Journal Article

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

Miretti, Marcos M, Li, Heng, Herrero, Javier, Gräf, Stefan, Herberth, Marlis, Johnson, Nathan, Howe, Kevin L, Durbin, Richard, Turner, Daniel J, Beck, Stephan, Birney, Ewan, Tavaré, Simon, Rakyan, Vardhman K, Flicek, Paul, Bäckdahl, Liselotte, Marioni, John C, Down, Thomas A, Jackson, David K, Thorne, Natalie P, Tomazou, Eleni M, Hubbard, Tim J P, Kulesha, Eugene

2008

Overview

An inability to estimate absolute DNA methylation levels has slowed progress in understanding the role of this epigenetic modification in health and disease. Down et al . describe an algorithm for analyzing methylated DNA immunoprecipitation profiles generated using either high-throughput sequencing or oligonucleotide arrays. DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm—Bayesian tool for methylation analysis (Batman)—for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: Agriculture / Algorithms / analysis / Base Sequence / Bayes Theorem / Bioinformatics / Biological and medical sciences / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / Cancer research / Chromatin Immunoprecipitation - methods / Chromosome Mapping - methods / Deoxyribonucleic acid / DNA / DNA - genetics / DNA Methylation / Epigenetics / Fundamental and applied biological sciences. Psychology / General aspects / Genetic aspects / Genetic screening / Genomes / Immune system / Life Sciences / Mammals / Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) / Medical research / Methods / Methylation / Molecular Sequence Data / Pattern Recognition, Automated - methods / Physiological aspects / Sequence Analysis, DNA - methods / Tennis / Testing