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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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Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication
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ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL
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Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization
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SMCHD1 Merges Chromosome Compartments and Assists Formation of Super-Structures on the Inactive X
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Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion
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Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis
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WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation
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Cohesin is required for long-range enhancer action at the Shh locus
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Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA
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Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos
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Loop extrusion: theory meets single-molecule experiments
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Self-citationHow subtle changes in 3D structure can create large changes in transcription
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Hi-C analyses with GENOVA: a case study with cohesin variants
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Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning
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Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase
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Enhancer release and retargeting activates disease-susceptibility genes
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Chromosome organization by one-sided and two-sided loop extrusion
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Self-citation
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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