{"doi":"10.1038/nature12644","title":"A high-resolution map of the three-dimensional chromatin interactome in human cells","abstract":null,"journal":"Nature","year":2013,"id":673173,"datarank":1.0766673624292797,"base_score":7.177782416195197,"endowment":7.177782416195197,"self_citation_contribution":1.0766673624292797,"citation_network_contribution":0.0,"self_endowment_contribution":1.0766673624292797,"citer_contribution":0.0,"corpus_percentile":81.9,"corpus_rank":2493,"citation_count":1309,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":418221,"name":"Yan Li","orcid":"0000-0002-7884-8074","position":1,"is_corresponding":false},{"id":81143,"name":"Jesse R. Dixon","orcid":"0000-0002-6273-2181","position":2,"is_corresponding":false},{"id":92301,"name":"Siddarth Selvaraj","orcid":null,"position":3,"is_corresponding":false},{"id":1113576,"name":"Zhen Ye","orcid":"0009-0009-6831-5846","position":4,"is_corresponding":false},{"id":228311,"name":"Ah Young Lee","orcid":"0000-0002-3489-7798","position":5,"is_corresponding":false},{"id":1758816,"name":"Chia-An Yen","orcid":null,"position":6,"is_corresponding":false},{"id":92307,"name":"Anthony D. Schmitt","orcid":"0000-0002-3818-1156","position":7,"is_corresponding":false},{"id":1758818,"name":"Celso A. Espinoza","orcid":null,"position":8,"is_corresponding":false},{"id":868657,"name":"Bing Ren","orcid":"0000-0003-0276-8577","position":9,"is_corresponding":false},{"id":68985,"name":"Fulai Jin","orcid":"0000-0003-0025-4337","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"A high-resolution map of the three-dimensional chromatin interactome in human cells","abstract":"A large number of cis-regulatory sequences have been annotated in the human genome, but defining their target genes remains a challenge. One strategy is to identify the long-range looping interactions at these elements with the use of chromosome conformation capture (3C)-based techniques. However, previous studies lack either the resolution or coverage to permit a whole-genome, unbiased view of chromatin interactions. Here we report a comprehensive chromatin interaction map generated in human fibroblasts using a genome-wide 3C analysis method (Hi-C). We determined over one million long-range chromatin interactions at 5-10-kb resolution, and uncovered general principles of chromatin organization at different types of genomic features. We also characterized the dynamics of promoter-enhancer contacts after TNF-α signalling in these cells. Unexpectedly, we found that TNF-α-responsive enhancers are already in contact with their target promoters before signalling. Such pre-existing chromatin looping, which also exists in other cell types with different extracellular signalling, is a strong predictor of gene induction. Our observations suggest that the three-dimensional chromatin landscape, once established in a particular cell type, is relatively stable and could influence the selection or activation of target genes by a ubiquitous transcription activator in a cell-specific manner.","is_dataset_classified":null,"base_score":7.177782416195197,"endowment":7.177782416195197,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24141950","pmcid":"PMC3838900","openalex_id":"https://openalex.org/W2065006553","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"T32 GM007198","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"P50 GM085764","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"P50 GM085764-03","title":null},{"funder_name":"NIEHS NIH HHS","grant_id":"U01 ES017166","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"T32 GM008666","title":null},{"funder_name":"National Institutes of Health","grant_id":"5U01ES017166-02","title":"The San Diego Epigenome Center"},{"funder_name":"National Institutes of Health","grant_id":"3P50GM085764-03S1","title":"Center for Systems Biology of Cellular Stress Responses"}],"total_grants":7,"fwci":51.5316,"citation_percentile":0.99944158,"influential_citations":0,"citation_trend":[{"year":2013,"count":3},{"year":2014,"count":98},{"year":2015,"count":128},{"year":2016,"count":146},{"year":2017,"count":139},{"year":2018,"count":141},{"year":2019,"count":135},{"year":2020,"count":133},{"year":2021,"count":124},{"year":2022,"count":68},{"year":2023,"count":65},{"year":2024,"count":59},{"year":2025,"count":52},{"year":2026,"count":17}],"oa_status":"closed","license":"Springer TDM","oa_locations":[{"url":"http://www.nature.com/articles/nature12644.pdf","host_type":"publisher"},{"url":"http://www.nature.com/articles/nature12644","host_type":"publisher"},{"url":"https://doi.org/10.1038/nature12644","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/24141950","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3838900","host_type":"repository"},{"url":"https://www.nature.com/articles/nature12644","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC3838900","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3838900?pdf=render","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/pmc3838900?pdf=render","host_type":""},{"url":"http://dx.doi.org/10.1038/nature12644","host_type":""},{"url":"https://dx.doi.org/10.1038/nature12644","host_type":""}],"fields_of_study":["Genomics and Chromatin Dynamics","Plant Molecular Biology Research","RNA Research and Splicing","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Cell Line","Chromatin","Chromosome Mapping","Enhancer Elements, Genetic","Gene Expression Regulation","Humans","Promoter Regions, Genetic","Protein Binding","Tumor Necrosis Factor-alpha","Signal Transduction","Genome, Human","Imaging, Three-Dimensional"],"keywords":["Chromatin","ChIA-PET","Enhancer","Chromosome conformation capture","Bivalent chromatin","Biology","Computational biology","CTCF","Scaffold/matrix attachment region","Genome","Interactome","Gene","Transcription factor","Genetics","Promoter","ChIP-sequencing","Human genome","Chromatin remodeling","Gene expression","Genome, Human","Tumor Necrosis Factor-alpha","Chromosome Mapping","Article","Cell Line","Enhancer Elements, Genetic","Imaging, Three-Dimensional","Gene Expression Regulation","Humans","Promoter Regions, Genetic","Protein Binding","Signal Transduction"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-16T12:36:25.582733Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}