Giresi P G, Zaba L C, et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position [J]. Nat Methods, 2013, 10(12): 1213-8.

[6] Johnson D S, Mortazavi A, Myers R M, et al. Genome-wide mapping of in vivo protein-DNA interactions [J]. Science, 2007, 316(5830): 1497-502.

[7] Fuhrmann M, Gockel N, Arizono M, et al. Super-Resolution Microscopy Opens New Doors to Life at the Nanoscale [J]. J Neurosci, 2022, 42(45): 8488-97.

[8] Franek M, Kilar A, Fojtík P, et al. Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations [J]. J Cell Sci, 2021, 134(15).

[9] Xu J, Ma H, Jin J, et al. Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells [J]. Cell Rep, 2018, 24(4): 873-82.

[10] Xie L, Dong P, Chen X, et al. 3D ATAC-PALM: super-resolution imaging of the accessible genome [J]. Nat Methods, 2020, 17(4): 430-6.

[11] Farhy C, Hariharan S, Ylanko J, et al. Improving drug discovery using image-based multiparametric analysis of the epigenetic landscape [J]. Elife, 2019, 8.

[12] Alvarez-Kuglen M, Ninomiya K, Qin H, et al. ImAge quantitates aging and rejuvenation [J]. Nat Aging, 2024, 4(9): 1308-27.

[13] Chen F, Li X, Bai M, et al. Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING [J]. Nat Protoc, 2025, 20(1): 220-47.

[14] Xue J, Chen F, Su L, et al. Pairwise Proximity-Differentiated Visualization of Single-Cell DNA Epigenetic Marks [J]. Angew Chem Int Ed Engl, 2021, 60(7): 3428-32.

[15] Kint S, Van Criekinge W, Vandekerckhove L, et al. Single cell epigenetic visualization assay [J]. Nucleic Acids Res, 2021, 49(8): e43.

[16] Ren X, Deng R, Zhang K, et al. Single-Cell Imaging of m(6) A Modified RNA Using m(6) A-Specific In Situ Hybridization Mediated Proximity Ligation Assay (m(6) AISH-PLA) [J]. Angew Chem Int Ed Engl, 2021, 60(42): 22646-51.

[17] Mao D, Tang X, Zhang R, et al. Multichrome encoding-based multiplexed, spatially resolved imaging reveals single-cell RNA epigenetic modifications heterogeneity [J]. Nat Commun, 2025, 16(1): 958.

[18] Fan S, Li X, Liu H, et al. Molecule Differentiation Encoding Microscopy to Dissect Dense Biomolecules in Cellular Nanoenvironments Below Spatial Resolution [J]. Angew Chem Int Ed Engl, 2025: e202425136.

[19] Chen F, Bai M, Cao X, et al. Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications [J]. Nat Commun, 2021, 12(1): 1965.

[20] Lu T, Ang C E, Zhuang X. Spatially resolved epigenomic profiling of single cells in complex tissues [J]. Cell, 2022, 185(23): 4448-64.e17.

[21] Zhang T, Yang H, Yu Q, et al. Dynamic, Single-cell Monitoring of RNA Modifications Response to Viral Infection Using a Genetically Encoded Live-cell RNA Methylation Sensor [J]. Angew Chem Int Ed Engl, 2025, 64(9): e202418003.

[22] Muñoz-López Á, Buchmuller B, Wolffgramm J, et al. Designer Receptors for Nucleotide-Resolution Analysis of Genomic 5-Methylcytosine by Cellular Imaging [J]. Angew Chem Int Ed Engl, 2020, 59(23): 8927-31.

[23] Stepanov A I, Shuvaeva A A, Putlyaeva L V, et al. Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe [J]. Cell Mol Life Sci, 2024, 81(1): 381.

[24] Feng Y, Wang Y, Wang X, et al. Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription [J]. Genome Biol, 2020, 21(1): 296.

引用本文

王梦灵, 郝翟, 张左玲, 王琛, 宋沁馨, 邹秉杰, 单细胞表观遗传成像方法研究进展[J]. 国际医学与数据杂志, 2025; 9: (2) : 20-26.

入驻平台

回到首页

搜索文章: