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Related Concept Videos

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Updated: Jan 15, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.

Jiayi Li1,2,3, Shenglun Chen1,2,4, Zhixing Wu1,2,5,6

  • 1Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China.

Briefings in Bioinformatics
|January 13, 2026
PubMed
Summary
This summary is machine-generated.

CircRM, a new computational tool, profiles RNA modifications in circular RNAs using nanopore sequencing. It reveals unique modification patterns on circular RNAs, distinct from linear RNAs.

Keywords:
circular RNAepitranscriptomicsnanopore direct RNA sequencing

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Identification of Circular RNAs using RNA Sequencing
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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Circular RNAs (circRNAs) are key regulatory molecules.
  • RNA modifications significantly influence circRNA function.
  • Existing methods lack resolution for circRNA modification profiling.

Purpose of the Study:

  • To develop a computational method for profiling RNA modifications in circRNAs.
  • To characterize the epitranscriptomic landscape of circRNAs at single-molecule resolution.
  • To identify circRNA-specific modification patterns and features.

Main Methods:

  • Developed CircRM, a computational tool leveraging nanopore direct RNA sequencing.
  • Integrated circRNA detection, read-level modification detection, and methylation rate quantification.
  • Applied CircRM to profile three major RNA modifications (m5C, m6A, m1A) in circRNAs.

Main Results:

  • Identified 427 high-confidence circRNAs and characterized m5C, m6A, and m1A modifications.
  • Revealed distinct modification patterns in circRNAs compared to linear RNAs, with enrichment near back-splice junctions.
  • Demonstrated conserved and cell-type-specific modification patterns across different cell lines.

Conclusions:

  • CircRM provides a powerful computational approach for studying circRNA modifications.
  • CircRNAs possess a unique epitranscriptomic landscape with RNA-type-specific regulations.
  • Findings advance the understanding of circular RNA biology and RNA modification mechanisms.