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meRanTK: methylated RNA analysis ToolKit.

Dietmar Rieder1, Thomas Amort2, Elisabeth Kugler1

  • 1Division of Bioinformatics and.

Bioinformatics (Oxford, England)
|November 7, 2015
PubMed
Summary

meRanTK is a new bioinformatics tool for analyzing RNA cytosine methylation. This software enables efficient mapping and calling of methylation in RNA bisulfite sequencing (RNA-BSseq) and Aza-IP data.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Posttranscriptional cytosine methylation in poly(A)RNA is significant but poorly understood.
  • High-throughput sequencing methods like RNA-BSseq, Aza-IP, and miCLIP allow transcriptome-wide studies of RNA modifications.
  • Specialized software for analyzing RNA-BSseq and Aza-IP data is currently lacking.

Purpose of the Study:

  • To develop the first publicly available toolkit for analyzing high-throughput RNA cytosine methylation data.
  • To address the specific requirements of RNA bisulfite sequencing (RNA-BSseq) and Aza-IP data analysis.
  • To provide a tool for fast, accurate, and comprehensive methylation calling and differential analysis.

Main Methods:

  • Development of meRanTK, a novel bioinformatics toolkit.

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  • Implementation of splice-aware bisulfite sequencing read mapping.
  • Inclusion of comprehensive methylation calling and differential methylation analysis capabilities.
  • Statistical analysis for single- and multi-replicate experiments.

    • Main Results:

    • meRanTK offers fast and user-friendly splice-aware mapping of bisulfite sequencing reads.
    • The toolkit provides comprehensive methylation calling and identification of differentially methylated cytosines.
    • Application of meRanTK to RNA-BSseq or Aza-IP data yields accurate results in standard-compliant formats.

    Conclusions:

    • meRanTK is the first specialized software tool for high-throughput RNA cytosine methylation data analysis.
    • The toolkit facilitates efficient and accurate analysis of RNA-BSseq and Aza-IP data.
    • meRanTK supports statistical analysis for identifying differentially methylated cytosines in various experimental designs.