m6ATEpre: Predicting YTHDF1-mediated mRNA Translation Efficiency Regulated by m6A Sites via Multi-omics Data Integration

Teng ZHANG; Ming ZHANG; Shao-Wu ZHANG; Lian LIU

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m6ATEpre: Predicting YTHDF1-mediated mRNA Translation Efficiency Regulated by m6A Sites via Multi-omics Data Integration

VernacularTitle:m6ATEpre：基于多组学数据整合的YTHDF1介导调控翻译效率的m6A修饰位点预测
Author: Teng ZHANG ¹ ; Ming ZHANG ¹ ; Shao-Wu ZHANG ² ; Lian LIU ³
Author Information

1. School of Computer, Jiangsu University of Science and Technology, Zhenjiang 212100, China
2. MOE Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi’an 710072, China
3. School of Artificial Intelligence and Computer Science, Shaanxi Normal University, Xi’an 710119, China
Publication Type:Journal Article
Keywords: m6A modification; YTHDF1-mediated translation efficiency; multi-omics data integration; feature representation
From: Progress in Biochemistry and Biophysics 2026;53(4):1087-1102
CountryChina
Language:English
Abstract: ObjectiveThe most prevalent mRNA modification, N6-methyladenosine (m⁶A) plays an important role in various RNA metabolism, including gene expression and translation. By recruiting different “reader” proteins and their cofactors, m⁶A modification can affect messenger RNA (mRNA) degradation, splicing, nuclear export and translation. However, the selective mechanism by which m⁶A sites regulate mRNA translation through m⁶A reader YTHDF1 binding remains poorly understood, due to a lack of computational methods for identifying context-specific m⁶A sites that regulate translation. To address this, we developed a novel computational framework named m⁶ATEpre, the first tool designed to predict cell-specific m⁶A sites that regulate translation efficiency. Methodsm⁶ATEpre integrates multi-omics data, introduces a novel feature representation strategy for m⁶A site sequences, and employs an autoencoder to effectively capture embedded feature representations. Specifically, m⁶ATEpre first integrated MeRIP-seq data and PAR-CLIP data through overlapping m⁶A sites with YTHDF1 binding sites and identified YTHDF1-mediated m⁶A sites. Then, m⁶ATEpre detected the translation gene by analyzing the Ribo-seq data under YTHDF1 knockdown vs control condition. Genes whose translation is mediated by YTHDF1 in an m⁶A-dependent manner were identified by a significant decrease in translation efficiency upon YTHDF1 knockdown. Next, we proposed a binary vector indicating the presence or absence of YTHDF1 binding motifs to characterize each m⁶A site sequence. This represents a novel feature representation strategy for m⁶A sites. m⁶ATEpre utilized the autoencoder to extract the potentially important feature representations and constructed a multilayer perceptron neural networks model to predict potential m⁶A sites that regulating translation efficiency. ResultsA comprehensive evaluation of m⁶ATEpre was conducted through a series of experiments. We compared its performance against that of a similar prediction task model, as well as other classifiers. The results indicate that m⁶ATEpre achieved the best prediction performance. In addition, we analyzed different feature representation strategies and performed ablation experiments to validate the rationality of the model design. The results demonstrate that our proposed feature representation strategy has a greater advantage in improving prediction performance. In the HeLa cell line, bioinformatic analysis of the metagene distribution and sequence minimum free energy of m⁶A sites regulating translation efficiency (m⁶A-reg-TE sites) revealed their specific properties in translation regulation. Functional enrichment analysis indicated that m⁶A-reg-TE genes are associated with specific biological processes and KEGG pathways. By integrating the binding sites of YTHDF1 co-factors with m⁶A-reg-TE sites, we revealed that YTHDF1-mediated and m⁶A-dependent translation efficiency regulation requires the cooperation of multiple translation-regulatory RNA-binding proteins among its co-factors in the HeLa cell line. Furthermore, we extended our predictions to the dataset of the HEK293T cell line. Similarly, bioinformatic analysis of the metagene distribution and functional enrichment revealed the cell-specific characteristic of these predicted m⁶A-reg-TE sites in HEK293T cells. Likewise, integrated analysis of multiple YTHDF1 co-factors and m⁶A-reg-TE sites predicted in the HEK293T cell line reveals their m⁶A-dependent cooperation in regulating translation efficiency. Conclusionm⁶ATEpre is a timely tool that will advance our understanding of the mechanisms of m⁶A regulation in translation efficiency. The source code and datasets used in this work can be downloaded from https://www.scidb.cn/s/bAZZFr.