DEEPReditor-CMG: A deep-learning-based predictive RNA editor for crop mitochondria genomes

Qin, S.; Xu, Z.; Wang, Y.; Wang, Z.; Cao, Y.; Hou, C.; Yang, J.; Liu, Y.; Xiao, Y.; Dai, Z.; Zhou, W.; Li, Q.

doi:10.1101/2025.10.09.681429

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bioRxiv · 10.1101/2025.10.09.681429

DEEPReditor-CMG: A deep-learning-based predictive RNA editor for crop mitochondria genomes

Qin, S.·Xu, Z.·Wang, Y.·Wang, Z.·Cao, Y.·Hou, C.·Yang, J.·Liu, Y.·Xiao, Y.·Dai, Z.·Zhou, W.·Li, Q.

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Abstract

C-to-U RNA editing is a pervasive phenomenon in crop mitochondria, playing a pivotal role in the processing of functional proteins encoded by mitochondrial genes and serving as a crucial regulatory mechanism for nuclear control over mitochondrial gene expression. However, identifying editing sites across the mitochondrial genome with high precision remains a formidable challenge. To address this challenge and uncover the potential regulatory patterns of C-to-U RNA editing, this study compiled a comprehensive dataset of mitochondrial genome sequences from 13 crops, including Arabidopsis thaliana, Lactuca sativa var. Capitata, Oryza sativa Japonica, and Zea mays, among others, annotated with editing sites from NCBI. Utilizing TensorFlow 2.0, we constructed a rigorous hyperparameter optimization framework, which facilitated the development of the DEEPReditor-CMG model, demonstrating superior predictive capabilities. Based on the DEEPReditor-CMG model and three interspecies relationship indices, we discovered that species with closer phylogenetic relationships exhibit more similar C-to-U RNA editing mechanisms, providing valuable insights into the evolutionary conservation of RNA editing mechanisms. We further developed executable programs for predicting C-to-U RNA editing sites in crop mitochondrial genomes, leveraging the conserved nature of the crop RNA editing machinery to maximize prediction reliability and uncover new editing sites with great potential. This research not only deepens our understanding of C-to-U RNA editing and post-transcriptional regulatory mechanisms in crop mitochondria but also paves a novel avenue for investigating RNA editing mechanisms. Experimental data, computational code, and applications are publicly accessible at https://github.com/Qinsidong/DEEPReditor-CMG. HighlightsHigh-precision prediction model for C-to-U RNA editing in crops--DEEPReditor-CMG Three interspecies relationship indices describing C to U RNA editing Prediction tools based on the conservation of crop RNA editing mechanisms Open-sourced experimental data, computational code, and applications

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Qin, S., Xu, Z., Wang, Y., Wang, Z., Cao, Y., Hou, C., Yang, J., Liu, Y., Xiao, Y., Dai, Z., Zhou, W., Li, Q.. 2025-10-13. DEEPReditor-CMG: A deep-learning-based predictive RNA editor for crop mitochondria genomes. https://doi.org/10.1101/2025.10.09.681429

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