Deconstructing the Cancer Epigenome using Reduced Representation Bisulfite Sequencing (RRBS)

2025 · doi:10.1101/2025.05.12.653548
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This paper presents a step-by-step computational and analytical pipeline for reduced representation bisulfite sequencing (RRBS) data to study how DNA methylation relates to disease processes, including cancer. It describes high-level stages spanning raw-read quality control, trimming, alignment, methylation extraction, differential methylation analysis, annotation, and downstream analyses, emphasizing that RRBS requires modified processing approaches due to deviations from standard sequencing protocols. A key limitation noted is that the computational workflow is specifically tailored for RRBS, implying that typical DNA-seq analysis methods are not directly applicable. Relevance to endometriosis: the paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

Reduced Representation Bisulfite Sequencing (RRBS) represents a relatively inexpensive methodology for investigating the influence of DNA methylation on the development and progression of diseases including cancer. RRBS is a targeted approach which combines the use of restriction enzyme selection, bisulfite conversion, and high throughput sequencing technologies. The computational processing and analysis of RRBS data therefore requires modified approaches compared to typical DNA sequencing, due to deviations from standard laboratory protocols. This chapter presents a step-by-step pipeline for the processing of raw RRBS reads including quality control, trimming, alignment, methylation extraction, differential methylation analysis, annotation, and downstream analysis. This pipeline is designed to ensure optimal processing for accurate results and to provide downstream analysis tools that can extract biological insights from the data.
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Abstract Reduced Representation Bisulfite Sequencing (RRBS) represents a relatively inexpensive methodology for investigating the influence of DNA methylation on the development and progression of diseases including cancer. RRBS is a targeted approach which combines the use of restriction enzyme selection, bisulfite conversion, and high throughput sequencing technologies. The computational processing and analysis of RRBS data therefore requires modified approaches compared to typical DNA sequencing, due to deviations from standard laboratory protocols. This chapter presents a step-by-step pipeline for the processing of raw RRBS reads including quality control, trimming, alignment, methylation extraction, differential methylation analysis, annotation, and downstream analysis. This pipeline is designed to ensure optimal processing for accurate results and to provide downstream analysis tools that can extract biological insights from the data. Competing Interest Statement The authors have declared no competing interest. Footnotes nglendinning01{at}qub.ac.uk; chung.911{at}osu.edu

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