ArticleCell2018
The Energetics and Physiological Impact of Cohesin Extrusion.
Erratum issuedOpen access · bronzeAbstract read
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Article in Cell, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 295 papers.
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295citing papers in PubMed
73.2field-weighted citation impact, top 1% of its field
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Who cites it
295 citing papers in PubMed, 619 citations in OpenAlex.
- Roles of meiotic and mitotic cohesin in stem cell gene regulation and genome stability.Molecular therapy. Nucleic acids · 2026Review
- Folding a broken genome: the versatile roles of cohesin in genome maintenance.Nature reviews. Genetics · 2026Review
- Unraveling the lexicon of complex mutational phenomena in human cancers.Nature cancer · 2026Review
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- Systematic evaluation of the heterogeneity of topologically associating domain boundaries in a large genomic context in humans.NAR genomics and bioinformatics · 2026Article
- Chiron3D: an interpretable deep learning framework for understanding the DNA code of chromatin looping.Bioinformatics (Oxford, England) · 2026Article
- High-resolution chromatin mapping reveals that CTCF anchors meiotic loops to the chromosome axis.Nature communications · 2026Article
- A hierarchy of spatial confinements governs chromatin dynamics and genomic encounters.bioRxiv : the preprint server for biology · 2026Article
- Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring.Molecular biology and evolution · 2026Article
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.Molecular cell · 2026Article
- Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells.bioRxiv : the preprint server for biology · 2026Article
- Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.Briefings in bioinformatics · 2026Article
- Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae.The EMBO journal · 2026Article
- Sequence design for three-dimensional genome folding using Akita Semifreddo.bioRxiv : the preprint server for biology · 2026Article
- Igh nuclear speckle association promotes V(D)J recombination.Nature communications · 2026Article
- RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions.Nature communications · 2026Article
- 3D genetic architecture of schizophrenia risk across three neuronal subtypes.Molecular psychiatry · 2026Article
- A functional overlap between actively transcribed genes and chromatin insulator elements.The EMBO journal · 2026Article
- DIS3 mutations enhance AID-driven translocations during B-cell activation, promoting transformation to multiple myeloma.Nature communications · 2026Article
235 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
33 authors at 7 institutions in 2 countries.
Laura VianLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Aleksandra PękowskaLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Suhas S P RaoThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Kyong-Rim Kieffer-KwonLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Seolkyoung JungLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Laura BaranelloGene Regulation, Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA.
Su-Chen HuangThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Laila El KhattabiLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Marei DoseLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Nathanael PruettLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Adrian L SanbornThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
Andres CanelaLaboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA.
Yaakov MamanLaboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA.
Anna OksanenLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Wolfgang ReschLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Xingwang LiThe Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA.
Byoungkoo LeeThe Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA.
Alexander L KovalchukLaboratory of Immunogenetics, NIAID, NIH, Rockville, MD 20852, USA.
Zhonghui TangThe Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA.
Steevenson NelsonLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.
Michele Di PierroCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
Ryan R ChengCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
Ido MacholThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Brian Glenn St HilaireThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Neva C DurandThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Muhammad S ShamimThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Elena K StamenovaThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
José N OnuchicCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
Yijun RuanThe Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA.
Andre NussenzweigLaboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA.
David LevensGene Regulation, Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA.
Erez Lieberman AidenThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China. Electronic address: erez@erez.com.
Rafael CasellasLymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA. Electronic address: rafael.casellas@nih.gov.
National Institute of Arthritis and Musculoskeletal and Skin Diseases · USBaylor College of Medicine · USUniversity of Connecticut · USCenter for Theoretical Biological Physics · USNational Human Genome Research Institute · USNational Institutes of Health · USNational Institute of Allergy and Infectious Diseases · US
Funding
Shared Resource ManagementP30CA034196 · NCI · JACKSON LABORATORY · PI Anna Karolina Palucka · 1985 to 2026
$61.9MThe genome-wide function of supercoiling and alternative DNA conformationsZIABC011011 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI LEVENS, DAVID L. · 2009 to 2025
$16.1MCenter for Cell CircuitsP50HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI REGEV, AVIV · 2011 to 2015
$15.6MCenter for Cell CircuitsRM1HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI BLAINEY, PAUL CLARK, HACOHEN, NIR · 2016 to 2020
$14.9MMolecular Biophysics Training Program at StanfordT32GM008294 · NIGMS · STANFORD UNIVERSITY · PI HUANG, KERWYN C. · 1989 to 2019
$7.4MPROGRAM IN HUMAN MOLECULAR GENETICST32GM008307 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI SHAULSKY, GAD · 1990 to 2020
$6.6MGENOME WIDE MAPPING OF LOOPS USING IN SITU HI-CUM1HG009375 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI LIEBERMAN-AIDEN, EREZ · 2017 to 2021
$4.7MNucleome Positioning System for Spatiotemporal Genome Organization and RegulationU54DK107967 · NIDDK · JACKSON LABORATORY · PI WEI, CHIA-LIN · 2015 to 2019
$3.6MExploring how the genome folds through proximity ligation and sequencingDP2OD008540 · OD · BROAD INSTITUTE, INC. · PI LIEBERMAN-AIDEN, EREZ · 2011 to 2016
$3.0MCharacterization of RNA-Chromatin Interactome by RNA-DNA Ligation and SequencingR01CA186714 · NCI · JACKSON LABORATORY · PI RUAN, YIJUN · 2014 to 2016
$2.2MAID biologyZ01AR041148 · NIAMS · NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES · PI CASELLAS, RAFAEL C · 2005 to 2008
$1.8MTranscription, Chromatin and DNA RepairZ01AR041149 · NIAMS · NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES · PI CASELLAS, RAFAEL C · 2005 to 2008
$1.8MIntramural NIH HHS Z01 AR041148Intramural NIH HHS Z01 AR041149NCI NIH HHS P30 CA034196NCI NIH HHS R01 CA186714NHGRI NIH HHS P50 HG006193NHGRI NIH HHS R25 HG007631NHGRI NIH HHS RM1 HG006193NHGRI NIH HHS UM1 HG009375NIDDK NIH HHS U54 DK107967NIGMS NIH HHS T32 GM008294NIGMS NIH HHS T32 GM008307NIH HHS DP2 OD008540
Abstract
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.
Indexed as
GenomeAdenosine TriphosphateAnimalsB-LymphocytesCCCTC-Binding FactorCell Cycle ProteinsCell LineChondroitin Sulfate ProteoglycansChromatinChromosomal Proteins, Non-HistoneChromosomesCohesinsDNA-Binding ProteinsHumansMiceMutagenesisAdenosine TriphosphateCCCTC-Binding FactorCell Cycle ProteinsChondroitin Sulfate ProteoglycansChromatinChromosomal Proteins, Non-HistoneCohesinsDNA-Binding ProteinsNipbl protein, mouseNuclear ProteinsPhosphoproteinsRad21 protein, mouseSMC3 protein, mouseTranscription Factorschromosomal translocationsclass switchingcohesinCTCFDNA damageloop extrusionNipblnuclear architecturetopoisomerase II
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