2. Academic Validation
  3. Mature chromatin packing domains persist after RAD21 depletion in 3D

Mature chromatin packing domains persist after RAD21 depletion in 3D

  • Sci Adv. 2025 Jan 24;11(4):eadp0855. doi: 10.1126/sciadv.adp0855.
Wing Shun Li 1 2 3,  Lucas M Carter 3 4,  Luay Matthew Almassalha 3 5,  Ruyi Gong 2 3,  Emily M Pujadas-Liwag 3 4,  Tiffany Kuo 3 4,  Kyle L MacQuarrie 6 7,  Marcelo Carignano 2,  Cody Dunton 2 3,  Vinayak Dravid 1 8 9 10 11,  Masato T Kanemaki 12 13 14,  Igal Szleifer 2 3 8,  Vadim Backman 2 3
Affiliations

Affiliations

  • 1 Applied Physics Program, Northwestern University, Evanston, IL 60208, USA.
  • 2 Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
  • 3 Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA.
  • 4 IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA.
  • 5 Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL 60611, USA.
  • 6 Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
  • 7 Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
  • 8 Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
  • 9 Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA.
  • 10 Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208, USA.
  • 11 International Institute for Nanotechnology (IIN), Northwestern University, Evanston, IL 60208, USA.
  • 12 Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
  • 13 Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
  • 14 Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
PMID: 39854464 DOI: 10.1126/sciadv.adp0855
Abstract

Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin is essential for 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 multiomic 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. In addition, we present evidence that cohesin-mediated loop extrusion generates nascent domains that undergo maturation through nucleosome posttranslational modifications. Our results demonstrate that a 3D genomic structure, composed of packing domains, is generated through cohesin activity and nucleosome modifications.

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