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.
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References
Cohn WE, Volkin E (1951) Nucleoside-5′-phosphates from ribonucleic acid. Nature 167:483–484. https://doi.org/10.1038/167483a0
Behm-Ansmant I, Helm M, Motorin Y (2011) Use of specific chemical reagents for detection of modified nucleotides in RNA. J Nucleic Acids 2011:1–17. https://doi.org/10.1017/s1355838299981335
Incarnato D, Oliviero S (2017) The RNA epistructurome: uncovering RNA function by studying structure and post-transcriptional modifications. Trends Biotechnol 35:318–333. https://doi.org/10.1016/j.tibtech.2016.11.002
Incarnato D, Morandi E, Simon LM, Oliviero S (2018) RNA framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications. Nucleic Acids Res 46:e97–e97. https://doi.org/10.1093/nar/gky486
Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, Dai Q, Segni AD, Salmon-Divon M, Clark WC, Zheng G, Pan T, Solomon O, Eyal E, Hershkovitz V, Han D, Doré LC, Amariglio N, Rechavi G, He C (2016) The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature 530:441–446. https://doi.org/10.1038/nature16998
Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515:143–146. https://doi.org/10.1038/nature13802
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. https://doi.org/10.1186/gb-2009-10-3-r25
Linder B, Grozhik AV, Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR (2015) Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat Methods 12:767–772. https://doi.org/10.1038/nmeth.3453
Zhou KI, Clark WC, Pan DW, Eckwahl MJ, Dai Q, Pan T (2018) Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing. RNA Biol 15:892–900. https://doi.org/10.1080/15476286.2018.1462654
Acknowledgments
This work was supported by funding from the University of Groningen (Groningen, Netherlands) and the Groningen Biomolecular Sciences and Biotechnology Institute (GBB) to D.I.
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Manfredonia, I., Incarnato, D. (2021). RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework. In: McMahon, M. (eds) RNA Modifications. Methods in Molecular Biology, vol 2298. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1374-0_1
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DOI: https://doi.org/10.1007/978-1-0716-1374-0_1
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