RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework

Ilaria Manfredonia; Danny Incarnato

doi:10.1007/978-1-0716-1374-0_1

RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework

Methods Mol Biol. 2021:2298:3-13. doi: 10.1007/978-1-0716-1374-0_1.

Authors

Ilaria Manfredonia¹, Danny Incarnato²

Affiliations

¹ Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
² Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands. [email protected].

PMID: 34085235
DOI: 10.1007/978-1-0716-1374-0_1

Abstract

RNA post-transcriptional modifications (PTMs) are progressively gaining relevance in the study of coding-independent functions of RNA. RNA PTMs act as dynamic regulators of several aspects of the RNA physiology, from translation to half-life. Rising interest is supported by the advance of high-throughput techniques enabling the detection of these modifications on a transcriptome-wide scale. To this end, here we illustrate the usefulness of RNA Framework, a comprehensive toolkit for the analysis of RNA PTM mapping experiments, by reanalyzing two published transcriptome-scale datasets of N1-methyladenosine (m¹A) and pseudouridine (Ψ) mapping, based on two different experimental strategies.

Keywords: High-throughput sequencing; N1-methyladenosine; Pseudouridine; RNA immunoprecipitation; RNA post-transcriptional modifications; m1A.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenosine / genetics
Data Analysis
High-Throughput Nucleotide Sequencing / methods
Pseudouridine / genetics
RNA / genetics*
RNA Processing, Post-Transcriptional / genetics*
Sequence Analysis, RNA / methods
Transcriptome / genetics

Substances

Pseudouridine
RNA
Adenosine