{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["4D Nucleome Consortium"],"funding":["NIDDK NIH HHS","NIDA NIH HHS","NHLBI NIH HHS","NHGRI NIH HHS","NCI NIH HHS","NIGMS NIH HHS"],"pubmed_abstract":["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 connec"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2024.09.17.613111"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11526861"],"repository":["biostudies-literature"],"pubmed_title":["An integrated view of the structure and function of the human 4D nucleome."],"pmcid":["PMC11526861"],"funding_grant_id":["U54 DK107980","U01 DK127405","U01 CA200059","U54 DK107981","U01 CA200147","UM1 HG011593","U01 DA040612","U01 CA200060","UM1 HG011585","UM1 HG011536","U01 HL129998","T32 GM008042","U01 DK127420","U54 DK107977","U54 DK107967","U54 DK107979","U01 DA052715","U01 DA052769","U01 HL130007","U01 HL157989","U54 DK107965"],"pubmed_authors":["Wen X","Ruan Y","Abraham A","Alver BH","Wu Q","Zhang L","Kumar P","Zhang R","Plewczynski D","Bhat P","Krietenstein N","van Steensel B","Zhan Y","Chien S","Willemin A","Winick-Ng W","Gibcus JH","Wang P","Yue F","Dekker J","Minsk MK","Wang T","Cook AL","Wang X","Wang Y","Oksuz BA","Esposito A","Yang L","Li D","Noble WS","Park P","Barnett RJ","van Schaik T","Szczepinska T","Xu J","Conte M","Navelkar R","Szabo D","Li Y","Yang Y","Zhong S","Rando OJ","Hu M","Brueckner L","Yildirim A","Gilbert DM","4D Nucleome Consortium","Liu J","Yu M","Belmont AS","Kukalev A","Lee L","Zhao W","Sasaki T","Bianco S","Pollard KS","Kim M","Nicodemi M","Liu Y","Boninsegna L","Janssens DH","Henikoff S","Pombo A","Zhao P","Veit A","Thieme CJ","Kempfer R","Emerson DJ","Schroeder A","Gehlenborg N","Alber F","Sengupta K","Phillips-Cremins JE","Kuang S","Peric-Hupkes D","Venev SV","Quinodoz SA","Chai H","Guttman M","Ren B","Marchal C","Zhang Y","Ehmsen S","Chilinski M","Ma J","Bakker C","Azcarate II","Ronchetti W","Chiariello AM"],"additional_accession":[]},"is_claimable":false,"name":"An integrated view of the structure and function of the human 4D nucleome.","description":"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 connec","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Oct","modification":"2026-06-03T03:14:12.926Z","creation":"2025-04-19T04:26:19.865Z"},"accession":"S-EPMC11526861","cross_references":{"pubmed":["39484446"],"doi":["10.1101/2024.09.17.613111"]}}