Prediction of mRNA subcellular localization using deep recurrent neural networks

Abstract Motivation Messenger RNA subcellular localization mechanisms play a crucial role in post-transcriptional gene regulation. This trafficking is mediated by trans-acting RNA-binding proteins interacting with cis-regulatory elements called zipcodes. While new sequencing-based technologies allow the high-throughput identification of RNAs localized to specific subcellular compartments, the precise mechanisms at play, and their dependency on specific sequence elements, remain poorly understood. Results We introduce RNATracker, a novel deep neural network built to predict, from their sequence alone, the distributions of mRNA transcripts over a predefined set of subcellular compartments. RNATracker integrates several state-of-the-art deep learning techniques (e.g. CNN, LSTM and attention layers) and can make use of both sequence and secondary structure information. We report on a variety of evaluations showing RNATracker’s strong predictive power, which is significantly superior to a variety of baseline predictors. Despite its complexity, several aspects of the model can be isolated to yield valuable, testable mechanistic hypotheses, and to locate candidate zipcode sequences within transcripts. Availability and implementation Code and data can be accessed at https://www.github.com/HarveyYan/RNATracker. Supplementary information Supplementary data are available at Bioinformatics online.