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Related Experiment Video

Updated: Jan 11, 2026

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry
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Uli-epic: profiling RNA modifications from ultra-low input samples.

Weizhi He1, Chu Xu1, Wen Chen2

  • 1Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.

Genome Biology
|November 11, 2025
PubMed
Summary

We developed Uli-epic, a low-input RNA method for profiling epitranscriptomic modifications like pseudouridine (Ψ) and m6A. This technique requires minimal RNA, enabling sensitive detection in neural stem cells and sperm.

Keywords:
BID-seqFetal growth restrictionGLORILinear amplificationM6AUli-epicUltra-low inputΨ

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • High-throughput sequencing methods for RNA modifications often demand large RNA quantities.
  • Harsh chemical treatments in existing protocols limit their applicability for precious or limited samples.

Purpose of the Study:

  • To introduce Uli-epic, an innovative library construction strategy for low-input epitranscriptomic profiling.
  • To enable sensitive detection of RNA modifications using picogram to nanogram amounts of RNA.

Main Methods:

  • Uli-epic library construction strategy.
  • BID-seq (Biotin-dependent) and GLORI (Guanine-Ligation-based) assays for RNA modification detection.
  • Application in neural stem cells and sperm RNA from mouse models.

Main Results:

  • Uli-epic enables epitranscriptomic profiling with as little as 100 pg to 1 ng of RNA.
  • Pseudouridine (Ψ) sites were investigated in neural stem cells and sperm using Uli-epic BID-seq with 500 pg of RNA.
  • m6A modifications were quantified in neural stem cells and sperm using Uli-epic GLORI with 10 ng of RNA.

Conclusions:

  • Uli-epic significantly reduces RNA input requirements for epitranscriptomic analysis.
  • The method facilitates the study of RNA modifications in sensitive cell types and conditions, such as fetal growth restriction.
  • Uli-epic provides a versatile platform for advancing epitranscriptomic research with limited RNA samples.