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Related Experiment Video

Updated: Oct 14, 2025

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues
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Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution.

Kyung Lock Kim1,2,3, Peter van Galen1,2,4, Volker Hovestadt1,2,5

  • 1Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.

Cell Reports Methods
|November 4, 2021
PubMed
Summary

This study introduces a microscopy platform to quantify RNA modifications like N6-methyladenosine (m6A) in single cells. The platform links m6A levels to cell phenotypes, revealing changes during leukemia cell differentiation.

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Cell Biology

Background:

  • Epigenetic modifications regulate mRNA stability and translation.
  • Understanding RNA modifications at the single-cell level is crucial for cell biology.

Purpose of the Study:

  • To develop a microscopy-based platform for quantifying RNA modifications in single cells.
  • To correlate RNA modification patterns with single-cell phenotypes and gene expression.

Main Methods:

  • Direct capture of mRNA from cell lysates onto oligo-dT-coated coverslips.
  • Label-free, amplification-free visual detection and sequencing of individual m6A-modified transcripts.
  • Integration of a nanoscale device for single-cell isolation and multi-modal analysis (m6A detection, gene expression, cell surface markers).
  • Coupling single-molecule m6A detection with fluorescence in situ hybridization (FISH).

Main Results:

  • Demonstrated a microscopy platform for single-cell RNA modification quantification.
  • Observed reduced cellular m6A levels during MUTZ3 leukemia cell differentiation (CD34+ to CD14+).
  • Successfully related individual gene mRNA and m6A levels to specific single-cell phenotypes using FISH.

Conclusions:

  • The developed platform enables direct, amplification-free quantification of RNA modifications in single cells.
  • This technology allows for the investigation of RNA modification dynamics in relation to cellular states and differentiation.
  • The single-cell multi-modal assay suite is valuable for studying RNA modifications in rare cell populations.