A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor

Area of Science:

• Epigenetics
• Bioinformatics
• Genomics

Background:

• Long-read sequencing advances epigenetics with single-base resolution DNA modification detection.
• DNA methylation plays crucial roles in gene regulation, imprinting, and disease.
• Specialized software is needed for analyzing unique long-read data characteristics like modBAM format and extended read lengths.

Purpose of the Study:

• To present NanoMethViz, a package for analyzing long-read DNA methylation data.
• To demonstrate a workflow for converting modBAM files for downstream analysis.
• To showcase exploratory data analysis and differentially methylated region (DMR) discovery using NanoMethViz and dmrseq.

Main Methods:

• Loading and visualizing long-read methylation data with NanoMethViz.
• Converting modBAM files for compatibility with Bioconductor tools (bsseq, DSS, dmrseq, edgeR).
• Applying dmrseq for DMR identification and integrating results with gene-level visualizations.

Main Results:

• Exploratory analysis revealed sample differences and aggregate methylation profiles.
• DMR analysis identified regions associated with known imprinted genes.
• Visualizations provided single-read resolution of methylation patterns on parental alleles.

Conclusions:

• NanoMethViz offers a streamlined workflow for long-read methylation data analysis.
• The package supports flexible integration with various statistical tools for DMR discovery.
• This approach enhances the study of DNA methylation in gene regulation, imprinting, and disease.