A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

Authors
Down, Thomas A.; Rakyan, Vardhman K.; Turner, Daniel J.; Flicek, Paul; Li, Heng; Kulesha, Eugene; Gräf, Stefan; Johnson, Nathan; Herrero, Javier; Tomazou, Eleni M.; Thorne, Natalie P.; Bäckdahl, Liselotte; Herberth, Marlis; Howe, Kevin L.; Jackson, David K.; Miretti, Marcos Mateo; Marioni, John C.; Birney, Ewan; Hubbard, Tim J. P.; Durbin, Richard; Tavaré, Simon; Beck, Stephan G.
Publication Year
2008
Language
English
Format
article
Status
Published version
Description
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 Unido
Fil: Rakyan, Vardhman K.. Institute of Cell and Molecular Science; Reino Unido
Fil: Turner, Daniel J.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Flicek, Paul. European Bioinformatics Institute; Reino Unido
Fil: Li, Heng. Wellcome Trust Sanger Institute; Reino Unido
Fil: Kulesha, Eugene. European Bioinformatics Institute; Reino Unido
Fil: Gräf, Stefan. European Bioinformatics Institute; Reino Unido
Fil: Johnson, Nathan. European Bioinformatics Institute; Reino Unido
Fil: Herrero, Javier. European Bioinformatics Institute; Reino Unido
Fil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Thorne, Natalie P.. University of Cambridge; Reino Unido
Fil: Bäckdahl, Liselotte. University College London; Reino Unido
Fil: Herberth, Marlis. University of Cambridge; Reino Unido
Fil: Howe, Kevin L.. University of Cambridge; Reino Unido
Fil: Jackson, David K.. Wellcome Trust Sanger Institute; Reino Unido
Fil: 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 Unido
Fil: Marioni, John C.. University of Cambridge; Reino Unido
Fil: Birney, Ewan. European Bioinformatics Institute; Reino Unido
Fil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Durbin, Richard. Wellcome Trust Sanger Institute; Reino Unido
Fil: Tavaré, Simon. University of Cambridge; Reino Unido
Fil: Beck, Stephan G.. University College London; Reino Unido
Subject
tissue-specific methylation
tDMRs
Bayesian deconvolution
Genética y Herencia
Ciencias Biológicas
CIENCIAS NATURALES Y EXACTAS
Access level
Restricted access
License
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repository
CONICET Digital (CONICET)
Institution
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identifier
oai:ri.conicet.gov.ar:11336/60202