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Updated: Sep 3, 2025
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Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
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Lighting Up Nucleic Acid Modifications in Single Cells with DNA-Encoded Amplification
Feng Chen1, Jing Xue1, Min Bai1
1Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
Accounts of Chemical Research
|July 29, 2022
Summary
New methods visualize nucleic acid modifications (NAMs) in single cells, revealing their spatial distribution and accessibility. These advances offer insights into epigenetic regulation and disease states.
Area of Science:
- Molecular Biology
- Epigenetics
- Biochemistry
- Genomics
- Cell Biology
Background:
- Nucleic acid modifications (NAMs) regulate gene expression and cellular functions.
- NAMs exhibit diverse abundances, spatial proximity, and dynamic accessibility within cells.
- Understanding NAMs' subcellular distribution and accessibility in single cells remains challenging.
Purpose of the Study:
- To develop and overview novel methods for single-cell analysis of NAMs.
- To investigate the subcellular distribution, spatial proximity, and accessibility of NAMs.
- To explore the role of NAMs in biological processes and disease states at the single-cell level.
Main Methods:
- Development of DNA-encoded amplification (DEA) strategies for NAM imaging.
- Base-encoded amplifying FISH (BEA-FISH) for visualizing low-abundance NAMs.
- Pairwise proximity-differentiated amplifying FISH (PPDA-FISH) for simultaneous NAM proximity analysis.
- Cellular macromolecule-tethered DNA walking indexing (Cell-TALKING) for multi-NAM analysis.
- Single-cell hydrogel encoding amplification (scHEA) for global DNA accessibility analysis.
Main Results:
- BEA-FISH enables visualization of previously undetectable low-abundance NAMs.
- PPDA-FISH allows simultaneous counting of different NAMs in close proximity.
- Cell-TALKING probes multiple NAMs within specific nanoenvironments.
- scHEA distinguishes breast cancer cells based on global 5hmC and 5hmU levels.
Conclusions:
- Novel DEA-based methods provide single-site sensitivity for NAM imaging in single cells.
- These techniques overcome limitations of conventional methods for NAM analysis.
- The developed approaches offer new avenues for understanding NAMs' roles in health and disease.
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