ArticleNature2026
An integrated view of the structure and function of the human 4D nucleome.
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Article in Nature, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38citing papers in PubMed
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Who cites it
38 citing papers in PubMed.
- Mapping subcellular microenvironments using oligonucleotide-directed proximity labeling.Current opinion in chemical biology · 2026Review
- Integrative modeling of the genome structure and dynamics in fission yeast.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Nuclear speckles: a fundamental layer of gene regulation.Trends in cell biology · 2026Review
- Elucidating structure-function relationships in the mammalian nucleolus.Nature reviews. Molecular cell biology · 2026Review
- Epistemological parameters in the recent era of nuclear organization and function.Molecular biology of the cell · 2026Review
- Mega-enhancers compartmentalize transcriptionally active long genes in the brain.Nature cell biology · 2026Article
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Nuclear speckle-associated perispeckle networks partition active chromatin into gene expression niches.Cell reports · 2026Article
- Toward a 4D genome annotation of CHO cells for biomanufacturing.Trends in biotechnology · 2026Review
- Pig Matrix: a matched multiomics 3D regulatory genomics database for evolutionary and comparative analyses in pigs.Molecular biology and evolution · 2026Article
- The cardiac 4D nucleome: nuclear and chromatin dynamics across development, disease and ageing.Nature reviews. Cardiology · 2026Review
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- A foundation model to help understand the regulatory implications of 3D genome organization.Nature methods · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.Genome biology · 2026Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals.bioRxiv : the preprint server for biology · 2026Article
- Article
- In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2.Molecular & cellular proteomics : MCP · 2026Article
- 3D genome architecture and epigenetic regulation of lineage identity in advanced prostate cancer.Endocrinology · 2026Review
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Authors and funding
90 authors.
Job DekkerDepartment of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA. job.dekker@umassmed.edu.ORCID 0000-0001-5631-0698
Betul Akgol OksuzDepartment of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Yang ZhangRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
Ye WangDepartment of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
Miriam K MinskDepartment of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
Shuzhen KuangGladstone Institutes, San Francisco, CA, USA.
Liyan YangDepartment of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Johan H GibcusDepartment of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID 0000-0002-0851-7560
Nils KrietensteinNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
Oliver J RandoDepartment of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID 0000-0003-1516-9397
Jie XuDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA.
Derek H JanssensBasic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0003-1079-9525
Steven HenikoffHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0000-0002-7621-8685
Alexander KukalevEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.ORCID 0000-0001-5847-3773
Willemin AndréaEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.ORCID 0000-0002-4370-6914
Warren Winick-NgEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.ORCID 0000-0002-8716-5558
Rieke KempferEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
Ana PomboEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.ORCID 0000-0002-7493-6288
Miao YuDepartment of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.ORCID 0009-0003-2147-3413
Pradeep KumarDepartment of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.ORCID 0000-0002-1060-1286
Liguo ZhangDepartment of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Andrew S BelmontDepartment of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.ORCID 0000-0002-6540-0801
Takayo SasakiSan Diego Biomedical Research Institute, San Diego, CA, USA.ORCID 0000-0001-7609-9316
Tom van SchaikDivision of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Laura BruecknerDivision of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Daan Peric-HupkesDivision of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Bas van SteenselDivision of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.ORCID 0000-0002-0284-0404
Ping WangDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA.
Haoxi ChaiLife Sciences Institute, Zhejiang University, Hangzhou, P.R. China.
Minji KimDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.ORCID 0000-0002-7282-8224
Yijun RuanLife Sciences Institute, Zhejiang University, Hangzhou, P.R. China.ORCID 0009-0008-5273-5195
Ran ZhangDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Sofia A QuinodozDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID 0000-0003-1862-5204
Prashant BhatDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID 0000-0003-3832-4871
Mitchell GuttmanDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID 0000-0003-4748-9352
Wenxin ZhaoShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Shu ChienShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-0332-285X
Yuan LiuShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-1835-6147
Sergey V VenevDepartment of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID 0000-0002-1507-7460
Dariusz PlewczynskiLaboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.ORCID 0000-0002-3840-7610
Ibai Irastorza AzcarateEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
Dominik SzabóEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
Christoph J ThiemeEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.ORCID 0000-0002-1566-0971
Teresa SzczepińskaEpigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.ORCID 0000-0001-9749-1253
Mateusz ChilińskiLaboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.ORCID 0000-0001-6641-8504
Kaustav SenguptaLaboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.
Mattia ConteDepartment of Physics, University of Naples "Federico II", and INFN, Naples, Italy.ORCID 0000-0002-6670-9800
Andrea EspositoDepartment of Physics, University of Naples "Federico II", and INFN, Naples, Italy.ORCID 0000-0002-5903-8439
Alex AbrahamDepartment of Physics, University of Naples "Federico II", and INFN, Naples, Italy.
Ruochi ZhangRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.ORCID 0000-0002-1103-5044
Yuchuan WangRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
Xingzhao WenProgram in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-1463-0359
Qiuyang WuShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Yang YangRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
Jie LiuDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Lorenzo BoninsegnaDepartment of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
Asli YildirimDepartment of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
Yuxiang ZhanDepartment of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
Andrea Maria ChiarielloDepartment of Physics, University of Naples "Federico II", and INFN, Naples, Italy.ORCID 0000-0002-6112-0167
Simona BiancoDepartment of Physics, University of Naples "Federico II", and INFN, Naples, Italy.ORCID 0000-0001-5819-060X
Lindsay LeeDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
Ming HuDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.ORCID 0000-0003-0987-2916
Yun LiDepartment of Biostatistics, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.ORCID 0000-0002-9275-4189
R Jordan BarnettDepartment of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
Ashley L CookDepartment of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
Daniel J EmersonDepartment of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
Claire MarchalIn silichrom Ltd, Newbury, UK.
Peiyao ZhaoSan Diego Biomedical Research Institute, San Diego, CA, USA.
Peter J ParkDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID 0000-0001-9378-960X
Burak H AlverDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID 0000-0002-5019-7652
Andrew J SchroederDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Rahi NavelkarDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Clara BakkerDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID 0000-0001-9600-4628
William RonchettiDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Shannon EhmsenDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Alexander D VeitDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Nils GehlenborgDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Ting WangDepartment of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.ORCID 0000-0002-6800-242X
Daofeng LiDepartment of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.ORCID 0000-0001-7492-3703
Xiaotao WangDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA. wangxiaotao@fudan.edu.cn.ORCID 0000-0002-3531-2157
Mario NicodemiDepartment of Physics, University of Naples "Federico II", and INFN, Naples, Italy. mario.nicodemi@na.infn.it.ORCID 0000-0002-8416-6416
Bing RenDepartment of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA. bren@nygenome.org.
Sheng ZhongShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. szhong@ucsd.edu.ORCID 0000-0001-6419-7453
Jennifer E Phillips-CreminsDepartment of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA. jennifer.cremins@wustl.edu.ORCID 0000-0002-4702-0450
David M GilbertSan Diego Biomedical Research Institute, San Diego, CA, USA. gilbert@sdbri.org.ORCID 0000-0001-8087-9737
Katherine S PollardGladstone Institutes, San Francisco, CA, USA. katherine.pollard@gladstone.ucsf.edu.ORCID 0000-0002-9870-6196
Frank AlberDepartment of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA. falber@g.ucla.edu.
Jian MaRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. jianma@cs.cmu.edu.ORCID 0000-0002-4202-5834
William S NobleDepartment of Genome Sciences, University of Washington, Seattle, WA, USA. william-noble@uw.edu.ORCID 0000-0001-7283-4715
Feng YueDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA. Yue@northwestern.edu.ORCID 0000-0002-7954-5462
Funding
4D Nucleome Network Data Coordination and Integration CenterU01CA200059 · NCI · HARVARD MEDICAL SCHOOL · PI PARK, PETER J · 2015 to 2024
$24.4MThe second phase of NIH Common Fund 4D Nucleome Network Organizational HubU01CA200147 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZHONG, SHENG · 2015 to 2024
$22.0MCenter for 3D Structure and Physics of the GenomeU54DK107980 · NIDDK · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI DEKKER, JOB, MIRNY, LEONID A · 2015 to 2019
$14.9MUniversity of Washington Center for Nuclear Organization and FunctionU54DK107979 · NIDDK · UNIVERSITY OF WASHINGTON · PI NOBLE, WILLIAM STAFFORD · 2015 to 2019
$11.8MCenter for 3D Structure and Physics of the GenomeUM1HG011536 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI DEKKER, JOB, MIRNY, LEONID A · 2020 to 2024
$11.8MMultiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data IntegrationUM1HG011593 · NHGRI · CARNEGIE-MELLON UNIVERSITY · PI ALBER, FRANK, BELMONT, ANDREW STEVEN · 2020 to 2024
$10.4MSan Diego Center for 4D Nucleome ResearchU54DK107977 · NIDDK · LUDWIG INSTITUTE FOR CANCER RES LTD · PI MURRE, CORNELIS, REN, BING · 2015 to 2019
$9.4MMapping Technology DevelopmentU54DK107965 · NIDDK · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI BELMONT, ANDREW STEVEN · 2015 to 2019
$8.6MCenter for Integrated Multi-modal and Multi-scale Nucleome ResearchUM1HG011585 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DULAC, CATHERINE, LEIN, ED · 2020 to 2024
$6.7MDynamics of chromosome organization and chromatin states in single cellsU01DK127420 · NIDDK · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAI, LONG, ELOWITZ, MICHAEL B · 2020 to 2024
$5.7MEngineering and Imaging 3D genome structure-function dynamics across time scalesU01DK127405 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI BLOBEL, GERD A, PHILLIPS-CREMINS, JENNIFER ELIZABETH · 2020 to 2024
$5.7MMapping the 3D Genome LandscapeU54DK107981 · NIDDK · UNIVERSITY OF SOUTHERN CALIFORNIA · PI ALBER, FRANK · 2015 to 2019
$4.2MNCI NIH HHS U01 CA200059NCI NIH HHS U01 CA200060NCI NIH HHS U01 CA200147NHGRI NIH HHS R00 HG013343NHGRI NIH HHS UM1 HG011536NHGRI NIH HHS UM1 HG011585NHGRI NIH HHS UM1 HG011593NHLBI NIH HHS U01 HL129998NHLBI NIH HHS U01 HL130007NHLBI NIH HHS U01 HL157989NIDA NIH HHS U01 DA040612NIDA NIH HHS U01 DA052715NIDA NIH HHS U01 DA052769NIDDK NIH HHS U01 DK127405NIDDK NIH HHS U01 DK127420NIDDK NIH HHS U54 DK107965NIDDK NIH HHS U54 DK107967NIDDK NIH HHS U54 DK107977NIDDK NIH HHS U54 DK107979NIDDK NIH HHS U54 DK107980NIDDK NIH HHS U54 DK107981
Abstract
The dynamic three-dimensional (3D) organization of the human genome (the 4D nucleome) is linked to genome function. Here we describe efforts by the 4D Nucleome Project
Indexed as
Cell NucleusGenome, HumanCell LineChromatinDNA ReplicationFibroblastsGenomicsHuman Embryonic Stem CellsHumansSingle-Cell AnalysisTranscription, GeneticChromatin
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