Master transcription factor binding sites constitute the core of early replication control elements.

Area of Science:

• Genomics
• Epigenetics
• Developmental Biology

Background:

• Eukaryotic genomes follow a replication timing (RT) program, crucial for development.
• Mechanisms controlling RT and its role in cell fate transitions are not fully understood.
• Early Replication Control Elements (ERCEs) were previously linked to early RT, transcription, and chromatin organization.

Purpose of the Study:

• To dissect the functional components of ERCEs.
• To elucidate the mechanisms by which ERCEs regulate replication timing and transcription.
• To understand the role of ERCEs in chromatin organization and cell fate transitions.

Main Methods:

• CRISPR-based deletion of subERCEs and transcription start sites in mouse embryonic stem cells (mESCs).
• Analysis of replication timing (RT) profiles.
• Assessment of genome-wide transcription levels.
• Evaluation of 3D chromatin architecture and compartmentalization.

Main Results:

• ERCEs are compound elements (subERCEs) driven by master transcription factor binding and long-range interactions.
• Deletion of subERCEs significantly impacted both transcription and RT.
• Deletion of transcription start sites abolished transcription with moderate effects on RT.
• SubERCEs function as both transcription enhancers and structural chromatin organizers supporting early RT.

Conclusions:

• SubERCEs are critical regulatory units within ERCEs.
• A model is proposed where subERCEs integrate transcription factor signals to orchestrate transcription, chromatin structure, and early replication timing.
• This mechanism may provide a feed-forward loop for robust epigenomic changes during cell fate transitions.