Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• Type II topoisomerases (TOP2s) manage DNA supercoiling crucial for cellular processes.
• TOP2s are found at chromatin loop anchors and TAD boundaries, sites linked to genomic instability.
• The precise role of TOP2s in 3D chromosome organization and topological constraint relief is not fully understood.

Purpose of the Study:

• To investigate the role of TOP2s in shaping 3D chromosome organization in human cells.
• To determine if TOP2s relieve topological constraints at specific genomic locations.
• To assess the impact of TOP2s on chromatin folding, gene expression, and nuclear lamina interactions.

Main Methods:

• Utilized 3D genomics techniques to map chromosome organization.
• Employed imaging methods for cellular visualization.
• Applied GapRUN for genome-wide profiling of positive supercoiling.
• Performed acute TOP2 depletion experiments.

Main Results:

• TOP2 depletion induced new large-scale contacts at boundaries between active and lamina-associated domains.
• Changes in higher-order chromatin folding correlated with altered chromatin-nuclear lamina interactions and gene expression.
• Depletion of TOP2 primarily affected transcriptionally anchored, positively supercoiled loops at the chromatin loop level.

Conclusions:

• TOP2s play a significant role in regulating chromosome organization at multiple scales.
• TOP2s fine-tune chromatin folding, influencing gene expression and nuclear organization.
• These findings highlight TOP2s as key regulators of genome architecture and stability.