A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

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. © 2008 Nature Publishing Group.Fil: Down, Thomas A.. Wellcome Trust Sanger Institute; Reino UnidoFil: Rakyan, Vardhman K.. Institute of Cell and Molecular Science; Reino UnidoFil: Turner, Daniel J.. Wellcome Trust Sanger Institute; Reino UnidoFil: Flicek, Paul. European Bioinformatics Institute; Reino UnidoFil: Li, Heng. Wellcome Trust Sanger Institute; Reino UnidoFil: Kulesha, Eugene. European Bioinformatics Institute; Reino UnidoFil: Gräf, Stefan. European Bioinformatics Institute; Reino UnidoFil: Johnson, Nathan. European Bioinformatics Institute; Reino UnidoFil: Herrero, Javier. European Bioinformatics Institute; Reino UnidoFil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute; Reino UnidoFil: Thorne, Natalie P.. University of Cambridge; Reino UnidoFil: Bäckdahl, Liselotte. University College London; Reino UnidoFil: Herberth, Marlis. University of Cambridge; Reino UnidoFil: Howe, Kevin L.. University of Cambridge; Reino UnidoFil: Jackson, David K.. Wellcome Trust Sanger Institute; Reino UnidoFil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Wellcome Trust Sanger Institute; Reino UnidoFil: Marioni, John C.. University of Cambridge; Reino UnidoFil: Birney, Ewan. European Bioinformatics Institute; Reino UnidoFil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute; Reino UnidoFil: Durbin, Richard. Wellcome Trust Sanger Institute; Reino UnidoFil: Tavaré, Simon. University of Cambridge; Reino UnidoFil: Beck, Stephan G.. University College London; Reino Unid

Miniaturization in functional genomics and proteomics

Proteins are the key components of the cellular machinery responsible for processing changes that are ordered by genomic information. Analysis of most human proteins and nucleic acids is important in order to decode the complex networks that are likely to underlie many common diseases. Significant improvements in current technology are also required to dissect the regulatory processes in high-throughtput and with low cost. Miniaturization of biological assays is an important prerequisite to achieve these goals in the near future