3DChrom

3DChrom reconstructs three-dimensional chromatin and topologically associating domain (TAD) structures from Hi-C interaction data using multidimensional scaling.

Key Features:

• Hi-C-Based 3D Chromatin Reconstruction: Generates three-dimensional models of chromatin and TADs from chromosome conformation capture (Hi-C) interaction matrices.
• Multidimensional Scaling Optimization: Uses a multidimensional scaling objective function capable of handling DNA bead-pairs with zero Hi-C contact values.
• Structural Metrics Calculation: Computes quantitative measures including radius of gyration, folding degree, and exponent parameters derived from Hi-C contact matrices.
• Integration with Genomic and Epigenomic Features: Allows structural analysis incorporating genetic and epigenetic features such as H3K4me3, transcription start sites, and RNA polymerase II.

Scientific Applications:

• 3D Genome Organization Analysis: Enables investigation of chromatin spatial organization within the cell nucleus.
• Topologically Associating Domain Studies: Supports structural analysis of TAD compactness and folding properties.
• Epigenomic Structure–Function Research: Facilitates exploration of relationships between chromatin structure and epigenetic regulatory features.

Methodology:

The method reconstructs chromatin structures from Hi-C interaction matrices using multidimensional scaling with a specialized objective function that accommodates DNA bead-pairs with zero contact frequencies, followed by computation of structural metrics such as radius of gyration and folding degree.