Introduction

The three-dimensional organization of chromatin in the nucleus is a critical determinant of gene regulation. Hi-C chromosome conformation capture sequencing reveals genome-wide chromatin contacts, enabling identification of topologically associating domains (TADs), chromatin loops, and A/B compartments. TADs are self-interacting genomic regions that constrain enhancer-promoter interactions. Chromatin loops bring distal regulatory elements into proximity. A/B compartments reflect the active (A) and repressive (B) chromatin states. Computational analysis of Hi-C data requires specialized normalization and feature detection algorithms.

Methods

Hi-C Matrix Generation

Synthetic Hi-C contact matrices were generated for 200 genomic bins at 40kb resolution (8Mb total) for two cell types. Contact frequencies follow a power-law distance decay. TAD structure was added as blocks of enhanced intra-domain contacts. Chromatin loops were added as point enrichments. A/B compartment structure was incorporated through preferential same-compartment contacts.

ICE Normalization

Iterative Correction and Eigenvector decomposition (ICE) normalization was applied for 20 iterations to remove systematic biases in Hi-C data including GC content, mappability, and restriction fragment length biases.

TAD Boundary Detection

Insulation scores were computed as the mean contact frequency in a sliding window (8 bins) around the diagonal. TAD boundaries were identified as local minima in the insulation score using peak detection with minimum distance of 5 bins.

Loop Calling

Chromatin loops were called as locally enriched contacts with enrichment ≥4x over local background (donut model). Loops were required to span at least 5 bins (200kb).

A/B Compartment Calling

Observed/expected (O/E) contact matrices were computed by normalizing for distance decay. Pearson correlation matrices of O/E values were computed, and the first eigenvector (PC1) was used to assign A (positive) and B (negative) compartments.

Loop Extrusion Simulation

Cohesin-mediated loop extrusion was simulated with 15 cohesins loading at random positions and extruding bidirectionally until stalling at CTCF sites. Contact maps were accumulated over 200 simulation steps.

Results

ICE normalization successfully removed systematic biases (bias range 0.3-3.2). TAD boundary detection identified 6 boundaries in Cell A and 7 in Cell B, with 3 shared boundaries, 4 gained, and 3 lost between cell types. Loop calling identified 13 loops in Cell A and 8 in Cell B. Compartment analysis revealed 110 bins (55%) switching between A and B compartments. Loop extrusion simulation produced contact patterns consistent with CTCF-anchored loop domains.

Discussion

ChromatinConformationEngine provides a complete framework for 3D genome analysis. The differential TAD and compartment analysis between cell types reveals cell-type-specific chromatin organization. The loop extrusion simulation provides mechanistic insight into cohesin-mediated genome folding. Future extensions include integration with ChIP-seq data for CTCF and cohesin binding, and multi-resolution analysis.

Code Availability

Full source code: https://github.com/BioTender-max/ChromatinConformationEngine

# pip install numpy scipy matplotlib
python chromatin_conformation_engine.py

Key Results

• Resolution: 40kb × 200 bins = 8Mb
• TAD boundaries: Cell A=6, Cell B=7, shared=3
• Compartment switches: 110 bins (55%)
• Loops: Cell A=13, Cell B=8
• CTCF sites simulated: 15