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icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation.

Pan Li1, Ruoyao Shi2, Qiangfeng Cliff Zhang1

  • 1MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Methods (San Diego, Calif.)
|October 14, 2019
PubMed
Summary

Researchers can now more accurately analyze RNA structures using icSHAPE-pipe, a new bioinformatics toolkit. This tool enhances RNA structure scoring and improves transcriptome-wide coverage for sequencing data analysis.

Keywords:
RNA secondary structureicSHAPEicSHAPE reactivity/structure score

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA molecules fold into complex structures crucial for regulating biological processes like transcription and translation.
  • Accurate RNA structure determination is essential but remains challenging due to limitations in current methodologies.
  • The icSHAPE (in vivo single-stranded RNA structure probing) method was previously developed to probe single-stranded RNA nucleotides within cells.

Purpose of the Study:

  • To introduce icSHAPE-pipe, a comprehensive bioinformatics toolkit designed for analyzing RNA structure sequencing data generated by icSHAPE experiments.
  • To provide researchers with a more accurate and efficient workflow for RNA structure analysis.
  • To improve the recovery of structural profiles and transcriptome-wide coverage from icSHAPE data.

Main Methods:

  • Development of icSHAPE-pipe, a software toolkit for processing and analyzing icSHAPE sequencing data.
  • Implementation of improved algorithms for calculating icSHAPE reactivity, serving as RNA structure scores for each base.
  • Integration of quality control features and automated report generation for sequencing data and analysis statistics.

Main Results:

  • icSHAPE-pipe demonstrates higher accuracy in calculating RNA structural information compared to the original icSHAPE data processing protocol.
  • The toolkit achieves significantly higher coverage of the transcriptome, enabling a more comprehensive analysis of RNA structures.
  • icSHAPE-pipe successfully performs quality control and generates detailed reports, streamlining the data analysis process.

Conclusions:

  • icSHAPE-pipe offers a convenient and robust workflow for researchers studying RNA structures using icSHAPE sequencing.
  • The toolkit enhances the accuracy and scope of RNA structure analysis, advancing our understanding of RNA's role in biological processes.
  • This advancement facilitates deeper insights into RNA structural dynamics and their functional implications in cellular contexts.