Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters

Area of Science:

• Genomics
• Molecular Biology
• Cell Biology

Background:

• Recurrent DNA break clusters (RDCs) are hotspots for replication-transcription collisions, particularly in neural progenitor cells.
• Understanding the mechanisms driving RDC formation is crucial for genome stability.

Purpose of the Study:

• To identify replication features that determine the location and orientation of RDCs.
• To investigate the role of DNA:RNA hybrids and replication-transcription interactions in RDC formation.

Main Methods:

• High-resolution replication sequencing in mouse neural progenitor cells under replication stress.
• Capture-ligation assay to map DNA double-strand breaks (DSBs).
• Strand-specific mapping of DNA-bound RNA and RNA polymerase activity.

Main Results:

• Most RDCs occur at timing transition regions (TTRs) with sparse origins and unidirectional forks.
• Leftward forks yield telomere-connected DSBs; rightward forks yield centromere-connected DSBs.
• Higher density of DNA:RNA hybrids and head-on replication-transcription collisions contribute significantly to DSBs.

Conclusions:

• Timing transition regions (TTRs) represent a fragile genomic class.
• The linear interplay between transcription and replication directly impacts genome stability, especially in neural progenitor cells.