HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data

Amna Farooq; Sindre Grønmyr; Omer Ali; Torbjørn Rognes; Katja Scheffler; Magnar Bjørås; Junbai Wang

doi:10.1016/j.csbj.2020.09.038

HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data

Comput Struct Biotechnol J. 2020 Oct 10:18:2877-2889. doi: 10.1016/j.csbj.2020.09.038. eCollection 2020.

Authors

Amna Farooq¹, Sindre Grønmyr^{1

2}, Omer Ali¹, Torbjørn Rognes^{2

3}, Katja Scheffler^{4

5}, Magnar Bjørås^{6

3

7}, Junbai Wang¹

Affiliations

¹ Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.
² Department of Informatics, University of Oslo, Oslo, Norway.
³ Department of Microbiology, Oslo University Hospital, Oslo, Norway.
⁴ Department of Neuromedicine and Movement Science and Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
⁵ Department of Neurology and Department of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.
⁶ Institute for Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
⁷ Department of Microbiology, University of Oslo, Oslo, Norway.

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/).

Keywords: Differential methylation; Hydroxy methylation; Hydroxymethylation-and methylation-sensitive tag sequencing; Methylation analysis; Whole genome bisulfite sequencing.