Efficient RNA nucleotide encoding enhances the accurate prediction of ac4C modifications

IF 4.3 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Methods Pub Date : 2025-08-31 DOI:10.1016/j.ymeth.2025.07.012

Na Li , Xiao Wang , Ming Zeng , Feng Cao , Ke Qiu , Jianbo Qiao

引用次数: 0

Abstract

RNA N4-acetylcytidine (ac4C) modification plays a vital role in gene regulation and cellular function. Accurate identification of ac4C sites is essential for elucidating their biological significance. However, existing prediction methods struggle to capture complex sequence patterns, limiting their accuracy. To address this, we propose GO-ac4C, an efficient prediction framework that integrates byte-pair encoding with nucleotide compositional features. GO-ac4C employs dynamic byte-pair encoding to learn optimal subsequence representations and enhances them with compositional features to effectively capture key motifs in RNA sequences. Experimental results demonstrate that GO-ac4C significantly outperforms state-of-the-art methods across multiple evaluation metrics and offers new insights into the mechanisms of RNA modification.

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高效的RNA核苷酸编码增强了对ac4C修饰的准确预测。

RNA n4 -乙酰胞苷（ac4C）修饰在基因调控和细胞功能中起着至关重要的作用。准确鉴定ac4C位点对于阐明其生物学意义至关重要。然而，现有的预测方法难以捕捉复杂的序列模式，限制了它们的准确性。为了解决这个问题，我们提出了GO-ac4C，一个有效的预测框架，集成了字节对编码和核苷酸组成特征。GO-ac4C采用动态字节对编码来学习最优子序列表示，并用组合特征对其进行增强，从而有效捕获RNA序列中的关键基序。实验结果表明，GO-ac4C在多个评估指标上明显优于最先进的方法，并为RNA修饰机制提供了新的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Methods 生物-生化研究方法

CiteScore

9.80

自引率

2.10%

发文量

222

审稿时长

11.3 weeks

期刊介绍： Methods focuses on rapidly developing techniques in the experimental biological and medical sciences. Each topical issue, organized by a guest editor who is an expert in the area covered, consists solely of invited quality articles by specialist authors, many of them reviews. Issues are devoted to specific technical approaches with emphasis on clear detailed descriptions of protocols that allow them to be reproduced easily. The background information provided enables researchers to understand the principles underlying the methods; other helpful sections include comparisons of alternative methods giving the advantages and disadvantages of particular methods, guidance on avoiding potential pitfalls, and suggestions for troubleshooting.