HiC-DCplus

HiC-DC+ implements genome-wide statistical analysis of Hi-C and HiChIP chromosome conformation capture data to call chromatin interactions and perform differential analyses for studying 3D genomic architecture and regulatory contacts.

Key Features:

• HiC-DC statistical framework: Efficient implementation of the HiC-DC statistical framework for interaction calling and modeling contact counts from Hi-C and HiChIP data.
• Preprocessing integration: Integrates with preprocessing tools to accept processed Hi-C and HiChIP input matrices.
• TAD and A/B compartment callers: Includes callers for Topologically Associating Domains (TADs) and A/B compartment identification.
• Enhancer–promoter interaction identification: Identifies enhancer–promoter interactions with superior accuracy on H3K27ac HiChIP data, validated using CRISPRi-FlowFISH.
• Differential analysis capabilities: Performs differential analysis of Hi-C and HiChIP datasets, recovering biological findings such as enhancer hubs, TAD aggregation, and promoter–enhancer loop dynamics linked to gene expression in contexts including cellular differentiation and cohesin perturbation.

Scientific Applications:

• 3D chromatin architecture mapping: Mapping genome-wide chromatin interactions from Hi-C and HiChIP to study three-dimensional genome organization.
• Regulatory interaction discovery: Discovery and quantification of enhancer–promoter interactions, including those detected in H3K27ac HiChIP and validated by CRISPRi-FlowFISH.
• Comparative conformation analysis: Comparative analysis of chromatin contacts across conditions, such as cellular differentiation and cohesin perturbation, to link loop changes with gene expression.
• Higher-order chromatin characterization: Identification and analysis of TADs and A/B compartments to study higher-order chromatin organization.

Methodology:

Implements the HiC-DC statistical framework to model Hi-C and HiChIP contact counts for interaction calling and differential analysis.