Mature chromatin packing domains persist after RAD21 depletion in 3D

Area of Science:

• Cellular and Molecular Biology
• Genomics
• Structural Biology

Background:

• Chromatin organization is crucial for genome function.
• Cohesin is known to be vital for genome connectivity (e.g., TADs and loops) but its role in physical chromatin structure remains unclear.
• Previous studies relied on Hi-C for connectivity, lacking direct physical visualization.

Purpose of the Study:

• To investigate the role of cohesin in regulating chromatin nanoscopic packing domains.
• To determine if chromatin packing domains are a direct physical representation of TADs.
• To visualize the impact of cohesin depletion on chromatin's physical structure.

Main Methods:

• Chromatin scanning transmission electron tomography (csTEM)
• Multiomic analysis
• Single-molecule localization microscopy (SMLM)
• RAD21 depletion (cohesin component)

Main Results:

• Chromatin packing domains are not direct physical manifestations of TADs.
• RAD21 depletion resulted in the loss of only 20% of packing domains.
• Cohesin depletion primarily affected small, nascent packing domains.
• Evidence suggests cohesin-mediated loop extrusion forms nascent domains that mature via nucleosome modifications.

Conclusions:

• Cohesin activity and nucleosome modifications are key drivers in generating a 3D genomic structure defined by packing domains.
• The physical structure of chromatin packing domains is distinct from TADs.
• Nascent chromatin domains are dynamically regulated by cohesin and posttranslational modifications.