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Two independent modes of chromatin organization revealed by cohesin removal
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Abstract
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.
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“Surprisingly however, deletion or degradation of cohesin or CTCF in differentiated cells has only mild effects on gene expression [344–349].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [348]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The A/B compartment structure does not disappear (and is in fact even strengthened) upon cohesin/CTCF depletion [344, 346–348], but, like TADs, dissolves in mitosis [459].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [348]
Experimental — accuracy not yet measuredIn the citing paper
“complementary polymer simulation studies and Hi-C studies employing acute depletion of CTCF and cohesin, which also support such a dynamic model.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [11]
In the citing paper
“Since multiple studies show that TADs and chromatin loops disappear without CTCF10,14 and cohesin,11,13–15 we reasoned that the most stable protein of CTCF and cohesin should set an upper limit on the stability of TADs and chromatin loops.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [11]
In the citing paper
“In contrast, cohesin loss leads to disappearance of TADs because extrusion no longer takes place.11,13–15”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [11]
In the citing paper
“although CTCF and cohesin both appear absolutely required for the formation of most TADs10-15”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [11]
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RetractedRodríguez-Carballo, E., Lopez‐Delisle, L., Yakushiji‐Kaminatsui, N., Ullate‐Agote, A., & Duboule, D. (2019) · BMC Biology · doi:10.1186/s12915-019-0677-x · Cited by 22
Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D
Nathanailidou, P., Taraviras, S. L., & Lygerou, Z. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.07.003 · Cited by 28
Characterizing chromatin folding coordinate and landscape with deep learning
Xie, W. J., Qi, Y., & Zhang, B. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008262 · Cited by 23
Barajas-Mora, E. M., Lee, L., Lu, H., Valderrama, J. A., Bjånes, E., Nizet, V., Feeney, A. J., Hu, M., & Murre, C. (2023) · Nature Immunology · doi:10.1038/s41590-022-01402-z · Cited by 26
Mechanism of phase condensation for chromosome architecture and function
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Cohesin forms fountains at active enhancers in C. elegans
Lüthi, B. N., Semple, J. I., Haemmerli, A., Thapliyal, S., Ghadage, K., Stojanovski, K., D’Asaro, D., Das, M., Gilbert, N., Glauser, D. A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-67302-6 · Cited by 28
Roles for Non-coding RNAs in Spatial Genome Organization
Khosraviani, N., Ostrowski, L., & Mekhail, K. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00336 · Cited by 27
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Competition Between Transcription and Loop Extrusion Modulates Promoter and Enhancer DynamicsPreprint
Platania, A., Erb, C., Barbieri, M., Molcrette, B., Grandgirard, E., de Kort, M. A. C., Meaburn, K. J., Taylor, T., Shchuka, V. M., Kocanova, S., et al. (2023) · SSRN Electronic Journal · doi:10.1101/2023.04.25.538222 · Cited by 32
SAFB restricts contact domain boundaries associated with L1 chimeric transcription
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Polycomb proteins as organizers of 3D genome architecture in embryonic stem cells
Pachano, T., Crispatzu, G., & Rada-Iglesias, Á. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz022 · Cited by 25
3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells
Papadogkonas, G., Papamatheakis, D.-A., & Spilianakis, C. G. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.921375 · Cited by 25
Postmitotic differentiation of human monocytes requires cohesin-structured chromatin
Minderjahn, J., Fischer, A. H., Maier, K., Mendes, K., Nuetzel, M., Raithel, J., Stanewsky, H., Ackermann, U., Månsson, R., Gebhard, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31892-2 · Cited by 24
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Three-dimensional nuclear organization in Arabidopsis thaliana
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SARS-CoV-2 Restructures the Host Chromatin ArchitecturePreprint
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Regulation of CTCF loop formation during pancreatic cell differentiation
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EBF1, PAX5, and MYC: regulation on B cell development and association with hematologic neoplasms
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Cohesin supercoils DNA during loop extrusion
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Functional genomic approaches to elucidate the role of enhancers during development
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A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6
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A cohesive look at leukemogenesis: The cohesin complex and other driving mutations in AML
Heimbruch, K. E., Meyer, A. E., Agrawal, P., Viny, A. D., & Rao, S. (2021) · Neoplasia · doi:10.1016/j.neo.2021.01.003 · Cited by 23
Metadata
- Authors
- Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., & Spitz, F.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Massachusetts Institute of Technology (US)
- Centre National de la Recherche Scientifique (FR)
- European Bioinformatics Institute (GB)
- Corresponding author
- Mirny, Leonid
- ORCID
- Venue
- Nature
- Published
- 2017-09-27
- Volume
- 551
- Issue
- 7678
- Pages
- 51-56
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5687303
- OpenAlex
- W2757387674
- Cited by
- 1,196
- References
- 78
- Citations by year
- 2026: 83 · 2025: 121 · 2024: 114 · 2023: 120 · 2022: 142 · 2021: 158 · 2020: 153 · 2019: 159 · 2018: 113 · 2017: 32
- FWCI
- 51.52
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- National Science Foundation (1504942)
- European Molecular Biology Laboratory
- European Commission (305626)
- Deutsche Forschungsgemeinschaft (1331/3-1, SP 1331/3-1)
- National Institutes of Health (DK 107980)
- National Institute of General Medical Sciences (R01GM114190)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK107980)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- chromatin organization, topologically associating domains, cohesin, NIPBL, loop extrusion, enhancer-promoter interactions, 3D genome organization, chromatin state, CTCF, interphase chromosomes, hepatocytes, genome compartmentalization
- MeSH terms
- Cohesins, Animals, Chromatin, Chromosomal Proteins, Non-Histone, Enhancer Elements, Genetic, Liver, Transcription Factors, Transcription, Genetic, Cell Cycle Proteins, Epigenesis, Genetic, Chromosome Positioning, Mice
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