methylation
Definition
Methylation is an epigenetic modification involving the addition of a methyl group (CH3) to DNA or proteins, most commonly occurring at cytosine bases in CpG dinucleotides. DNA methylation regulates gene expression without altering the underlying DNA sequence, typically silencing genes when occurring in promoter regions. This reversible modification plays crucial roles in development, genomic imprinting, X-chromosome inactivation, and chromatin structure maintenance. Aberrant methylation patterns are associated with cancer, aging, and various diseases. Methylation status can be inherited through cell divisions and influenced by environmental factors, making it a key mechanism linking genotype to phenotype and a critical target for therapeutic intervention.
Visualize methylation in Nodes Bio
Researchers can visualize methylation data as networks connecting differentially methylated regions to affected genes, transcription factors, and downstream pathways. Nodes Bio enables integration of methylation profiles with gene expression data to identify epigenetic regulatory networks. Users can map CpG islands to their target genes, visualize co-methylation patterns across samples, and explore how methylation changes propagate through signaling cascades to reveal disease mechanisms.
Visualization Ideas:
- Gene regulatory networks showing methylation-mediated transcriptional silencing
- Co-methylation networks identifying coordinated epigenetic changes across genomic regions
- Multi-omics integration networks connecting methylation status to gene expression and protein abundance
Example Use Case
A cancer research team investigating colorectal tumor samples discovers hypermethylation of tumor suppressor gene promoters. Using methylation array data, they identify 150 differentially methylated CpG sites between normal and tumor tissue. By integrating this with RNA-seq data, they map which methylation changes correlate with gene silencing. Network analysis reveals that hypermethylation of specific transcription factor binding sites creates a cascade effect, simultaneously silencing multiple DNA repair genes and contributing to genomic instability characteristic of the cancer subtype.