Liu Ji-Hong, Zhang Yizhou, Zhou Ning, He Jiale, Xu Jing, Cai Zhao, Yang Liang, Liu Yang
Medical Research Center Southern University of Science and Technology Hospital Shenzhen China.
School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong Southern University of Science and Technology Shenzhen China.
Imeta. 2024 Mar 19;3(3):e186. doi: 10.1002/imt2.186. eCollection 2024 Jun.
DNA methylation serves as the primary mode of epigenetic regulation in prokaryotes, particularly through transcriptional regulation. With the rapid implementation of third-generation sequencing technology, we are currently experiencing a golden age of bacterial epigenomics. However, there has been a lack of comprehensive research exploring the versatility and consequential impact of bacterial DNA methylome on cellular and physiological functions. There is a critical need for a user-friendly bioinformatics tool that can effectively characterize DNA methylation modification features and predict the regulation patterns. To address this gap, the current study introduces Bacmethy, an innovative tool that utilizes SMRT-seq data and offers a range of analytical modules. First, the tool classifies methylation sites in the genome, highlighting the distinct regulations present under varying modification fractions and location enrichment. Furthermore, this tool enables us to identify regulatory region methylation and potential and interactions between methylation sites and regulatory effectors. Using benchmark data sets and our data, we show that our tool facilitates the understanding of the distinctive traits of DNA methylation modifications and predicts transcriptional regulation effects on important physiological and pathological functions. Bacmethy code is freely available, and the Docker image is downloadable. Bacmethy has been made available as a user-friendly web server interface at https://bacmethy.med.sustech.edu.cn.
DNA甲基化是原核生物表观遗传调控的主要方式，尤其是通过转录调控。随着第三代测序技术的迅速应用，我们目前正处于细菌表观基因组学的黄金时代。然而，目前缺乏全面的研究来探索细菌DNA甲基化组对细胞和生理功能的多样性及相应影响。迫切需要一种用户友好的生物信息学工具，能够有效地表征DNA甲基化修饰特征并预测调控模式。为了填补这一空白，本研究引入了Bacmethy，这是一种利用单分子实时测序（SMRT-seq）数据并提供一系列分析模块的创新工具。首先，该工具对基因组中的甲基化位点进行分类，突出不同修饰比例和位置富集下存在的独特调控。此外，该工具使我们能够识别调控区域甲基化以及甲基化位点与调控效应器之间的潜在相互作用。使用基准数据集和我们自己的数据，我们表明我们的工具有助于理解DNA甲基化修饰的独特特征，并预测对重要生理和病理功能转录调控的影响。Bacmethy代码可免费获取，Docker镜像也可下载。Bacmethy已作为一个用户友好的网络服务器界面在https://bacmethy.med.sustech.edu.cn上线。
