YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

Area of Science:

• Epigenetics and Genomics
• Developmental Biology
• Chromatin Structure and Dynamics

Background:

• CCCTC-binding factor (CTCF) is a key architectural protein organizing higher-order chromatin folding in pluripotent stem cells.
• CTCF binding dynamics during development are increasingly recognized as crucial for cellular transitions.
• Understanding CTCF's role in chromatin reorganization during neural lineage commitment is essential.

Purpose of the Study:

• To investigate the genome-wide CTCF occupancy shifts during early neural lineage commitment.
• To elucidate the contribution of CTCF dynamics to 3D chromatin folding reconfiguration.
• To identify other architectural proteins involved in neural progenitor cell (NPC) chromatin organization.

Main Methods:

• Genome-wide CTCF occupancy profiling.
• Chromatin conformation capture techniques to analyze 3D chromatin folding.
• siRNA-mediated knockdown of Yin Yang 1 (YY1) to assess its functional role.
• Analysis of CTCF and YY1 binding sites in pluripotent stem cells and NPCs.

Main Results:

• A significant decrease in CTCF occupancy was observed during the transition from pluripotency to multipotent primary neural progenitor cells (NPCs).
• Pluripotency gene-enhancer interactions, often CTCF-anchored, were decommissioned in parallel with CTCF loss.
• CTCF binding sites in NPCs were largely pre-existing, with few de novo sites; YY1 was identified at NPC-specific gene-enhancer loops.
• YY1 knockdown specifically disrupted NPC enhancer-gene interactions, revealing its role in developmentally regulated looping within the CTCF framework.

Conclusions:

• CTCF occupancy dynamically decreases during neural lineage commitment, impacting pluripotency-associated chromatin loops.
• Yin Yang 1 (YY1) acts as an architectural protein mediating developmentally regulated looping interactions in NPCs.
• YY1-mediated interactions are nested within a pre-existing topological framework established by constitutive CTCF interactions.