DNA methylation
Definition
DNA methylation is an epigenetic modification involving the addition of a methyl group (CH3) to cytosine bases, typically at cytosine-guanine dinucleotides (CpG sites). This covalent modification regulates gene expression without altering the underlying DNA sequence, primarily through recruitment of methyl-binding proteins and chromatin remodeling complexes that suppress transcription. DNA methylation patterns are established by DNA methyltransferases (DNMTs) and play crucial roles in development, genomic imprinting, X-chromosome inactivation, and silencing of repetitive elements. Aberrant methylation patterns are hallmarks of cancer and other diseases, where hypermethylation of promoter CpG islands can silence tumor suppressor genes, while global hypomethylation may activate oncogenes. Methylation profiling has become essential for understanding gene regulation, cellular differentiation, and disease mechanisms.
Visualize DNA methylation in Nodes Bio
Researchers can visualize DNA methylation data as networks connecting methylated genomic regions to affected genes, transcription factors, and downstream pathways. Nodes Bio enables integration of methylation profiles with gene expression data to identify correlations between methylation status and transcriptional changes. Users can map differentially methylated regions (DMRs) to regulatory networks, revealing how epigenetic modifications propagate through biological pathways and influence cellular phenotypes in disease contexts.
Visualization Ideas:
- Methylation-gene expression correlation networks showing epigenetic regulation of transcription
- CpG island methylation networks linked to silenced tumor suppressor genes and oncogenic pathways
- Multi-omics integration networks combining DNA methylation, histone modifications, and chromatin accessibility data
Example Use Case
A cancer research team investigates colorectal tumor progression by profiling DNA methylation across normal, adenoma, and carcinoma samples. They identify hypermethylation of the MLH1 promoter CpG island correlating with microsatellite instability. Using network analysis, they map how MLH1 silencing affects DNA mismatch repair pathway components and connects to mutations in downstream targets like BRAF and KRAS. The integrated methylation-expression network reveals that early-stage hypermethylation events predict progression risk and identifies potential epigenetic biomarkers for patient stratification in clinical trials.