Hi-C analyses with GENOVA: a case study with cohesin variants

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Chromosome conformation capture (3C) techniques, like Hi-C, are crucial for understanding genome-wide chromosome structure.
• Analyzing large Hi-C datasets requires specialized software, posing a challenge for researchers.
• Understanding the roles of cohesin subunits in 3D genome organization is an active area of research.

Purpose of the Study:

• To introduce GENOVA, a user-friendly R-package for the analysis and visualization of chromosome conformation capture (3C) data.
• To provide researchers with a tool that integrates common Hi-C analyses and supports major mapping pipeline outputs.
• To investigate the distinct roles of cohesin subunits SA1 and SA2 in shaping 3D genome architecture.

Main Methods:

• Development of GENOVA as an R-package implementing compartment and insulation score analyses.
• Creation of annotated heatmaps for visualizing locus-specific contact frequencies.
• Aggregation of Hi-C signals over user-defined genomic regions, including integration with ChIP-seq data.
• Analysis of Hi-C data from HAP1 cell lines with targeted knockout of cohesin subunits SA1 and SA2.

Main Results:

• GENOVA facilitates detailed exploration of Hi-C data, including compartment and insulation analyses.
• Cells lacking SA1 (ΔSA1) exhibited increased intra-TAD interactions and enhanced compartmentalization.
• Cells lacking SA2 (ΔSA2) displayed longer loop structures and reduced genome compartmentalization.
• Cohesin subunit SA1 appears to facilitate longer loop formation, while SA2 is involved in intra-TAD interaction maintenance.

Conclusions:

• GENOVA is an accessible R-package for comprehensive Hi-C data analysis and visualization.
• Cohesin subunits SA1 and SA2 play differential roles in genome folding, impacting loop formation and compartmentalization.
• The 3D genome structure arises from a balance between loop extrusion and compartmentalization, modulated by cohesin complexes.