A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• RNA epigenetics, specifically N6-methyladenosine (m(6)A) modification, is an emerging field.
• MeRIP-Seq is a key technology for surveying m(6)A modifications transcriptome-wide.
• Existing MeRIP-Seq data analysis protocols require optimization due to data-specific characteristics.

Purpose of the Study:

• To provide a detailed and user-friendly protocol for analyzing MeRIP-Seq data.
• To present the application of the exomePeak R/Bioconductor package for RNA methylation analysis.
• To offer best practices and alternative strategies for MeRIP-Seq data processing.

Main Methods:

• Utilized the exomePeak R/Bioconductor package for MeRIP-Seq data analysis.
• Incorporated standard bioinformatics tools for raw reads alignment.
• Applied statistical methods for RNA methylation site detection and differential analysis.

Main Results:

• Developed a comprehensive workflow covering alignment, site detection, motif discovery, differential analysis, and functional analysis.
• Demonstrated the utility of exomePeak for robust MeRIP-Seq data interpretation.
• Provided clear rationales, methods, and best practices for each analysis step.

Conclusions:

• The presented protocol and exomePeak package offer a standardized and efficient approach to MeRIP-Seq data analysis.
• This resource will aid researchers in exploring the epitranscriptome and RNA modifications.
• The exomePeak package is freely available, promoting accessibility in RNA epigenetics research.