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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Related Experiment Video

Updated: Jan 9, 2026

Optimized Quantitative Assessment of Enhancer RNA Stability in Mouse Embryonic Stem Cells
03:34

Optimized Quantitative Assessment of Enhancer RNA Stability in Mouse Embryonic Stem Cells

Published on: November 21, 2025

204

Optimized Quantitative Assessment of Enhancer RNA Stability in Mouse Embryonic Stem Cells.

Jiin Moon1, Hyohi Lee1, Yeonju Jang1

  • 1Department of Convergent Bioscience and Informatics, and Graduate School of Biological Sciences, Chungnam National University (CNU).

Journal of Visualized Experiments : Jove
|December 8, 2025
PubMed
Summary

Enhancer RNAs (eRNAs) are rapidly degraded in mouse embryonic stem cells (mESCs), with a half-life of approximately 2-3 minutes. This study presents a new method to quantify eRNA stability and turnover in pluripotent cells.

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Area of Science:

  • * Molecular Biology
  • * Epigenetics
  • * Stem Cell Biology

Background:

  • * Enhancer RNAs (eRNAs) are non-coding transcripts from active enhancers, crucial for gene regulation.
  • * eRNA stability and degradation dynamics are poorly understood, especially in dynamic embryonic stem cells (ESCs).

Purpose of the Study:

  • * To present a quantitative method for assessing the decay kinetics and half-life of eRNAs in mouse ESCs.
  • * To investigate the stability of both intergenic and intragenic eRNAs.

Main Methods:

  • * Inhibition of transcription using Actinomycin D in mouse ESCs.
  • * RNA collection at multiple time points followed by cDNA synthesis (random hexamer and oligo(dT) primers).
  • * Quantitative analysis of decay curves using a one-phase exponential decay model.

Main Results:

  • * eRNAs in mouse ESCs exhibit rapid turnover.
  • * The estimated half-life for eRNAs is approximately 2-3 minutes.

Conclusions:

  • * The developed protocol offers a robust framework for studying eRNA stability in pluripotent stem cells.
  • * Findings provide insights into enhancer activity and RNA dynamics in ESCs.