ArticleScientific reports2013
Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
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- Large-scale integration of DNA methylation and gene expression array platforms identifies bothEpigenetics · 2022Article
- Recognition of driver genes with potential prognostic implications in lung adenocarcinoma based on H3K79me2.Computational and structural biotechnology journal · 2022Article
- Metabotropic Glutamate Receptor 2 and Dopamine Receptor 2 Gene Expression Predict Sensorimotor Gating Response in the Genetically Heterogeneous NIH-HS Rat Strain.Molecular neurobiology · 2020Article
- Identification of Key Histone Modifications and Their Regulatory Regions on Gene Expression Level Changes in Chronic Myelogenous Leukemia.Frontiers in cell and developmental biology · 2020Article
- Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare.BMC genomics · 2018Article
- Differences in 5-HT2A and mGlu2 Receptor Expression Levels and Repressive Epigenetic Modifications at the 5-HT2A Promoter Region in the Roman Low- (RLA-I) and High- (RHA-I) Avoidance Rat Strains.Molecular neurobiology · 2018Article
- DNA hypomethylation of Synapsin II CpG islands associates with increased gene expression in bipolar disorder and major depression.BMC psychiatry · 2016Article
- Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.Nucleic acids research · 2016Article
- Article
- MicroRNAs in placental health and disease.American journal of obstetrics and gynecology · 2015Review
- Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development.Molecular genetics and genomics : MGG · 2015Article
- Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types.Scientific reports · 2015Article
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genome-wide variation of multiple epigenetic modifications in CpG islands (CGIs) and the interactions between them are of great interest. Here, we optimized an entropy-based strategy to quantify variation of epigenetic modifications and explored their interaction across mouse embryonic stem cells, neural precursor cells and brain. Our results showed that four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3 and H3K27me3) of CGIs in the mouse genome undergo combinatorial variation during neuron differentiation. DNA methylation variation was positively correlated with H3K27me3 variation, and negatively correlated with H3K4me2/3 variation. We identified 5,194 CGIs differentially modified by epigenetic modifications (DEM-CGIs). Among them, the differentially DNA methylated CGIs overlapped significantly with the CGIs differentially modified by H3K27me3. Moreover, DEM-CGIs may contribute to co-regulation of related developmental genes including core transcription factors. Our entropy-based strategy provides an effective way of investigating dynamic cross-talk among epigenetic modifications in various biological processes at the macro scale.
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