ArticleScience (New York, N.Y.)2021
3D genomics across the tree of life reveals condensin II as a determinant of architecture type.
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Article in Science (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 173 papers.
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173citing papers in PubMed
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173 citing papers in PubMed, 295 citations in OpenAlex.
- Condensin complexes: from chromatin organization to disease.Nucleus (Austin, Tex.) · 2026Review
- Single-molecule chromatin tracing reveals a diversity of megabase heterochromatin domains.Nature structural & molecular biology · 2026Article
- A translocation within the Ogataea species complex alters local subtelomeric chromatin while maintaining overall genome organization.G3 (Bethesda, Md.) · 2026Article
- Modified meiosis in the tardigrade Hypsibius exemplaris maintains heterozygosity across the genome.Genetics · 2026Article
- Non-coding DNA dynamics and its roles as a physical barrier in genome safeguarding across early development and evolution.Heredity · 2026Review
- Applying the Poincaré Disc Method to Analyze the Hierarchical Structure of TADs in Hi-C Data.Genes · 2026Article
- A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species.Nature methods · 2026Article
- Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea.Nature communications · 2026Article
- Annotating Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients.bioRxiv : the preprint server for biology · 2026Article
- Modified meiosis in the tardigradebioRxiv : the preprint server for biology · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Divergent 3D genome architecture of male germ cells across vertebrates.Nature communications · 2026Article
- First genome-wide centromere map of Trypanosoma cruzi suggests linear and 3D compartment boundaries and spatial clustering.BMC genomics · 2026Article
- Structural basis of condensin II activation.Research square · 2026Article
- Condensin I but not Condensin II is crucial for mitotic chromosome mechanics.Nature communications · 2026Article
- Condensin IDC has a functional ATPase that is required for X-Chromosome dosage compensation in C. elegans.Genetics · 2026Article
- Article
- The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.Nucleic acids research · 2026Article
- Exploring the energy landscape of bacterial chromosome segregation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A Translocation within thebioRxiv : the preprint server for biology · 2026Article
113 more citing papers are in PubMed but not listed here.
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Authors and funding
64 authors at 20 institutions in 11 countries.
Claire Hoencamp *Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0003-2047-4724
Olga Dudchenko *The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0001-9163-9544
Ahmed M O Elbatsh *Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0001-8012-3999
Sumitabha Brahmachari *Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.ORCID 0000-0002-9091-6180
Jonne A Raaijmakers *Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0003-1759-8347
Tom van Schaik *Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0001-7850-5074
Ángela Sedeño Cacciatore *Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0002-2751-0428
Vinícius G Contessoto *Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.ORCID 0000-0002-1891-9563
Roy G H P van Heesbeen *Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Bram van den BroekBioImaging Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0003-1037-907X
Aditya N MhaskarDivision of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0002-9323-437X
Hans TeunissenDivision of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Brian Glenn St HilaireThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
David WeiszThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0001-5868-6672
Arina D OmerThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0003-1336-2505
Melanie PhamThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0002-6083-271X
Zane ColaricThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Zhenzhen YangShanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China.
Suhas S P RaoThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Namita MitraThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Christopher LuiThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0002-2904-6745
Weijie YaoThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Ruqayya KhanThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0001-7549-8761
Leonid L MorozWhitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA.ORCID 0000-0002-1333-3176
Andrea KohnWhitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA.
Judy St LegerDepartment of Biosciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA.ORCID 0000-0002-6213-3429
Alexandria MenaSeaWorld San Diego, San Diego, CA 92109, USA.
Karen HolcroftMoody Gardens, Galveston, TX 77554, USA.
Maria Cristina GambettaCenter for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.ORCID 0000-0002-9450-3551
Fabian LimDepartment of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.ORCID 0000-0001-5628-7707
Emma FarleyDepartment of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.ORCID 0000-0002-9241-247X
Nils SteinLeibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), 06466 Seeland, Germany.ORCID 0000-0003-3011-8731
Alexander HaddadThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Daniel ChaussNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Ayse Sena MutluDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0002-2849-7210
Meng C WangDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0002-5898-6007
Neil D YoungFaculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia.ORCID 0000-0001-8756-229X
Evin HildebrandtAvian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA.ORCID 0000-0002-2149-3970
Hans H ChengAvian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA.ORCID 0000-0003-2071-4644
Christopher J KnightHopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA.ORCID 0000-0002-7522-4127
Theresa L U BurnhamDepartment of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA.ORCID 0000-0002-5641-737X
Kevin A HovelCoastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA.ORCID 0000-0002-1643-1847
Andrew J BeelDepartment of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.ORCID 0000-0002-3044-0651
Pierre-Jean MatteiDepartment of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Roger D KornbergDepartment of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.ORCID 0000-0002-2425-7519
Wesley C WarrenDepartment of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.ORCID 0000-0003-2255-2730
Gregory CaryThe Jackson Laboratory, Bar Harbor, ME 04609, USA.ORCID 0000-0003-3573-5229
José Luis Gómez-SkarmetaCentro Andaluz de Biología del Desarrollo CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain.
Veronica HinmanDepartment of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.ORCID 0000-0003-3414-1357
Kerstin Lindblad-TohBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0001-8338-0253
Federica Di PalmaDepartment of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
Kazuhiro MaeshimaGenome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.ORCID 0000-0003-3909-0341
Asha S MultaniDepartment of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.ORCID 0000-0002-6989-8627
Sen PathakDepartment of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.ORCID 0000-0002-2458-6048
Liesl Nel-ThemaatDepartment of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Richard R BehringerDepartment of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Parwinder KaurUWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.ORCID 0000-0003-0201-0766
René H MedemaDivision of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Bas van SteenselDivision of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0002-0284-0404
Elzo de WitDivision of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.ORCID 0000-0003-2883-1415
José N OnuchicCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.ORCID 0000-0002-9448-0388
Michele Di PierroCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.ORCID 0000-0002-2889-2632
Erez Lieberman AidenThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA. b.rowland@nki.nl erez@erez.com.ORCID 0000-0003-0634-6486
Benjamin D RowlandDivision of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands. b.rowland@nki.nl erez@erez.com.ORCID 0000-0002-0694-8463
Baylor College of Medicine · USOncode Institute · NLThe Netherlands Cancer Institute · NLThe University of Texas MD Anderson Cancer Center · USCenter for Theoretical Biological Physics · USStanford University · USBroad Institute · USMichigan Department of Agriculture and Rural Development · USSan Diego State University · USThe University of Western Australia · AUUniversity of California San Diego · USUniversity of Florida · USCancer Genomics Centre · NLCarnegie Mellon University · USCentro Andaluz de Biología del Desarrollo · ESCornell University · USHoward Hughes Medical Institute · USJackson Laboratory · USNational Institute of Genetics · JPNational Institutes of Health · US
Funding
Mapping Technology DevelopmentU54DK107965 · NIDDK · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI BELMONT, ANDREW STEVEN · 2015 to 2019
$8.6MDecode the chemical language that orchestrates cellular and organismal homeostasisDP1DK113644 · NIDDK · BAYLOR COLLEGE OF MEDICINE · PI WANG, MENG CARLA · 2016 to 2020
$5.5MThree-Dimensional Structure of Eukaryote ChromosomesR01DK121366 · NIDDK · STANFORD UNIVERSITY · PI LEVITT, MICHAEL · 2018 to 2021
$4.8MGENOME WIDE MAPPING OF LOOPS USING IN SITU HI-CUM1HG009375 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI LIEBERMAN-AIDEN, EREZ · 2017 to 2021
$4.7MTargeting a lipid-mediated pro-longevity pathway as Alzheimer's therapyRF1AG062257 · NIA · BAYLOR COLLEGE OF MEDICINE · PI WANG, JIN, WANG, MENG CARLA · 2018 to 2020
$4.0MSpBase: A Database System For Echinoderm Genome InformationP41HD071837 · NICHD · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAMERON, ROBERT ANDREW · 2012 to 2017
$3.0MPrebiotic Regulation of LongevityR01AT009050 · NCCIH · BAYLOR COLLEGE OF MEDICINE · PI WANG, MENG CARLA · 2016 to 2020
$2.6MDeciphering the regulatory principles governing enhancer specificityDP2HG010013 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FARLEY, EMMA KIRSTEN · 2017 to 2021
$2.5MNeighborhood SES and Emotional Distress in Old AgeR01AG022537 · NIA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ANESHENSEL, CAROL S. · 2003 to 2009
$2.4MNeuron-SELEX: Development of neuron-specific nanoscale toolkits for single-cell recognitionR01NS114491 · NINDS · UNIVERSITY OF FLORIDA · PI MOROZ, LEONID L · 2020 to 2024
$2.0MLIPID SIGNALING IN REGULATION OF LONGEVITYR01AG045183 · NIA · BAYLOR COLLEGE OF MEDICINE · PI WANG, MENG CARLA · 2013 to 2017
$1.8MNCCIH NIH HHS R01 AT009050NHGRI NIH HHS DP2 HG010013NHGRI NIH HHS UM1 HG009375NIA NIH HHS R01 AG022537NIA NIH HHS R01 AG045183NIA NIH HHS RF1 AG062257NICHD NIH HHS P41 HD071837NIDDK NIH HHS DP1 DK113644NIDDK NIH HHS R01 DK121366NIDDK NIH HHS U54 DK107965NINDS NIH HHS R01 NS114491
Abstract
We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
Indexed as
Biological EvolutionGenomeAdenosine TriphosphatasesAlgorithmsAnimalsCell NucleolusCell NucleusCentromereChromosomesChromosomes, HumanDNA-Binding ProteinsEukaryotaGenome, HumanGenomicsHeterochromatinHumansAdenosine Triphosphatasescondensin complexesDNA-Binding ProteinsHeterochromatinMultiprotein Complexes
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