resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers资源methylome分析适合基因敲除研究潜在的表观基因组修饰符.pdfVIP

Wilson et al. GigaScience 2012, 1:3 /content/1/1/3 RESEARCH Open Access Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers 1* 1 1 2 1 3 Gareth A Wilson , Pawandeep Dhami , Andrew Feber , Daniel Cortázar , Yuka Suzuki , Reiner Schulz , Primo Schär2 and Stephan Beck1* Abstract Background: Methylated DNA immunoprecipitation (MeDIP) is a popular enrichment based method and can be combined with sequencing (termed MeDIP-seq) to interrogate the methylation status of cytosines across entire genomes. However, quality control and analysis of MeDIP-seq data have remained to be a challenge. Results: We report genome-wide DNA methylation profiles of wild type (wt) and mutant mouse cells, comprising 3 biological replicates of Thymine DNA glycosylase (Tdg) knockout (KO) embryonic stem cells (ESCs), in vitro differentiated neural precursor cells (NPCs) and embryonic fibroblasts (MEFs). The resulting 18 methylomes were analysed with MeDUSA (Methylated DNA Utility for Sequence Analysis), a novel MeDIP-seq computational analysis pipeline for the identification of differentially methylated regions (DMRs). The observed increase of hypermethylation in MEF promoter-associated CpG islands supports a previously proposed role for Tdg in the protection of regulatory regions from epigenetic silencing. Further analysis of genes and regions associated with the DMRs by gene ontology, pathway, and ChIP analyses revealed further insights into Tdg function, including an association of TDG with low-methylated distal regulatory regions. Conclusions: We demonstrate that MeDUSA is able to detect both large-scale changes between cells from different stages of differentiation a