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Open Access Research

Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers

Gareth A Wilson1*, Pawandeep Dhami1, Andrew Feber1, Daniel Cortázar2, Yuka Suzuki1, Reiner Schulz3, Primo Schär2 and Stephan Beck1*

Author Affiliations

1 Medical Genomics, UCL Cancer Institute, University College London, London, UK

2 Institute of Biochemistry and Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland

3 Department of Medical and Molecular Genetics, King’s College London, London, UK

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GigaScience 2012, 1:3  doi:10.1186/2047-217X-1-3

Published: 12 July 2012

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 and also small but significant changes between the methylomes of cells that only differ in the KO of a single gene. These changes were validated utilising publicly available datasets and confirm TDG's function in the protection of regulatory regions from epigenetic silencing.

Keywords:
Methylome; MeDIP-seq; Epigenetics; Epigenomics; DNA methylation; Computational pipeline; MeDUSA