Author: You Zhou, Kathi Zarnack
N6-methyladenosine (m6A) is the most abundant internal modification in mRNA. It impacts many different aspects of an mRNA's life, e.g. nuclear export, translation, stability, etc.
m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation (miCLIP) and the improved miCLIP2 are m6A antibody-based methods that allow the transcriptome-wide mapping of m6A sites at a single-nucleotide resolution. In brief, UV crosslinking of the m6A antibody to the modified RNA leads to truncation of reverse transcription or C-to-T transitions in the case of readthrough. However, due to the limited specificity and high cross-reactivity of the m6A antibodies, the miCLIP data comprise a high background signal, which hampers the reliable identification of m6A sites from the data.
For accurately detecting m6A sites, we implemented an AdaBoost-based machine learning model (m6Aboost) for classifying the miCLIP2 peaks into m6A sites and background signals. The model was trained on high-confidence m6A sites that were obtained by comparing wildtype and Mettl3 knockout mouse embryonic stem cells (mESC) lacking the major methyltransferase Mettl3. For classification, the m6Aboost model uses a series of features, including the experimental miCLIP2 signal (truncation events and C-to-T transitions) as well as the transcript region (5'UTR, CDS, 3'UTR) and the nucleotide sequence in a 21-nt window around the miCLIP2 peak.
The package m6Aboost includes the trained model and the functionalities to prepare the data, extract the required features and predict the m6A sites.
Nadine Körtel, Cornelia Rücklé, You Zhou, Anke Busch, Peter Hoch-Kraft, F X Reymond Sutandy, Jacob Haase, Mihika Pradhan, Michael Musheev, Dirk Ostareck, Antje Ostareck-Lederer, Christoph Dieterich, Stefan Hüttelmaier, Christof Niehrs, Oliver Rausch, Dan Dominissini, Julian König, Kathi Zarnack, Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning, Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Page e92, https://doi.org/10.1093/nar/gkab485
Documentation (vignette and user manual) is available at the m6Aboost's Bioconductor landing page at http://bioconductor.org/packages/m6Aboost.