The DOI matches its Crossref record; 56 of the 57 references it cites were found in a registry or an index.
The Energetics and Physiological Impact of Cohesin Extrusion
Open accessAbstract
Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural "stripes," where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.
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In the citing paper
“Stripe domains tend to anchor at a single CTCF binding site (as opposed to two divergent CTCF sites in the classic case for TADs), which points towards a nearby site for the cohesin-loading factor NIPBL [456, 457].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [456]
In the citing paper
“The presence of so-called stripes or flames on Hi-C maps indicates that unidirectional extrusion from an enhancer is quite common [116,117,118].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [116]
In the citing paper
“The stripes were enriched in super enhancers (Extended Data Fig. 8a-8b), consistent with previous findings 34.”
From Subtype-specific 3D genome alteration in acute myeloid leukaemia (2022) · cites this paper as [34]
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Metadata
- Authors
- Vian, L., Pękowska, A., Rao, S. S. P., Kieffer-Kwon, K.-R., Jung, S., Baranello, L., Huang, S.-C., El Khattabi, L., Dose, M., Pruett, N., Sanborn, A. L., Canela, A., Maman, Y., Oksanen, A., Resch, W., Li, X., Lee, B., Kovalchuk, A. L., Tang, Z., Nelson, S., Di Pierro, M., Cheng, R. R., Machol, I., St Hilaire, B. G., Durand, N. C., Shamim, M. S., Stamenova, E. K., Onuchic, J. N., Ruan, Y., Nussenzweig, A., Levens, D., Aiden, E. L., & Casellas, R.
- Affiliations
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (US)
- Baylor College of Medicine (US)
- National Institutes of Health (US)
- University of Connecticut (US)
- Center for Theoretical Biological Physics (US)
- Corresponding author
- Aiden, Erez Lieberman
- Casellas, Rafael
- ORCID
- Pękowska, Aleksandra
- Rao, Suhas S.P.
- Jung, Seolkyoung
- Baranello, Laura
- Dose, Marei
- Pruett, Nathanael
- Sanborn, Adrian L.
- Maman, Yaakov
- Resch, Wolfgang
- Li, Xingwang
- Lee, Byoungkoo
- Kovalchuk, Alexander L.
- Tang, Zhonghui
- Cheng, Ryan R.
- Machol, Ido
- Durand, Neva C.
- Shamim, Muhammad S.
- Onuchic, José N.
- Ruan, Yijun
- Levens, David
- Aiden, Erez Lieberman
- Casellas, Rafael
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-05
- Volume
- 173
- Issue
- 5
- Pages
- 1165-1178.e20
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6251724
- OpenAlex
- W2800216985
- Cited by
- 581
- References
- 57
- Citations by year
- 2026: 48 · 2025: 57 · 2024: 63 · 2023: 65 · 2022: 68 · 2021: 90 · 2020: 78 · 2019: 80 · 2018: 32
- FWCI
- 25.16
- Type
- journal article
- Language
- en
- Update notices
- erratum (2018-09-20)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- UWA Profiles and Research Repository (UWA) (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- NIAMS, NCI
- NIAID
- NIH Helix Systems
- Paul and Daisy Soros Fellowship
- Fannie and John Hertz Foundation Fellowship
- Cornelia de Lange Syndrome Foundation
- NIH New Innovator Award (1DP2OD008540-01)
- NSF Physics Frontiers Center Award (PHY-1427654)
- NHGRI Center for Excellence for Genomic Sciences (HG006193)
- Welch Foundation (Q-1866, C-1792)
- NVIDIA Research Center Award
- IBM University Challenge Award
- Google Research Award
- Cancer Prevention Research Institute of Texas Scholar Award (R1304)
- USDA Agriculture and Food Research Initiative Grant (2017-05741)
- McNair Medical Institute Scholar Award
- NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375)
- President’s Early Career Award in Science and Engineering
- NSF (PHY-1427654, CHE-1614101)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- 3D genome organization, super-enhancers, chromosomal translocation, plasmacytoma, oncogene deregulation
- MeSH terms
- CCCTC-Binding Factor, Cohesins, Adenosine Triphosphate, Animals, B-Lymphocytes, Cell Line, Chromatin, Chromosomal Proteins, Non-Histone, Chromosomes, DNA-Binding Proteins, Humans, Nuclear Proteins, Phosphoproteins, Chondroitin Sulfate Proteoglycans, Transcription Factors, Transcription, Genetic, Mutagenesis, Genome, Cell Cycle Proteins, Mice
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