Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution
| Autor: | Shashank Sathe, Jaclyn M. Einstein, Gene W. Yeo, Daniel A. Lorenz |
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| Rok vydání: | 2019 |
| Předmět: |
0303 health sciences
Resolution (mass spectrometry) 030302 biochemistry & molecular biology RNA Endogeny Computational biology Methylation Biology Transcript isoforms 03 medical and health sciences Nanopore TheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITY Nanopore sequencing Molecular Biology 030304 developmental biology |
| Zdroj: | RNA. 26:19-28 |
| ISSN: | 1469-9001 1355-8382 |
| DOI: | 10.1261/rna.072785.119 |
| Popis: | Direct RNA sequencing holds great promise for the de novo identification of RNA modifications at single-coordinate resolution; however, interpretation of raw sequencing output to discover modified bases remains a challenge. Using Oxford Nanopore's direct RNA sequencing technology, we developed a random forest classifier trained using experimentally detected N6-methyladenosine (m6A) sites within DRACH motifs. Our software MINES (m6A Identification using Nanopore Sequencing) assigned m6A methylation status to more than 13,000 previously unannotated DRACH sites in endogenous HEK293T transcripts and identified more than 40,000 sites with isoform-level resolution in a human mammary epithelial cell line. These sites displayed sensitivity to the m6A writer, METTL3, and eraser, ALKBH5, respectively. MINES (https://github.com/YeoLab/MINES.git) enables m6A annotation at single coordinate–level resolution from direct RNA nanopore sequencing. |
| Databáze: | OpenAIRE |
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