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The mechanisms by which such elements work are largely unknown. Two SEs termed DR\/DQ-SE and XL9-SE are situated within the human MHC class II locus between the HLA-DRB1 and HLA-DQA1 genes and are highly enriched for disease-causing SNPs. To test the function of these elements, we used CRISPR\/Cas9 to generate a series of mutants that deleted the SE. Deletion of DR\/DQ-SE resulted in reduced expression of HLA-DRB1 and HLA-DQA1 genes. The SEs were found to interact with each other and the promoters of HLA-DRB1 and HLA-DQA1. DR\/DQ-SE also interacted with neighboring CTCF binding sites. Importantly, deletion of DR\/DQ-SE reduced the local chromatin interactions, implying that it functions as the organizer for the local three-dimensional architecture. These data provide direct mechanisms by which an MHC-II SE contributes to expression of the locus and suggest how variation in these SEs may contribute to human disease and altered immunity.<\/jats:p>","DOI":"10.1084\/jem.20190668","type":"journal-article","created":{"date-parts":[[2019,11,21]],"date-time":"2019-11-21T19:37:07Z","timestamp":1574365027000},"update-policy":"https:\/\/doi.org\/10.1084\/jem.crossmarkpolicy","source":"Crossref","is-referenced-by-count":32,"title":["A super enhancer controls expression and chromatin architecture within the MHC class II locus"],"prefix":"10.1084","volume":"217","author":[{"given":"Parimal","family":"Majumder","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7140-633X","authenticated-orcid":false,"given":"Joshua T.","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6306-4584","authenticated-orcid":false,"given":"Andrew R.","family":"Rahmberg","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaurav","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tian","family":"Mi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7716-8504","authenticated-orcid":false,"given":"Christopher D.","family":"Scharer","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2432-1840","authenticated-orcid":false,"given":"Jeremy M.","family":"Boss","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"291","published-online":{"date-parts":[[2019,11,21]]},"reference":[{"key":"2023072610010157800_bib1","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1084\/jem.157.3.1053","article-title":"Human B cell variants immunoselected against a single Ia antigen subset have lost expression of several Ia antigen subsets","volume":"157","author":"Accolla","year":"1983","journal-title":"J. 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