Abstract
BackgroundMethylated 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.ResultsWe 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.ConclusionsWe 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.
Highlights
Methylated DNA immunoprecipitation (MeDIP) is a popular enrichment based method and can be combined with sequencing to interrogate the methylation status of cytosines across entire genomes
Of the methylcytosines detected in human somatic cells, more than 99% have been shown to be in a CpG context
Data description Here, we present a comprehensive resource comprising data and tools for the study of genome-wide methylation profiles in mouse. 18 methylomes were generated using a dataset of over 251 million uniquely mapped fragments (>502 million mapped paired-end reads) and were processed using our novel MeDIP-seq computational analysis pipeline (Methylated DNA Utility for Sequence Analysis, or MeDUSA)
Summary
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. DNA methylation is an important epigenetic modification, playing a vital role in genome dynamics. Methylation predominantly occurs symmetrically on both DNA strands at palindromic CpG dinucleotides, but the preference between CpG and non-CpG methylation appears to vary with the degree of cell differentiation [2]. Of the methylcytosines detected in human somatic cells (fetal lung fibroblasts), more than 99% have been shown to be in a CpG context. In embryonic stem cells there is abundant methylation in non-CpG contexts, comprising approximately 25% of the total number of methylcytosines detected [3]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
