Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects

Liu, Ji-Hong1,2; Zhang, Yizhou1,2; Zhou, Ning3; He, Jiale1,2; Xu, Jing1; Cai, Zhao2; Yang, Liang2,4; Liu, Yang1

2024-06-01

10.1002/imt2.186

IMETA   影响因子和分区

2770-5986

2770-596X

["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 cis and trans 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 .","Bacmethy tool provides a one-stop analysis and visualization pipeline for effectively characterizing bacterial DNA methylation modification features and predicting the regulation patterns. Bacmethy offers both a local run function and an online interface analysis service, providing significant convenience for researchers without coding abilities. Bacmethy provides useful information for decoding the underlying molecular mechanisms of how DNA methylation regulates bacterial cellular and physiological functions. image","Bacmethy tool provides a one-stop analysis and visualization pipeline for effectively characterizing bacterial DNA methylation modification features and predicting the regulation patterns. Bacmethy offers both a local run function and an online interface analysis service, providing significant convenience for researchers without coding abilities. Bacmethy provides useful information for decoding the underlying molecular mechanisms of how DNA methylation regulates bacterial cellular and physiological functions."]

bacteria DNA methylation SMRT-seq transcriptional regulation undermethylation

ESCI

英语

第一 ; 通讯

Shenzhen Overseas High-level Talent Team[KQTD20200909113758004] ; Nanshan District Health System Technology Major Project[NSZD2023064] ; Nanshan District Scientific Research Program[2021NS028] ; President of Southern University of Science and Technology Hospital Foundation[2020-D4] ; null[32300060] ; null[32270196] ; null[32200053]

Microbiology

Microbiology

WOS:001187291700001

WILEY

Web of Science

1.Southern Univ Sci & Technol Hosp, Med Res Ctr, Shenzhen 518055, Peoples R China
2.Southern Univ Sci & Technol, Key Univ Lab Metab & Hlth Guangdong, Sch Med, Shenzhen 518055, Peoples R China
3.Southern Univ Sci & Technol Hosp, Clin Lab, Shenzhen, Peoples R China
4.Southern Univ Sci & Technol, Shenzhen Peoples Hosp 3, Natl Clin Res Ctr Infect Dis, Affiliated Hosp 2, Shenzhen, Peoples R China

Liu, Ji-Hong,Zhang, Yizhou,Zhou, Ning,et al. Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects[J]. IMETA,2024,3(3).

Liu, Ji-Hong.,Zhang, Yizhou.,Zhou, Ning.,He, Jiale.,Xu, Jing.,...&Liu, Yang.(2024).Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects.IMETA,3(3).

Liu, Ji-Hong,et al."Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects".IMETA 3.3(2024).