epigenome
Definition
The epigenome encompasses all chemical modifications to DNA and histone proteins that regulate gene expression without altering the underlying DNA sequence. These modifications include DNA methylation, histone acetylation, methylation, phosphorylation, and chromatin remodeling patterns. Unlike the static genome, the epigenome is dynamic and responsive to environmental factors, developmental stages, and disease states. Epigenomic changes control which genes are accessible for transcription, thereby determining cell identity and function. Understanding the epigenome is crucial for deciphering gene regulation mechanisms, developmental biology, cancer progression, and inheritance of acquired traits. Aberrant epigenetic modifications are implicated in numerous diseases, making the epigenome a critical target for therapeutic intervention and biomarker discovery.
Visualize epigenome in Nodes Bio
Researchers can visualize epigenomic regulatory networks by mapping relationships between epigenetic modifications, transcription factors, and target genes. Nodes Bio enables integration of ChIP-seq, ATAC-seq, and methylation data to construct multi-layered networks showing how chromatin states influence gene expression patterns. Users can identify epigenetic regulators as key network hubs and trace their downstream effects across biological pathways, facilitating discovery of epigenetic drivers in disease contexts.
Visualization Ideas:
- Epigenetic modifier-gene regulatory networks showing histone acetyltransferases and methyltransferases connected to target genes
- Multi-layer networks integrating DNA methylation status, chromatin accessibility, and gene expression levels
- Temporal epigenomic networks tracking chromatin state transitions during cell differentiation or disease progression
Example Use Case
A cancer research team investigates how DNA methylation patterns silence tumor suppressor genes in colorectal cancer. They integrate whole-genome bisulfite sequencing data with gene expression profiles and histone modification maps. By visualizing these multi-omics datasets as networks in Nodes Bio, they identify clusters of co-methylated genes regulated by specific transcription factors. The network reveals that aberrant methylation of a master regulator disrupts an entire pathway controlling cell differentiation, providing a potential therapeutic target for demethylating agents.