3D-GNOME

3D-GNOME models three-dimensional chromatin architecture and predicts structural alterations in genome organization caused by structural variants.

Key Features:

• Structural Variant–Aware Genome Modeling: Incorporates structural variants to simulate their effects on chromatin spatial organization.
• Reference 3D Genome Structure: Uses Chromosome Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) data from the GM12878 cell line to construct a baseline chromatin conformation model.
• Custom Structural Data Integration: Accepts user-provided structural data or lists of structural variants for customized genome structure modeling.
• Chromatin Interaction Visualization: Generates contact diagrams to compare reference chromatin structures with structures altered by structural variants.

Scientific Applications:

• 3D Genome Organization Studies: Enables analysis of spatial chromatin organization and its variation across genomic contexts.
• Gene Regulation Research: Supports investigation of how structural variants modify chromatin architecture and influence transcriptional regulation.
• Disease Mechanism Analysis: Facilitates exploration of disease-associated genomic structural rearrangements affecting genome organization.

Methodology:

The method constructs three-dimensional chromatin models using ChIA-PET interaction data from the GM12878 cell line and integrates structural variant information to simulate alterations in genome spatial organization.