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Leger, Adrien; Amaral, Paulo P; Pandolfini, Luca; Capitanchik, Charlotte; Capraro, Federica; Miano, Valentina; Migliori, Valentina; Toolan-Kerr, Patrick; Sideri, Theodora; Enright, Anton J; Tzelepis, Konstantinos; van Werven, Folkert J; Luscombe, Nicholas M; Barbieri, Isaia; Ule, Jernej; Fitzgerald, Tomas; Birney, Ewan; Leonardi, Tommaso; Kouzarides, Tony
Nature communications, 12/2021, Letnik: 12, Številka: 1Journal Article
RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. In recent years, a growing number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework that identifies modifications from these data. Our strategy compares an RNA sample of interest against a non-modified control sample, not requiring a training set and allowing the use of replicates. We show that Nanocompore can detect different RNA modifications with position accuracy in vitro, and we apply it to profile m A in vivo in yeast and human RNAs, as well as in targeted non-coding RNAs. We confirm our results with orthogonal methods and provide novel insights on the co-occurrence of multiple modified residues on individual RNA molecules.
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in: SICRIS
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