nucleosome
Definition
A nucleosome is the fundamental repeating unit of eukaryotic chromatin, consisting of approximately 147 base pairs of DNA wrapped 1.65 turns around an octamer of histone proteins (two copies each of H2A, H2B, H3, and H4). This structure compacts DNA and serves as a critical regulatory platform for gene expression through epigenetic modifications. Post-translational modifications to histone tails, such as acetylation, methylation, and phosphorylation, alter chromatin accessibility and recruit regulatory proteins. Nucleosome positioning and dynamics directly influence transcription factor binding, DNA replication, and repair processes. Understanding nucleosome architecture and modifications is essential for epigenomics research, as aberrant nucleosome regulation is implicated in cancer, developmental disorders, and other diseases.
Visualize nucleosome in Nodes Bio
Researchers can use Nodes Bio to visualize networks connecting nucleosome modifications to gene expression changes and downstream phenotypes. Map relationships between histone modification enzymes (writers, erasers, readers), chromatin remodelers, transcription factors, and target genes. Integrate ChIP-seq, ATAC-seq, and RNA-seq data to identify causal pathways linking specific nucleosome states to cellular outcomes, revealing how epigenetic changes propagate through regulatory networks.
Visualization Ideas:
- Histone modification enzyme networks showing writers, erasers, and readers connected to target genes
- Chromatin accessibility networks linking nucleosome positioning to transcription factor binding sites
- Multi-omics integration networks connecting nucleosome states (ChIP-seq) with gene expression (RNA-seq) and phenotypic outcomes
Example Use Case
A cancer researcher investigating drug resistance in melanoma discovers that resistant cells show altered H3K27me3 patterns at specific genomic loci. Using Nodes Bio, they map the network connecting the EZH2 methyltransferase, affected nucleosome positions, downstream target genes, and resistance-associated pathways. The visualization reveals that nucleosome remodeling at the MITF locus activates a transcriptional program driving resistance. This network analysis identifies combination therapy targets: EZH2 inhibitors plus MITF pathway blockers to overcome resistance mechanisms.