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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
Published on: February 24, 2015
MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility
Carolina E Pardo1, Ian M Carr, Christopher J Hoffman
1Department of Biochemistry and Molecular Biology, University of Florida Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, Gainesville, FL 32610-3633, USA.
Nucleic Acids Research
|October 21, 2010
Summary
This study introduces MethylViewer, a program for analyzing DNA methylation data from bisulfite sequencing and protein-DNA interaction mapping. MethylViewer enables high-resolution mapping of DNA methylation and protein binding sites, aiding cancer research.
Area of Science:
- Epigenetics and Genomics
- Molecular Biology
- Cancer Research
Background:
- Bisulfite sequencing is crucial for nucleotide-resolution DNA methylation analysis.
- Probing with cytosine DNA methyltransferases followed by bisulfite sequencing (MAPit) maps protein-DNA interactions.
- Existing methods require enhanced tools for analyzing complex methylation patterns.
Purpose of the Study:
- To develop a versatile software tool, MethylViewer, for analyzing bisulfite sequencing and MAPit data.
- To enable simultaneous analysis of multiple DNA sequence motifs, including those with degenerate bases.
- To facilitate high-resolution mapping of DNA methylation and protein-DNA interactions.
Main Methods:
- Utilized MAPit methylation footprinting with M.CviPI methyltransferase.
- Applied the developed MethylViewer program for data analysis.
- Analyzed hMLH1 chromatin in colorectal cancer cells (HCT116, RKO) and PHO5 promoter in yeast.
Main Results:
- MethylViewer allows simultaneous querying of cytosine methylation at up to four user-defined motifs.
- High-resolution mapping of endogenous CG methylation and accessible GC sites on single DNA molecules was achieved.
- Disruption of nucleosome positioning on single molecules was detected in yeast.
Conclusions:
- MethylViewer provides an integrated solution for analyzing bisulfite sequencing and MAPit datasets.
- The software enables rapid, accurate, and detailed analysis for diverse biological systems.
- This tool enhances the study of DNA methylation and protein-DNA interactions in epigenetics and disease.
