Analyzing mRNA Epigenetic Sequencing Data with TRESS

Zhenxing Guo; Andrew M Shafik; Peng Jin; Zhijin Wu; Hao Wu

doi:10.1007/978-1-0716-2962-8_12

Analyzing mRNA Epigenetic Sequencing Data with TRESS

Methods Mol Biol. 2023:2624:163-183. doi: 10.1007/978-1-0716-2962-8_12.

Authors

Zhenxing Guo¹, Andrew M Shafik², Peng Jin², Zhijin Wu³, Hao Wu⁴

Affiliations

¹ Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA.
² Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
³ Department of Biostatistics, Brown University, Providence, RI, USA.
⁴ Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA. hao.wu@emory.edu.

PMID: 36723816
DOI: 10.1007/978-1-0716-2962-8_12

Abstract

RNA epigenetics has emerged as an active topic to study gene regulation mechanisms. In this regard, the MeRIP-seq technology allows profiling transcriptome-wide mRNA modifications, in particular m⁶A. The primary goals for the analysis of MeRIP-seq data are the identification of m⁶A-methylated regions under each condition and across different biological conditions. Here we describe detailed procedures to guide researchers in MeRIP-seq data analyses by providing step-by-step instructions of the dedicated bioconductor package TRESS.

Keywords: Differential RNA methylation; MeRIP-seq; Peak detection; RNA epigenetics.

MeSH terms

Epigenesis, Genetic*
Methylation
RNA* / genetics
RNA, Messenger / genetics
Sequence Analysis, RNA / methods

Substances

RNA, Messenger
RNA