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Dryad

Mature chromatin packing domains persist after RAD21 depletion in 3D

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Jan 18, 2025 version files 222.42 MB

Abstract

Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin is essential for topologically associated domains (TAD) and loop connectivity features in Hi-C, but the corresponding change in physical structure has not been studied using electron microscopy. Pairing chromatin scanning transmission electron tomography with multi-omics analysis, and single molecule localization microscopy, we study the role of cohesin in regulating the conformationally defined chromatin nanoscopic packing domains. Our results indicate that packing domains are not physical manifestation of TADs. Using electron microscopy, we found that only 20% of packing domains are lost upon RAD21 depletion. The effect of RAD21 depletion is restricted to small, poorly packed (nascent) packing domains. Additionally, we present evidence that cohesin mediated loop-extrusion generates nascent domains that undergo maturation through nucleosome posttranslational modifications. Our results demonstrate that 3D genomic structure, comprised of packing domains, is generated through cohesin activity and nucleosome modifications.