{"doi":"10.1016/j.molcel.2022.01.023","title":"HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization","abstract":null,"journal":"Molecular Cell","year":2022,"id":593435,"datarank":0.6698862177981877,"base_score":4.465908118654584,"endowment":4.465908118654584,"self_citation_contribution":0.6698862177981877,"citation_network_contribution":0.0,"self_endowment_contribution":0.6698862177981877,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":86,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"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":558587,"name":"Yu Xiang","orcid":"0000-0001-9199-3383","position":1,"is_corresponding":false},{"id":1518819,"name":"Derek T. Peters","orcid":null,"position":2,"is_corresponding":false},{"id":962663,"name":"Choiselle Marius","orcid":null,"position":3,"is_corresponding":false},{"id":559684,"name":"Tongyu Sun","orcid":null,"position":4,"is_corresponding":false},{"id":559682,"name":"Ruocheng Shan","orcid":null,"position":5,"is_corresponding":false},{"id":246226,"name":"Jianhong Ou","orcid":"0000-0002-8652-2488","position":6,"is_corresponding":false},{"id":595858,"name":"Xin Lin","orcid":"0000-0001-6913-4654","position":7,"is_corresponding":false},{"id":235524,"name":"Feng Yue","orcid":"0000-0002-5856-3506","position":8,"is_corresponding":false},{"id":282280,"name":"Wei Li","orcid":"0000-0002-2163-7903","position":9,"is_corresponding":false},{"id":415273,"name":"Kevin W. Southerland","orcid":"0000-0002-0306-2130","position":10,"is_corresponding":false},{"id":249984,"name":"Yarui Diao","orcid":"0000-0001-5842-4082","position":11,"is_corresponding":false},{"id":1322357,"name":"Xiaolin Wei","orcid":"0000-0001-6313-7790","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization","abstract":"The long-range interactions of cis-regulatory elements (cREs) play a central role in gene regulation. cREs can be characterized as accessible chromatin sequences. However, it remains technically challenging to comprehensively identify their spatial interactions. Here, we report a new method HiCAR (Hi-C on accessible regulatory DNA), which utilizes Tn5 transposase and chromatin proximity ligation, for the analysis of open-chromatin-anchored interactions with low-input cells. By applying HiCAR in human embryonic stem cells and lymphoblastoid cells, we demonstrate that HiCAR identifies high-resolution chromatin contacts with an efficiency comparable with that of in situ Hi-C over all distance ranges. Interestingly, we found that the \"poised\" gene promoters exhibit silencer-like function to repress the expression of distal genes via promoter-promoter interactions. Lastly, we applied HiCAR to 30,000 primary human muscle stem cells and demonstrated that HiCAR is capable of analyzing chromatin accessibility and looping using low-input primary cells and clinical samples.","is_dataset_classified":null,"base_score":4.465908118654584,"endowment":4.465908118654584,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35196517","pmcid":"PMC8934281","openalex_id":"https://openalex.org/W4214521951","authors":[],"funders":[{"funder_name":"NHGRI NIH HHS","grant_id":"R35 HG011328","title":null},{"funder_name":"NHLBI NIH HHS","grant_id":"U01 HL156064","title":null},{"funder_name":"NCATS NIH HHS","grant_id":"UL1 TR002553","title":null}],"total_grants":3,"fwci":6.111,"citation_percentile":0.97770064,"influential_citations":0,"citation_trend":[{"year":2022,"count":10},{"year":2023,"count":12},{"year":2024,"count":32},{"year":2025,"count":22},{"year":2026,"count":10}],"oa_status":"green","license":"http://www.elsevier.com/open-access/userlicense/1.0/","oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8934281","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8934281","host_type":"repository"},{"url":"https://api.elsevier.com/content/article/PII:S1097276522000983?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S1097276522000983?httpAccept=text/plain","host_type":"publisher"},{"url":"https://doi.org/10.1016/j.molcel.2022.01.023","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/35196517","host_type":"repository"}],"fields_of_study":["Genomics and Chromatin Dynamics","RNA Research and Splicing","Chromosomal and Genetic Variations"],"mesh_terms":["Chromatin","DNA","Gene Expression Regulation","Humans","Promoter Regions, Genetic","Regulatory Sequences, Nucleic Acid"],"keywords":["Chromatin","Biology","ChIA-PET","CTCF","Computational biology","Chromosome conformation capture","Promoter","Gene","Cell biology","Genetics","Embryonic stem cell","Transposase","Genome","Gene expression","Chromatin remodeling","Enhancer","Transposable element","Chromatin organization","Chromatin Accessibility","Hicar","Silencer-like Promoter","Low-input Multi-omic"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"},{"name":"gen"},{"name":"igsr"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-27T11:00:07.325012Z","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":[]}