Unveiling RNA Modifications: High-throughput Sequencing Approaches to Chart the Epitranscriptome and Dissect Its Role in Gene Expression

In recent years, the development of sophisticated methodologies based on second- and third-generation sequencing has enabled the RNA community to explore RNA modifications on a genome-wide scale. In this context, the Nanopore platform has been a game-changer, allowing for the sequencing of native transcripts while potentially retrieving information on the identity and position of numerous modifications along RNA molecules. As the field progresses, there is growing interest and effort in developing methodologies to fully exploit this information, aiming to achieve a precise and comprehensive map of RNA modifications at single-molecule and single-nucleotide resolution. These advancements will significantly contribute to address outstanding questions about the biology of individual modifications and their role in shaping gene expression, such as their dynamic regulation over time and in response to external and internal stimuli, as well as their role in the combinatorial epitranscriptional code.This topic will explore novel Nanopore sequencing-based frameworks for RNA modification detection, including comparative approaches using specific baselines and computational methodologies that enhance state-of-the-art detection performance. Additionally, it will cover studies evaluating the performance of both existing and novel methodologies for RNA modifications profiling, with particular emphasis on the development of datasets tailored for this purpose and benchmarking against orthogonal techniques, such as Illumina RNA-seq-based protocols. Furthermore, this topic will investigate methodologies that extend beyond the detection of single modification sites in polyadenylated linear transcripts, such as those designed for studying other classes of RNA molecules, identifying differential modification sites, or simultaneously profiling multiple RNA modifications. Additionally, it will cover approaches leveraging exogenous RNA modifications for nascent RNA profiling, providing insights into RNA transcriptional and post-transcriptional dynamics. Finally, this topic will highlight studies that offer new insights into the biology of the epitranscriptome through the application of Nanopore sequencing. Particularly relevant to this research topic are studies on the role of RNA modifications in RNA therapeutics, as well as their involvement in establishing transcriptional regulatory networks and mediating crosstalk between distinct and distal steps of gene expression. Topic editors: Mattia Furlan, Simone Maestri Source: https://www.frontiersin.org/research-topics/70584/unveiling-rna-modifications-high-throughput-sequencing-approaches-to-chart-the-epitranscriptome-and-dissect-its-role-in-gene-expression