DNA methylation profiling using whole-genome bisulfite sequencing data

초록

Whole-genome bisulfite sequencing (WGBS) enables DNA methylation profiling across the genome at single base resolution, but bisulfite-converted reads require specialized processing to generate reliable methylation information. This technical protocol integrates established bioinformatic tools into a reproducible workflow for converting raw WGBS data into CpG-level methylation profiles and differentially methylated region (DMR) calls. The workflow operates on CpG methylation values ordered by genomic coordinates to generate de novo DMRs. We illustrate the workflow using whole blood-derived WGBS data from Beagle dogs, showing how candidate DMRs are filtered, summarized by direction, and consolidated into a final DMR set. By linking raw data processing to regional methylation interpretation, the protocol offers a reproducible framework for downstream genomic annotation and functional analysis.

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