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Li-BrU-seq: A Low-Input and Simplified Metabolic Labeling Method for Nascent RNA Sequencing.

Yi-Feng Huang1, Jun-Tong He1, Ye-Lin Lan1

  • 1State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.

ACS Chemical Biology
|March 3, 2026
PubMed
Summary

We developed Li-BrU-seq, a new method for profiling nascent RNA. This technique offers high sensitivity and specificity for low-input samples, overcoming limitations of existing RNA sequencing methods.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Transcriptional dynamics are crucial for biological processes like cell fate and stress responses.
  • Nascent RNA sequencing is vital for studying gene expression but faces challenges like high cell input and cytotoxicity.
  • Existing methods struggle with low-input samples and can introduce artifacts.

Purpose of the Study:

  • To introduce Li-BrU-seq, an optimized 5-bromouridine (BrU)-based profiling strategy for low-input samples.
  • To demonstrate Li-BrU-seq's superior performance compared to existing protocols.
  • To provide a versatile and accessible platform for nascent RNA analysis.

Main Methods:

  • Development of a systematically optimized 5-bromouridine (BrU)-based RNA profiling strategy.
  • Streamlining the enrichment workflow for efficient low-input RNA analysis.
  • Benchmarking Li-BrU-seq against previous protocols for specificity and sensitivity.

Main Results:

  • Li-BrU-seq achieves higher enrichment specificity and sensitivity than existing methods.
  • High-quality transcriptomic profiling is possible from low-input material (500 ng total RNA or ~25,000 cells).
  • The method supports flexible temporal resolution without stress-induced artifacts, unlike 4sU-based methods.

Conclusions:

  • Li-BrU-seq is an accessible and versatile platform for nascent RNA analysis.
  • The method expands the scope of transcriptomic profiling to low-input, rare, and sensitive biological systems.
  • Li-BrU-seq overcomes key limitations of current nascent RNA sequencing technologies.