ArticleGigaScience2012
Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers.
Article in GigaScience, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 54 citations in OpenAlex.
- TET3 protects theiScience · 2025Article
- The TDG protein environment connects active DNA demethylation with chromatin and RNA biology.Cellular and molecular life sciences : CMLS · 2025Article
- The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers.Cancer cell international · 2024Review
- MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis.Bioinformatics (Oxford, England) · 2023Article
- MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation.Botanical studies · 2023Article
- Computational challenges in detection of cancer using cell-free DNA methylation.Computational and structural biotechnology journal · 2022Review
- Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline.Frontiers in plant science · 2021Review
- Cell-Free DNA-Methylation-Based Methods and Applications in Oncology.Biomolecules · 2020Review
- DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis.Clinical epigenetics · 2019Review
- Role of epigenomic mechanisms in the onset and management of insulin resistance.Reviews in endocrine & metabolic disorders · 2019Review
- The Impact and Mechanism of Methylated Metabotropic Glutamate Receptors 1 and 5 in the Hippocampus on Depression-Like Behavior in Prenatal Stress Offspring Rats.Journal of clinical medicine · 2018Article
- Article
- Profiling genome-wide DNA methylation.Epigenetics & chromatin · 2016Review
- Article
- MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq.Scientific reports · 2015Article
- Comprehensive analysis of DNA methylation data with RnBeads.Nature methods · 2014Article
- Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development.Genome research · 2014Article
- Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases.Genome medicine · 2014Article
- Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics.Genome medicine · 2014Article
- DNA methylation analysis of murine hematopoietic side population cells during aging.Epigenetics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.