biostudies-literatureUnknown4D Nucleome ConsortiumNIDDK NIH HHSNIDA NIH HHSNHLBI NIH HHSNHGRI NIH HHSNCI NIH HHSNIGMS NIH HHSThe dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connecbioRxiv : the preprint server for biology2024.09.17.613111https://www.ebi.ac.uk/biostudies/studies/S-EPMC11526861biostudies-literatureAn integrated view of the structure and function of the human 4D nucleome.PMC11526861U54 DK107980U01 DK127405U01 CA200059U54 DK107981U01 CA200147UM1 HG011593U01 DA040612U01 CA200060UM1 HG011585UM1 HG011536U01 HL129998T32 GM008042U01 DK127420U54 DK107977U54 DK107967U54 DK107979U01 DA052715U01 DA052769U01 HL130007U01 HL157989U54 DK107965Wen XRuan YAbraham AAlver BHWu QZhang LKumar PZhang RPlewczynski DBhat PKrietenstein Nvan Steensel BZhan YChien SWillemin AWinick-Ng WGibcus JHWang PYue FDekker JMinsk MKWang TCook ALWang XWang YOksuz BAEsposito AYang LLi DNoble WSPark PBarnett RJvan Schaik TSzczepinska TXu JConte MNavelkar RSzabo DLi YYang YZhong SRando OJHu MBrueckner LYildirim AGilbert DM4D Nucleome ConsortiumLiu JYu MBelmont ASKukalev ALee LZhao WSasaki TBianco SPollard KSKim MNicodemi MLiu YBoninsegna LJanssens DHHenikoff SPombo AZhao PVeit AThieme CJKempfer REmerson DJSchroeder AGehlenborg NAlber FSengupta KPhillips-Cremins JEKuang SPeric-Hupkes DVenev SVQuinodoz SAChai HGuttman MRen BMarchal CZhang YEhmsen SChilinski MMa JBakker CAzcarate IIRonchetti WChiariello AMfalseAn integrated view of the structure and function of the human 4D nucleome.The dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connec2024-01-01T00:00:00Z2024 Oct2026-06-03T03:14:12.926Z2025-04-19T04:26:19.865ZS-EPMC115268613948444610.1101/2024.09.17.613111