Computational Epitranscriptomics: Bioinformatic Approaches for the Analysis of RNA Modifications

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Background

Coding and non-coding transcripts can be decorated by dozens of different epitranscriptional modifications, with major consequences on the fate of marked RNAs, including their processing, stability, translation, localization, and export. For a number of modifications, specific writers, erasers, and readers have been identified, which could be responsible for the dynamic regulation of these marks.

While a number of epitranscriptional modifications have been known for decades, this area of research is blossoming recently due to the development of methods for their genome-wide identification. These methods, often followed by high-throughput sequencing, typically involve the identification of signatures left by their reverse-transcription, or are based on the purification of marked RNAs through modification-specific antibodies.

Despite the growing number of studies in this field, the functional role of epitranscriptional modifications, including the most common ones, remains to be fully elucidated. In addition, we are just beginning charting and understanding the implications of the aberrant regulation of these marks. Finally, the methods developed for the identification and the integrative analysis of the patterning of RNA modifications with other layers of regulation, present several unresolved issues.

This Research Topic aims at collecting Original Research articles, Methods papers, Perspectives or Reviews focused on the computational analysis of bulk or genome-wide epitranscriptional data, including (while not limited to) the following:

● Analysis workflows, including reads alignment, quality control, filtering or downstream analyses aimed at the identification of RNA modifications
● Peak calling methods for the identification or differential analysis of RNA modifications
● Computational analysis of direct sequencing data (such as Nanopore) for the analysis of epitranscriptional marks
● Methods to predict the positioning of RNA modifications based on sequence features
● Methods to analyze the interplay between epitranscriptional marks and RNA secondary structure
● Methods to unravel the consequences of RNA modifications on the fate of marked transcripts

This article collection is a specific activity performed in the framework of the COST Action CA16120 EPITRAN - European Epitranscriptomics Network. Contributions are also welcome from non EPITRAN members.

Keywords: RNA, RNA modification, bioinformatics, high-throughput sequencing

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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