MethylViewer

MethylViewer analyzes cytosine DNA methylation patterns from bisulfite sequencing and MAPit data to map endogenous and enzyme-induced methylation and infer protein–DNA interactions.

Key Features:

• Bisulfite sequencing and MAPit support: Analyzes bisulfite-converted sequence data and MAPit (methylation analysis by probing with methyltransferases) datasets to assess cytosine methylation.
• Multi-motif analysis: Supports analysis of up to four different methylation sites, including CpG, GpC, CpNpG, or any user-defined motifs.
• Degenerate motif handling: Matches and analyzes motifs containing degenerate bases.
• Non-native methyltransferase compatibility: Processes data generated using non-native DNA methylases such as M.CviPI to enable analysis of enzyme-induced methylation.
• Simultaneous motif querying: Queries cytosine methylation status at multiple motifs within bisulfite-converted sequences concurrently.
• Primer design integration: Provides integrated primer design for bisulfite sequencing experiments.
• Data export and figure generation: Exports data for statistical analysis and generates publication-quality images.
• Nucleosome and footprint detection: Detects disruptions in nucleosome positioning and supports methylation footprinting to map protein–DNA interactions.

Scientific Applications:

• Protein–DNA interaction mapping: Maps protein–DNA interactions via methylation footprinting using endogenous and enzyme-induced methylation patterns.
• Endogenous and enzyme-induced methylation analysis: Distinguishes and analyzes endogenous cytosine methylation and methylation introduced by exogenous methyltransferases such as M.CviPI.
• Nucleosome positioning studies: Detects disruptions in nucleosome positioning, as applied to PHO5 promoter studies in budding yeast.
• Cancer chromatin analysis: Applied to analysis of hMLH1 chromatin methylation in colorectal cancer cells.
• Bisulfite and MAPit dataset processing: Facilitates quantitative analysis and downstream statistical interpretation of bisulfite sequencing and MAPit datasets for publication.

Methodology:

Analyzes bisulfite-converted sequences by concurrently querying cytosine methylation across up to four motifs (including degenerate and user-defined motifs), processes datasets generated with non-native methyltransferases such as M.CviPI, performs integrated primer design, and exports data and publication-quality images for downstream statistical analysis.