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bioRxiv · 10.1101/2020.06.15.152728

Predicting Mean Ribosome Load for 5'UTR of any length using Deep Learning

Karollus, A.·Avsec, Z.·Gagneur, J.
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Abstract

The 5 untranslated region plays a key role in regulating mRNA translation and consequently protein abundance. Therefore, accurate modeling of 5UTR regulatory sequences shall provide insights into translational control mechanisms and help interpret genetic variants. Recently, a model was trained on a massively parallel reporter assay to predict mean ribosome load (MRL) - a proxy for translation rate - directly from 5UTR sequence with a high degree of accuracy. However, this model is restricted to sequence lengths investigated in the reporter assay and therefore cannot be applied to the majority of human sequences without a substantial loss of information. Here, we introduced frame pooling, a novel neural network operation that enabled the development of an MRL prediction model for 5UTRs of any length. Our model shows state-of-the-art performance on fixed length randomized sequences, while offering better generalization performance on longer sequences and on a variety of translation-related genome-wide datasets. Variant interpretation is demonstrated on a 5UTR variant of the gene HBB associated with beta-thalassemia. Frame pooling could find applications in other bioinformatics predictive tasks. Moreover, our model, released open source, could help pinpoint pathogenic genetic variants.

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Karollus, A., Avsec, Z., Gagneur, J.. 2020-06-16. Predicting Mean Ribosome Load for 5'UTR of any length using Deep Learning. https://doi.org/10.1101/2020.06.15.152728

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