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.
| Original language | English (US) |
|---|---|
| Article number | eadp0855 |
| Journal | Science Advances |
| Volume | 11 |
| Issue number | 4 |
| DOIs | |
| State | Published - Jan 24 2025 |
Funding
Chat-GPT 4.0 was used to assist in the review of the logic structure in the manuscript and with coding support for data visualization. No AI tools or external reviewers were used for conceptualization, writing, synthesis, or direct analysis of results. Philanthropic support was received from R. and K. Goldman, the Christina Carinato Charitable Foundation, M. E. Holliday, I. Schneider, and D. Sachs. Computational analysis of Hi-C data was supported in part through the computational resources and staff contributions provided by the Genomics Compute Cluster, which is jointly supported by the Feinberg School of Medicine, the Center for Genetic Medicine, and Feinberg's Department of Biochemistry and Molecular Genetics, the Office of the Provost, the Office for Research, and Northwestern Information Technology. The Genomics Compute Cluster is part of Quest, Northwestern University's high-performance computing facility, with the purpose to advance research in genomics. We appreciate the support from the ENCODE Consortium in the generation and dissemination of publicly available datasets. In particular, we thank the lab of E. Lieberman-Aiden for the generation of the Micro-C dataset, the lab of M. Snyder for the generation of the ATAC-seq dataset in RAD21-depleted and control cells with the AID2 system, the lab of B. Bernstein for the generation of the Mint-C hIP-seq data, and the lab of C. Lee for the generation of the Chia-PET datasets. This work made use of the BioCryo facility (RRID:SCR_021288) of Northwestern University's NUANCE Center, which has received support from the SHyNE Resource (NSF ECC S-2025633), the IIN, and Northwestern's MRSEC program (NSF DMR-2308691). This work was supported by National Science Foundation grant EFMA-1830961 (E.M.P.-L., M.C., I.S., and V.B.), National Science Foundation grant EFMA-1830969 (E.M.P.-L. and V.B.), National Science Foundation grant ECC S-2025633, National Science Foundation grant DMR-2308691, National Institutes of Health grant R01CA228272 (W.S.L., T.K., I.S., and V.B.), National Institutes of Health grant U54 CA268084 (W.S.L., L.M.C., L.M.A., E.M.P.-L., T.K., K.L.M., M.C., I.S., and V.B.), National Institutes of Health grant U54 CA261694 (L.M.C. and V.B.), NIH Training Grant T32AI083216 (L.M.A.), NIH Training Grant T32GM132605 (T.K., L.M.C., and V.B.), Hyundai Hope on Wheels Hope Scholar Grant (K.L.M.), CURE Childhood Cancer Early Investigator Grant (K.L.M.), Alex's Lemonade Stand Foundation \"A\" award grant (K.L.M.), Ann and Robert H. Lurie Children's Hospital of Chicago under the Molecular and Translational Cancer Biology Neighborhood (K.L.M.), National Institutes of Health National Center for Advancing Translational Sciences KL2TR001424 (K.L.M.), and Northwestern University Starzl Scholar Award (L.M.A.).
ASJC Scopus subject areas
- General