miProBERT: identification of microRNA promoters based on the pre-trained model BERT

发起人 计算生物学 基因预测 小RNA 计算机科学 判别式 基因 生物 人工智能 遗传学 基因表达 基因组
作者
Xin Wang,Xin Gao,Guohua Wang,Dan Li
出处
期刊:Briefings in Bioinformatics [Oxford University Press]
卷期号:24 (3) 被引量:6
标识
DOI:10.1093/bib/bbad093
摘要

Abstract Accurate prediction of promoter regions driving miRNA gene expression has become a major challenge due to the lack of annotation information for pri-miRNA transcripts. This defect hinders our understanding of miRNA-mediated regulatory networks. Some algorithms have been designed during the past decade to detect miRNA promoters. However, these methods rely on biosignal data such as CpG islands and still need to be improved. Here, we propose miProBERT, a BERT-based model for predicting promoters directly from gene sequences without using any structural or biological signals. According to our information, it is the first time a BERT-based model has been employed to identify miRNA promoters. We use the pre-trained model DNABERT, fine-tune the pre-trained model on the gene promoter dataset so that the model includes information about the richer biological properties of promoter sequences in its representation, and then systematically scan the upstream regions of each intergenic miRNA using the fine-tuned model. About, 665 miRNA promoters are found. The innovative use of a random substitution strategy to construct a negative dataset improves the discriminative ability of the model and further reduces the false positive rate (FPR) to as low as 0.0421. On independent datasets, miProBERT outperformed other gene promoter prediction methods. With comparison on 33 experimentally validated miRNA promoter datasets, miProBERT significantly outperformed previously developed miRNA promoter prediction programs with 78.13% precision and 75.76% recall. We further verify the predicted promoter regions by analyzing conservation, CpG content and histone marks. The effectiveness and robustness of miProBERT are highlighted.
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