WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach

Abstract

N 6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotes, and plays a pivotal role in various biological processes, such as splicing, RNA degradation and RNA-protein interaction. We report here a prediction framework WHISTLE for transcriptome-wide m6A RNA-methylation site prediction. When tested on six independent datasets, our approach, which integrated 35 additional genomic features besides the conventional sequence features, achieved a major improvement in the accuracy of m6A site prediction (average AUC: 0.948 and 0.880 under the full transcript or mature messenger RNA models, respectively) compared to the state-of-the-art computational approaches MethyRNA (AUC: 0.790 and 0.732) and SRAMP (AUC: 0.761 and 0.706). It also out-performed the existing epitranscriptome databases MeT-DB (AUC: 0.798 and 0.744) and RMBase (AUC: 0.786 and 0.736), which were built upon hundreds of epitranscriptome high-throughput sequencing samples. To probe the putative biological processes impacted by changes in an individual m6A site, a network-based approach was implemented according to the 'guilt-by-association' principle by integrating RNA methylation profiles, gene expression profiles and protein-protein interaction data. Finally, the WHISTLE web server was built to facilitate the query of our high-accuracy map of the human m6A epitranscriptome, and the server is freely available at: www.xjtlu.edu.cn/biologicalsciences/whistle and http://whistle-epitranscriptome.com.

Figure 1.

Generation of positive and negative data. The transcriptome m⁶A sites under RRACH consensus motifs that have been reproduced in at least two of the five training datasets were used as positive m⁶A sites. The negative training data (non-m⁶A sites) was randomly selected from the non-positive RRACH adenosines on the full transcripts containing the positive sites.

Figure 2.

WHISTLE website. The WHISTLE website hosts a functionally annotated high-accuracy predicted map of the human m⁶A epitranscriptome. The WHISTLE website supports direct query of RNA-methylation sites with respect to a specific GO function or gene. The m⁶A RNA-methylation sites were predicted from m6A-CLIP data, miCLIP data, sequence features and genome-derived features. And then, the most dynamic RNA-methylation sites were annotated under the Gene Ontology framework using the guilt-by-association principle by integrating gene expression, RNA methylation and protein–protein interaction data. Please Supplementary Figure S2 for the complete data processing pipeline of WHISTLE.