Genome Organization Drives Chromosome Fragility

Area of Science:

• Genomics
• Molecular Biology
• Cancer Biology

Background:

• CCCTC-binding factor (CTCF) and cohesin form chromosome loop anchors crucial for genome organization.
• Topoisomerase 2B (TOP2B) is implicated in DNA double-strand break (DSB) formation.
• Genomic rearrangements are linked to various diseases, including cancer.

Purpose of the Study:

• To investigate the vulnerability of CTCF/cohesin-bound loop anchors to TOP2B-mediated DNA double-strand breaks (DSBs).
• To determine the relationship between DSBs at loop anchors and chromosomal rearrangements.
• To assess the dependence of DSB formation on transcription, replication, and cell type.

Main Methods:

• Analysis of CTCF and cohesin occupancy.
• Identification of TOP2B-mediated DNA cleavage sites.
• Genome-wide analysis of DSB locations and their correlation with topological domain borders and breakpoint clusters.
• Assessment of transcription and replication dependence.

Main Results:

• Evolutionarily conserved chromosome loop anchors bound by CTCF and cohesin are susceptible to TOP2B-mediated DSBs.
• Genomic polymorphisms altering CTCF/cohesin binding redirect cleavage sites to new loop anchors.
• DSBs at loop anchors are largely independent of transcription, replication, and cell type.
• DSBs occur throughout interphase, near topological domain borders, and at cancer-associated breakpoint clusters.

Conclusions:

• Chromosome loop anchors function as fragile sites, generating DSBs.
• These DSBs contribute to chromosomal rearrangements, particularly those observed in cancer.
• DSB formation at loop anchors is a fundamental process largely uncoupled from active transcription or replication.