Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Replication timing (RT) is linked to genome architecture, but regulatory cis-elements are unknown.
• Topologically associating domains (TADs) are key structural units of the genome.

Purpose of the Study:

• To identify cis-elements regulating replication timing and genome architecture.
• To investigate the role of TAD boundaries and intra-TAD elements in controlling these processes.

Main Methods:

• CRISPR-mediated deletions and inversions in mouse ESCs.
• Analysis of replication timing, A/B compartmentalization, TAD architecture, and transcription.

Main Results:

• CTCF-associated TAD boundaries are dispensable for replication timing.
• Deletion of CTCF-independent intra-TAD contact sites (ERCEs) caused domain-wide RT shifts, A-to-B compartment changes, weakened TADs, and transcriptional loss.
• ERCEs are essential for maintaining genome structure and function.

Conclusions:

• Discrete cis-regulatory elements (ERCEs) control domain-wide replication timing, compartmentalization, TAD architecture, and transcription.
• These findings reveal fundamental principles linking genome structure and function.