WHISTLE: A Functionally Annotated High-Accuracy Map of Human m⁶A Epitranscriptome

N⁶-Methyladenosine (m⁶A) is the most prevalent posttranscriptional modification in eukaryotes and plays a pivotal role in various biological processes, such as splicing, RNA degradation, and RNA–protein interaction. Accurately identification of the location of m⁶A is essential for related downstream studies. In this chapter, we introduce a prediction framework WHISTLE, which enables us to acquire so far the most accurate map of the transcriptome-wide human m⁶A RNA-methylation sites (with an average AUC: 0.948 and 0.880 under the full transcript or mature messenger RNA models, respectively, when tested on independent datasets). Besides, each individual m⁶A site was also functionally annotated according to the “guilt-by-association” principle by integrating RNA methylation data, gene expression data and protein–protein interaction data. A web server was constructed for conveniently querying the predicted RNA methylation sites and their putative biological functions. The website supports the query by genes, by GO function, table view, and the download of all the functionally annotated map of predicted map of human m⁶A epitranscriptome. The WHISTLE web server is freely available at: www.xjtlu.edu.cn/biologicalsciences/whistle and http://whistle-epitranscriptome.com.