{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T18:56:58Z","timestamp":1778093818329,"version":"3.51.4"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,9,22]],"date-time":"2021-09-22T00:00:00Z","timestamp":1632268800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970644"],"award-info":[{"award-number":["31970644"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Huazhong Agricultural University Scientific & Technological Self-innovation Foundation","award":["11041810351"],"award-info":[{"award-number":["11041810351"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2662017JC048"],"award-info":[{"award-number":["2662017JC048"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Pujiang Program","award":["21PJ1401700"],"award-info":[{"award-number":["21PJ1401700"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Enhancer RNAs (eRNAs) are a class of non-coding RNAs transcribed from enhancers. As the markers of active enhancers, eRNAs play important roles in gene regulation and are associated with various complex traits and characteristics. With increasing attention to eRNAs, numerous eRNAs have been identified in different human tissues. However, the expression landscape, regulatory network and potential functions of eRNAs in animals have not been fully elucidated. Here, we systematically characterized 185\u00a0177 eRNAs from 5085 samples across 10 species by mapping the RNA sequencing data to the regions of known enhancers. To explore their potential functions based on evolutionary conservation, we investigated the sequence similarity of eRNAs among multiple species. In addition, we identified the possible associations between eRNAs and transcription factors (TFs) or nearby genes to decipher their possible regulators and target genes, as well as characterized trait-related eRNAs to explore their potential functions in biological processes. Based on these findings, we further developed Animal-eRNAdb (http:\/\/gong_lab.hzau.edu.cn\/Animal-eRNAdb\/), a user-friendly database for data searching, browsing and downloading. With the comprehensive characterization of eRNAs in various tissues of different species, Animal-eRNAdb may greatly facilitate the exploration of functions and mechanisms of eRNAs.<\/jats:p>","DOI":"10.1093\/nar\/gkab832","type":"journal-article","created":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T19:10:08Z","timestamp":1631301008000},"page":"D46-D53","source":"Crossref","is-referenced-by-count":26,"title":["Animal-eRNAdb: a comprehensive animal enhancer RNA database"],"prefix":"10.1093","volume":"50","author":[{"given":"Weiwei","family":"Jin","sequence":"first","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan\u00a0430070, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guanghui","family":"Jiang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan\u00a0430070, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanbo","family":"Yang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan\u00a0430070, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianye","family":"Yang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan\u00a0430070, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenqian","family":"Yang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan\u00a0430070, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan\u00a0430070, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaohui","family":"Niu","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan\u00a0430070, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rong","family":"Zhong","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhao","family":"Zhang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1895-2993","authenticated-orcid":false,"given":"Jing","family":"Gong","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan\u00a0430070, P.R. China"},{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,22]]},"reference":[{"key":"2022010507355138200_B1","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/0092-8674(83)90410-5","article-title":"Enhancer elements","volume":"33","author":"Khoury","year":"1983","journal-title":"Cell"},{"key":"2022010507355138200_B2","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nrg.2016.4","article-title":"Enhancers as non-coding RNA transcription units: recent insights and future perspectives","volume":"17","author":"Li","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"2022010507355138200_B3","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/j.ccell.2020.08.020","article-title":"A High-Resolution map of human enhancer RNA loci characterizes super-enhancer activities in cancer","volume":"38","author":"Chen","year":"2020","journal-title":"Cancer Cell"},{"key":"2022010507355138200_B4","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.gpb.2017.02.003","article-title":"Non-coding transcripts from enhancers: new insights into enhancer activity and gene expression regulation","volume":"15","author":"Chen","year":"2017","journal-title":"Genomics Proteomics Bioinform."},{"key":"2022010507355138200_B5","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.cell.2013.09.011","article-title":"Mapping human epigenomes","volume":"155","author":"Rivera","year":"2013","journal-title":"Cell"},{"key":"2022010507355138200_B6","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1101\/gad.308619.117","article-title":"The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription","volume":"32","author":"Mikhaylichenko","year":"2018","journal-title":"Genes Dev."},{"key":"2022010507355138200_B7","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1101\/gr.152306.112","article-title":"Enhancer transcripts mark active estrogen receptor binding sites","volume":"23","author":"Hah","year":"2013","journal-title":"Genome Res."},{"key":"2022010507355138200_B8","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1038\/s41594-020-0446-0","article-title":"Enhancer RNAs are an important regulatory layer of the epigenome","volume":"27","author":"Sartorelli","year":"2020","journal-title":"Nat. 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U.S.A."},{"key":"2022010507355138200_B11","doi-asserted-by":"crossref","first-page":"D932","DOI":"10.1093\/nar\/gkaa940","article-title":"HeRA: an atlas of enhancer RNAs across human tissues","volume":"49","author":"Zhang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507355138200_B12","doi-asserted-by":"crossref","first-page":"1356","DOI":"10.1002\/hep4.1413","article-title":"Novel lipid long intervening noncoding RNA, oligodendrocyte maturation-associated long intergenic noncoding RNA, regulates the liver steatosis gene stearoyl-coenzyme a desaturase as an enhancer RNA","volume":"3","author":"Benhammou","year":"2019","journal-title":"Hepatol. 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Sci."},{"key":"2022010507355138200_B15","first-page":"129","article-title":"A muscle-specific enhancer RNA mediates cohesin recruitment and regulates transcription in trans","author":"Tsai","year":"2018"},{"key":"2022010507355138200_B16","doi-asserted-by":"crossref","first-page":"4562","DOI":"10.1038\/s41467-019-12543-5","article-title":"Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer","volume":"10","author":"Zhang","year":"2019","journal-title":"Nat. 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Rep."},{"key":"2022010507355138200_B43","doi-asserted-by":"crossref","first-page":"D701","DOI":"10.1093\/nar\/gky1084","article-title":"Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB","volume":"47","author":"Hu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507355138200_B44","doi-asserted-by":"crossref","first-page":"D659","DOI":"10.1093\/nar\/gkz854","article-title":"Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation","volume":"48","author":"Yang","year":"2020","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D46\/42058098\/gkab832.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D46\/42058098\/gkab832.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T08:03:44Z","timestamp":1641369824000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D46\/6374163"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,22]]},"references-count":44,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,9,22]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab832","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,9,22]]}}}