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

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.

Recent advances in functional annotation and prediction of the epitranscriptome

“…By directly learning the RNA modification sites reported from high-throughput sequencing approaches, a large number of prediction models have been established for the computational identification of RNA modification sites from the primary sequences of the RNA molecule as well as by taking advantage of other information [71] , [92] , [93] . Thanks to the development of sequencing technology such as miCLIP and PA-m 6 A-seq for m 6 A, it becomes possible to train m 6 A site prediction models using machine learning approaches, which extract features from the primary sequences centered around the m 6 A sites to predict the probability of another nucleotide being a methylation site or not.…”

Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications

“…Special attention has also been paid to the prediction of RNA modifications in introns 23 , lncRNAs 24 as well as various tissues and cell lines [25][26][27] . Together, these works greatly advanced our understanding of the localization of multiple RNA modification types in different species under various conditions 28 . However, existing approaches suffered from the following limitations.…”

Transcriptomic Analysis of the Mechanisms for Alleviating Psoriatic Dermatitis Using Taodan Granules in an Imiquimod-Induced Psoriasis-like Mouse Model

“…RNA sequencing (RNA-seq), a progressive technique, is practical for identifying numerous genes regulated by specific medications ( Liu et al, 2020 ). In this study, we used an imiquimod (IMQ)-induced psoriasis-like mouse model to examine the mechanism of action of TDGs against psoriasis.…”