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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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Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian chromosomes with self-mapping fluorescent labels and track them at ultraresolution. We find that sequences separated by submegabase distances transition to proximity in tens of seconds. This rapid search is dependent on cohesin and is exhibited only within domains. Domain borders act as kinetic impediments to this search process, rather than structural boundaries. The genomic separation–dependent scaling of the search time for cis interactions violated predictions of diffusion, suggesting motor-driven folding. We also uncover cohesin-dependent processive motion at 2.7 kilobases per second. Together, these multiscale dynamics reveal the organization of the genome into kinetically associated domains.
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- Award ID(s):
- 2022182
- PAR ID:
- 10651800
- Publisher / Repository:
- American Association for the Advancement of Science
- Date Published:
- Journal Name:
- Science
- Volume:
- 389
- Issue:
- 6766
- ISSN:
- 0036-8075
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1126/science.adx2202
