Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics

Computational and Structural Biotechnology Journal
Lian LiuJia Meng

Abstract

Post-transcriptional RNA modification occurs on all types of RNA and plays a vital role in regulating every aspect of RNA function. Thanks to the development of high-throughput sequencing technologies, transcriptome-wide profiling of RNA modifications has been made possible. With the accumulation of a large number of high-throughput datasets, bioinformatics approaches have become increasing critical for unraveling the epitranscriptome. We review here the recent progress in bioinformatics approaches for deciphering the epitranscriptomes, including epitranscriptome data analysis techniques, RNA modification databases, disease-association inference, general functional annotation, and studies on RNA modification site prediction. We also discuss the limitations of existing approaches and offer some future perspectives.

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Methods Mentioned

BETA
MeRIP-seq
Immunoprecipitation
ChIP-Seq
RNA-Seq
PCR
electrophoresis
deamination

Software Mentioned

Exomepeak
DeepM6ASeq
m6A
MetaPlotR
BaySeqPeak
MeTDiff
BEERS
PseColl
exomePeak2
Driver

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