Prediction of Multiple Types of RNA Modifications via Biological Language Model.

Journal: IEEE/ACM transactions on computational biology and bioinformatics
Published Date: Oct 9, 2023

Abstract

It has been demonstrated that RNA modifications play essential roles in multiple biological processes. Accurate identification of RNA modifications in the transcriptome is critical for providing insights into the biological functions and mechanisms. Many tools have been developed for predicting RNA modifications at single-base resolution, which employ conventional feature engineering methods that focus on feature design and feature selection processes that require extensive biological expertise and may introduce redundant information. With the rapid development of artificial intelligence technologies, end-to-end methods are favorably received by researchers. Nevertheless, each well-trained model is only suitable for a specific RNA methylation modification type for nearly all of these approaches. In this study, we present MRM-BERT by feeding task-specific sequences into the powerful BERT (Bidirectional Encoder Representations from Transformers) model and implementing fine-tuning, which exhibits competitive performance to the state-of-the-art methods. MRM-BERT avoids repeated de novo training of the model and can predict multiple RNA modifications such as pseudouridine, m6A, m5C, and m1A in Mus musculus, Arabidopsis thaliana, and Saccharomyces cerevisiae. In addition, we analyse the attention heads to provide high attention regions for the prediction, and conduct saturated in silico mutagenesis of the input sequences to discover potential changes of RNA modifications, which can better assist researchers in their follow-up research.

Authors

  • Ying Zhang
    Department of Nephrology, Nanchong Central Hospital Affiliated to North Sichuan Medical College, Nanchong, China.
  • Fang Ge
    School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China.
  • Fuyi Li
    College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia.
  • Xibei Yang
    School of Computer Science and Engineering, Jiangsu University of Science and Technology, No. 2 Mengxi Road, Zhenjiang 212003, China.
  • Jiangning Song
    College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia College of Information Engineering, Northwest A&F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia.
  • Dong-Jun Yu

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