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Related Experiment Video

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A Nonsequencing Approach for the Rapid Detection of RNA Editing
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Profiling A-to-I RNA editing during mouse somatic reprogramming at the single-cell level.

Tianhang Lv1,2, Siyuan Jiang1,2, Xiaoshan Wang2

  • 1College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.

Heliyon
|July 31, 2023
PubMed
Summary

Adenosine-to-inosine (A-to-I) RNA editing varies dynamically in single cells during reprogramming. This RNA editing, regulated by ADAR1, influences gene expression and promotes mesenchymal-epithelial transition.

Keywords:
ADAR1Mouse somatic reprogrammingSingle-cell RNA editing

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Area of Science:

  • Molecular Biology
  • Genomics
  • Stem Cell Biology

Background:

  • Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) is a complex, heterogeneous process.
  • Adenosine-to-inosine (A-to-I) RNA editing is a key biological factor influencing cellular reprogramming.
  • Understanding the dynamics of RNA editing at the single-cell level is crucial for deciphering reprogramming mechanisms.

Purpose of the Study:

  • To investigate the role and dynamics of A-to-I RNA editing during single-cell reprogramming.
  • To identify specific genes and pathways affected by A-to-I RNA editing in this process.
  • To correlate RNA editing levels with the expression of RNA editing enzymes like ADAR1.

Main Methods:

  • Analysis of A-to-I RNA editing sites using high-depth, full-length single-cell RNA sequencing (scRNA-seq) data.
  • Quantification of A-to-I RNA editing frequency at the single-cell level.
  • Gene Ontology (GO) enrichment analysis to identify affected pathways.
  • Correlation analysis between RNA editing levels and gene expression.

Main Results:

  • A-to-I RNA editing frequency exhibits significant cell-to-cell variation and dynamic changes during reprogramming.
  • A-to-I RNA editing levels are positively correlated with the expression of the RNA editing enzyme ADAR1.
  • ADAR1-dependent A-to-I editing downregulates specific genes (e.g., Igtp, Irgm2) to inhibit interferon-beta response and protein complex stability pathways, promoting mesenchymal-epithelial transition (MET).
  • A negative correlation was observed between A-to-I editing frequency and the expression of genes like Nras and Ube2l6.

Conclusions:

  • A-to-I RNA editing is a dynamic regulatory mechanism in single-cell reprogramming.
  • ADAR1-mediated RNA editing plays a critical role in promoting MET by modulating gene expression and cellular pathways.
  • The findings provide novel insights into the molecular mechanisms governing cellular reprogramming and pluripotency induction.