Abstract
DNA methylation (5mC) and hydroxymethylation (5hmC) are chemical modifications of cytosine bases which play a crucial role in epigenetic gene regulation. However, cost, data complexity and unavailability of comprehensive analytical tools is one of the major challenges in exploring these epigenetic marks. Hydroxymethylation-and Methylation-Sensitive Tag sequencing (HMST-seq) is one of the most cost-effective techniques that enables simultaneous detection of 5mC and 5hmC at single base pair resolution. We present HMST-Seq-Analyzer as a comprehensive and robust method for performing simultaneous differential methylation analysis on 5mC and 5hmC data sets. HMST-Seq-Analyzer can detect Differentially Methylated Regions (DMRs), annotate them, give a visual overview of methylation status and also perform preliminary quality check on the data. In addition to HMST-Seq, our tool can be used on whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data sets as well. The tool is written in Python with capacity to process data in parallel and is available at (https://hmst-seq.github.io/hmst/).
Highlights
Epigenetic DNA methylation provides an additional layer for controlling cellular processes
It is divided into eight discrete modules, where the default settings for the parameters are aimed for HMST-seq data but parameters are flexible to accommodate representation bisulfite sequencing (RRBS) and Whole-genome bisulfite sequencing (WGBS) data in the package
Three main figures in the results provide a statistical summary of the genome-wide methylation status: 1) relative density of 5mC/5hmC in defined genomic regions (e.g, TSS, TES, gene body, enhancer, 50 distance, and intergenic regions) or genome-wide; 2) percentage of hyper-/ hypomethylated differentially methylated regions (DMRs) in TSS, TES, gene body, 50 distance, and intergenic regions; 3) a genomic average of 5mC/5hmC levels in TSS-Gene-TES regions or enhancer regions
Summary
Epigenetic DNA methylation provides an additional layer for controlling cellular processes. It is the most stable epigenetic mark that plays a significant role in gene regulation with impact on health and disease [1]. DNA methylation varies in response to cell differentiation, disease, and environmental factors. 5-methylcytosine (5mC) is the most abundant epigenetic mark. The aforementioned two methylation marks have essential roles in the development and regulation of cellular processes [3]. Abnormal methylation patterns have been observed in many human diseases and can be used in clinical outcome predictions [4]. Correct profiling of DNA methylation in a genome is key to understand the contribution of epigenetics in gene regulation
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