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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Related Experiment Video

Updated: Jun 24, 2026

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry
08:45

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry

Published on: April 21, 2022

Quantitative profiling of RNA modifications enriched in non-membrane-bound cellular structures using APEX-RNA-MS.

Kyung W Seo1, Dhruv Y Dhingani1, Ralph E Kleiner1

  • 1Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.

Cell Chemical Biology
|June 22, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces APEX-RNA-MS, a new method to map RNA modifications within cells. It reveals how RNA modifications change in cellular structures during stress, offering insights into RNA biology.

Keywords:
APEXDNA damageP-bodiesRNA mass spectrometryRNA modificationsproximity labelingstress granules

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Published on: December 5, 2016

Area of Science:

  • Molecular Biology
  • Cell Biology
  • Biochemistry

Background:

  • RNA modifications are crucial for biological processes.
  • Understanding their subcellular distribution is challenging.
  • Post-transcriptional regulation controls RNA function.

Purpose of the Study:

  • To develop a method for characterizing RNA modifications at subcellular resolution.
  • To investigate the distribution of RNA modifications near RNA-binding proteins in cellular condensates.
  • To analyze changes in RNA modifications during cellular stress responses.

Main Methods:

  • APEX-RNA-MS combines APEX2 proximity labeling with LC-MS.
  • Quantification of modified ribonucleotides.
  • RNA sequencing and RNA FISH were used for validation.

Main Results:

  • APEX-RNA-MS successfully mapped RNA modifications proximal to proteins in non-membrane-bound structures.
  • Changes in protein-proximal RNA modification levels were observed upon DNA damage and stress granule formation.
  • tRNA-specific modifications were found proximal to G3BP1, with tRNAs accumulating in stress granules.

Conclusions:

  • APEX-RNA-MS provides a versatile approach for studying subcellular RNA modification distribution.
  • The study offers new insights into the composition and function of cellular condensates.
  • Characterizing RNA modifications in dynamic cellular structures is now more feasible.