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Multichrome encoding-based multiplexed, spatially resolved imaging reveals single-cell RNA epigenetic modifications

Dongsheng Mao1, Xiaochen Tang2, Runchi Zhang1

  • 1Shanghai Tenth People's Hospital of Tongji University, Shanghai, PR China.

Nature Communications
|January 22, 2025
PubMed
Summary

Researchers developed a new imaging tool, PRoximity Exchange-assisted Encoding of Multichrome (PREEM), to map RNA epigenetic modifications in single cells. This method reveals cell-to-cell variability in N6-methyladenosine patterns, enhancing our understanding of gene expression.

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Cell Biology

Background:

  • Single-cell analysis is crucial for understanding cellular heterogeneity.
  • Epigenetic modifications, like RNA N6-methyladenosine (m6A), play key roles in gene expression and cellular function.
  • Existing imaging techniques have limitations in resolving multiple epigenetic modifications simultaneously at the single-cell level.

Purpose of the Study:

  • To develop a novel method for multiplexed, spatially resolved imaging of single-cell RNA epigenetic modifications.
  • To enable the mapping of multiple site-specific RNA m6A modifications at single-molecule resolution within individual cells.
  • To investigate the heterogeneity of RNA epigenetic modifications and their response to drug treatments.

Main Methods:

  • Developed a strategy using multichrome encoding and "AND" Boolean logic recognition, termed PRoximity Exchange-assisted Encoding of Multichrome (PREEM).
  • Implemented PREEM for multiplexed imaging of RNA N6-methyladenosine (m6A) modifications in single cells.
  • Utilized cyclic imaging with tailed DNA self-assembly to demonstrate scalability and adaptability.

Main Results:

  • Successfully mapped the expression and nuclear distribution of multiple site-specific RNA m6A modifications at single-molecule resolution in single cells.
  • Revealed previously unknown heterogeneity in RNA epigenetic modifications across individual cells.
  • Demonstrated changes in these modification patterns following treatment with various drugs.

Conclusions:

  • PREEM is an innovative tool that expands the capabilities of single-cell epigenetics research.
  • Enables joint analysis of multiple epigenetic targets, overcoming imaging channel limitations.
  • Enhances the understanding of cell-to-cell variability in epigenetic modifications, improving the exploration of cellular functions.