Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• The cohesin complex organizes the genome by forming loops and topologically associating domains (TADs).
• The impact of chromatin state on cohesin's genome structuring functions is not fully understood.

Purpose of the Study:

• To investigate how histone acetylation, induced by trichostatin A (TSA), affects cohesin's interaction with chromatin.
• To differentiate between cohesin populations involved in TAD formation and CTCF-anchored loops.

Main Methods:

• Induction of histone hyperacetylation using trichostatin A (TSA).
• Analysis of cohesin occupancy and chromatin interactions using a semi-in vitro system with TEV-cleavable RAD21.
• Distinguishing between TSA-sensitive and TSA-resistant cohesin populations.

Main Results:

• Histone hyperacetylation disrupts short-range interactions within TADs but preserves CTCF-anchored loops.
• Two distinct cohesin populations were identified: TSA-sensitive (extruding) and TSA-resistant (topologically bound).
• Proteolytic cleavage of cohesin at CTCF sites rendered it TSA-sensitive, confirming the role of topological engagement.

Conclusions:

• Cohesin exists in distinct biochemical states, influencing its role in genome organization.
• A TSA-sensitive, extruding cohesin form allows dynamic chromatin loop changes.
• A TSA-resistant, topologically bound cohesin form ensures the stability of CTCF-anchored loops against chromatin state alterations.