CpG island
Definition
CpG islands are genomic regions, typically 300-3000 base pairs long, with a high frequency of cytosine-guanine dinucleotides (CpG sites) relative to the rest of the genome. In mammals, CpG dinucleotides are generally depleted and methylated, but CpG islands remain largely unmethylated and are often located at gene promoters (approximately 70% of human promoters). These regions play crucial roles in gene regulation, as their methylation status directly influences transcriptional activity. Hypermethylation of CpG islands in promoter regions typically leads to gene silencing, while unmethylated islands permit transcription. CpG islands are essential for understanding epigenetic regulation, development, genomic imprinting, X-chromosome inactivation, and disease states, particularly cancer where aberrant methylation patterns can silence tumor suppressor genes.
Visualize CpG island in Nodes Bio
Researchers can use Nodes Bio to visualize relationships between CpG island methylation patterns and gene expression networks. By mapping methylation status of CpG islands to their associated genes and downstream pathways, users can identify epigenetic regulatory networks and discover how methylation changes propagate through biological systems. Network visualization reveals clusters of co-methylated genes and their functional relationships, enabling identification of epigenetic biomarkers and therapeutic targets.
Visualization Ideas:
- Gene regulatory networks showing CpG island methylation status linked to transcription factor binding and target gene expression
- Multi-omics integration networks connecting CpG island methylation data with RNA-seq expression levels and protein abundance
- Disease-specific epigenetic networks comparing CpG island methylation patterns between normal and diseased tissue samples across multiple genes
Example Use Case
A cancer research team investigating colorectal tumor progression analyzes genome-wide methylation data to identify hypermethylated CpG islands. They discover that CpG islands in the promoters of DNA repair genes MLH1 and MGMT show progressive hypermethylation across tumor stages. By integrating this methylation data with gene expression profiles and patient outcomes, they identify a network of epigenetically silenced genes associated with microsatellite instability and treatment resistance. This network analysis reveals potential epigenetic biomarkers for early detection and suggests combination therapies targeting DNA methyltransferases alongside conventional chemotherapy.