{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T02:32:22Z","timestamp":1772245942487,"version":"3.50.1"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,1,7]],"date-time":"2022-01-07T00:00:00Z","timestamp":1641513600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012041","name":"Versus Arthritis","doi-asserted-by":"publisher","award":["21428 22053 22198"],"award-info":[{"award-number":["21428 22053 22198"]}],"id":[{"id":"10.13039\/501100012041","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"\n Background:<\/jats:bold>\n Ankylosing Spondylitis (AS) is a common form of inflammatory spinal arthritis with a complex aetiology and high heritability, involving more than 100 genetic associations. These include several AS-associated single nucleotide polymorphisms (SNPs) upstream of\n RUNX3,<\/jats:italic>\n which encodes the multifunctional RUNT-related transcription factor (TF) 3. The lead associated SNP\n rs6600247<\/jats:italic>\n (\n p<\/jats:italic>\n = 2.6 \u00d7 10\n \u221215<\/jats:sup>\n ) lies \u223c13kb upstream of the\n RUNX3<\/jats:italic>\n promoter adjacent to a c-MYC TF binding-site. The effect of\n rs6600247<\/jats:italic>\n genotype on DNA binding and chromosome looping were investigated by electrophoretic mobility gel shift assays (EMSA), Western blotting-EMSA (WEMSA) and Chromosome Conformation Capture (3C).\n <\/jats:p>\n \n Results:<\/jats:bold>\n Interrogation of ENCODE published data showed open chromatin in the region overlapping\n rs6600247<\/jats:italic>\n in primary human CD14\n +<\/jats:sup>\n monocytes, in contrast to the Jurkat T cell line or primary human T-cells. The\n rs6600247<\/jats:italic>\n AS-risk allele is predicted to specifically disrupt a c-MYC binding-site. Using a 50bp DNA probe spanning\n rs6600247<\/jats:italic>\n we consistently observed reduced binding to the AS-risk \u201cC\u201d allele of both purified c-MYC protein and nuclear extracts (NE) from monocyte-like U937 cells. WEMSA on U937 NE and purified c-MYC protein confirmed these differences (\n n<\/jats:italic>\n = 3;\n p<\/jats:italic>\n &lt; 0.05). 3C experiments demonstrated negligible interaction between the region encompassing\n rs6600247<\/jats:italic>\n and the RUNX3 promoter. A stronger interaction frequency was demonstrated between the\n RUNX3<\/jats:italic>\n promoter and the previously characterised AS-associated SNP\n rs4648889<\/jats:italic>\n .\n <\/jats:p>\n \n Conclusion:<\/jats:bold>\n The lead SNP\n rs6600247,<\/jats:italic>\n located in an enhancer-like region upstream of the\n RUNX3<\/jats:italic>\n promoter, modulates c-MYC binding. However, the region encompassing\n rs6600247<\/jats:italic>\n has rather limited physical interaction with the promoter of\n RUNX3<\/jats:italic>\n . In contrast a clear chromatin looping event between the region encompassing\n rs4648889<\/jats:italic>\n and the\n RUNX3<\/jats:italic>\n promoter was observed. These data provide further evidence for complexity in the regulatory elements upstream of the\n RUNX3<\/jats:italic>\n promoter and the involvement of\n RUNX3<\/jats:italic>\n transcriptional regulation in AS.\n <\/jats:p>","DOI":"10.3389\/fgene.2021.741867","type":"journal-article","created":{"date-parts":[[2022,1,7]],"date-time":"2022-01-07T00:29:02Z","timestamp":1641515342000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Disruption of c-MYC Binding and Chromosomal Looping Involving Genetic Variants Associated With Ankylosing Spondylitis Upstream of the RUNX3 Promoter"],"prefix":"10.3389","volume":"12","author":[{"given":"Carla J.","family":"Cohen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Connor","family":"Davidson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlo","family":"Selmi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Bowness","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julian C.","family":"Knight","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B. Paul","family":"Wordsworth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matteo","family":"Vecellio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,1,7]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1038\/nm.4370","article-title":"SNP-mediated Disruption of CTCF Binding at the IFITM3 Promoter Is Associated with Risk of Severe Influenza in Humans","volume":"23","author":"Allen","year":"2017","journal-title":"Nat. Med."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1770","DOI":"10.3389\/fimmu.2018.01770","article-title":"Armed and Ready: Transcriptional Regulation of Tissue-Resident Memory CD8 T Cells","volume":"9","author":"Behr","year":"2018","journal-title":"Front. Immunol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1016\/s0140-6736(73)91360-3","article-title":"Ankylosing Spondylitis and HL-A 27","volume":"301","author":"Brewerton","year":"1973","journal-title":"The Lancet"},{"key":"B4","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1111\/imr.12840","article-title":"Interleukin\u201023 Pathway at the Enthesis: The Emerging story of Enthesitis in Spondyloarthropathy","volume":"294","author":"Bridgewood","year":"2020","journal-title":"Immunol. Rev."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1823","DOI":"10.1002\/art.1780401015","article-title":"Susceptibility to Ankylosing Spondylitis in Twins the Role of Genes, HLA, and the Environment","volume":"40","author":"Brown","year":"1997","journal-title":"Arthritis Rheum."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1329","DOI":"10.1038\/ng.2007.17","article-title":"Association Scan of 14,500 Nonsynonymous SNPs in Four Diseases Identifies Autoimmunity Variants","volume":"39","author":"Burton","year":"2007","journal-title":"Nat. Genet."},{"key":"B7","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1097\/bor.0000000000000239","article-title":"Subclinical Gut Inflammation in Ankylosing Spondylitis","volume":"28","author":"Ciccia","year":"2016","journal-title":"Curr. Opin. Rheumatol."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aax6085","article-title":"IRF5 Guides Monocytes toward an Inflammatory CD11c+ Macrophage Phenotype and Promotes Intestinal Inflammation","volume":"5","author":"Corbin","year":"2020","journal-title":"Sci. Immunol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1038\/ng.2667","article-title":"Identification of Multiple Risk Variants for Ankylosing Spondylitis through High-Density Genotyping of Immune-Related Loci","volume":"45","author":"Cortes","year":"2013","journal-title":"Nat. Genet."},{"key":"B10","doi-asserted-by":"publisher","first-page":"7146","DOI":"10.1038\/ncomms8146","article-title":"Major Histocompatibility Complex Associations of Ankylosing Spondylitis Are Complex and Involve Further Epistasis with ERAP1","volume":"6","author":"Cortes","year":"2015","journal-title":"Nat. Commun."},{"key":"B11","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1101\/gad.179804.111","article-title":"A Decade of 3C Technologies: Insights into Nuclear Organization","volume":"26","author":"de Wit","year":"2012","journal-title":"Genes Dev."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1038\/ni.3272","article-title":"Runx3 Specifies Lineage Commitment of Innate Lymphoid Cells","volume":"16","author":"Ebihara","year":"2015","journal-title":"Nat. Immunol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1945","DOI":"10.1084\/jem.20070133","article-title":"The Role of the Runx Transcription Factors in Thymocyte Differentiation and in Homeostasis of Naive T Cells","volume":"204","author":"Egawa","year":"2007","journal-title":"J. Exp. Med."},{"key":"B14","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/ng.3528","article-title":"Analysis of Five Chronic Inflammatory Diseases Identifies 27 New Associations and Highlights Disease-specific Patterns at Shared Loci","volume":"48","author":"Ellinghaus","year":"2016","journal-title":"Nat. Genet."},{"key":"B15","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1038\/s41588-021-00816-z","article-title":"Cis-regulatory Chromatin Loops Arise before TADs and Gene Activation, and Are Independent of Cell Fate during Early Drosophila Development","volume":"53","author":"Espinola","year":"2021","journal-title":"Nat. Genet."},{"key":"B16","doi-asserted-by":"publisher","first-page":"e33313","DOI":"10.1371\/journal.pone.0033313","article-title":"RUNX3 Regulates Intercellular Adhesion Molecule 3 (ICAM-3) Expression during Macrophage Differentiation and Monocyte Extravasation","volume":"7","author":"Estecha","year":"2012","journal-title":"PloS one"},{"key":"B17","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1038\/ng.873","article-title":"Interaction between ERAP1 and HLA-B27 in Ankylosing Spondylitis Implicates Peptide Handling in the Mechanism for HLA-B27 in Disease Susceptibility","volume":"43","author":"Evans","year":"2011","journal-title":"Nat. Genet."},{"key":"B18","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1038\/sj.emboj.7600085","article-title":"Runx3 Regulates Mouse TGF-\u03b2-Mediated Dendritic Cell Function and its Absence Results in Airway Inflammation","volume":"23","author":"Fainaru","year":"2004","journal-title":"Embo J."},{"key":"B19","doi-asserted-by":"publisher","first-page":"bax028","DOI":"10.1093\/database\/bax028","article-title":"GeneHancer: Genome-wide Integration of Enhancers and Target Genes in GeneCards","volume":"2017","author":"Fishilevich","year":"2017","journal-title":"Database : J. Biol. databases curation"},{"key":"B20","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1038\/s41576-019-0209-0","article-title":"Towards a Comprehensive Catalogue of Validated and Target-Linked Human Enhancers","volume":"21","author":"Gasperini","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"B21","doi-asserted-by":"publisher","first-page":"145421","DOI":"10.1016\/j.gene.2021.145421","article-title":"Super-enhancers for RUNX3 Are Required for Cell Proliferation in EBV-Infected B Cell Lines","volume":"774","author":"Hosoi","year":"2021","journal-title":"Gene"},{"key":"B22","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1038\/s41588-021-00799-x","article-title":"Independence of Chromatin Conformation and Gene Regulation during Drosophila Dorsoventral Patterning","volume":"53","author":"Ing-Simmons","year":"2021","journal-title":"Nat. Genet."},{"key":"B23","doi-asserted-by":"publisher","first-page":"4243","DOI":"10.1158\/0008-5472.can-09-3805","article-title":"Role of RUNX3 in Bone Morphogenetic Protein Signaling in Colorectal Cancer","volume":"70","author":"Lee","year":"2010","journal-title":"Cancer Res."},{"key":"B24","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1038\/gene.2017.11","article-title":"Epigenetic and Gene Expression Analysis of Ankylosing Spondylitis-Associated Loci Implicate Immune Cells and the Gut in the Disease Pathogenesis","volume":"18","author":"Li","year":"2017","journal-title":"Genes Immun."},{"key":"B25","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1016\/j.molcel.2019.12.021","article-title":"Chromosome Conformation Capture and beyond: Toward an Integrative View of Chromosome Structure and Function","volume":"77","author":"McCord","year":"2020","journal-title":"Mol. Cel."},{"key":"B26","doi-asserted-by":"publisher","first-page":"21.11","DOI":"10.1002\/0471142727.mb2111s74","article-title":"Mapping Chromatin Interactions by Chromosome Conformation Capture","volume":"21","author":"Miele","year":"2006","journal-title":"Current. Protocols. in. Mol. Biol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"624632","DOI":"10.3389\/fimmu.2021.624632","article-title":"From the Genetics of Ankylosing Spondylitis to New Biology and Drug Target Discovery","volume":"12","author":"Nancy","year":"2021","journal-title":"Front. Immunol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"195","DOI":"10.3389\/fgene.2012.00195","article-title":"Transcription Factor Binding at Enhancers: Shaping a Genomic Regulatory Landscape in Flux","volume":"3","author":"Palstra","year":"2012","journal-title":"Front. Gene"},{"key":"B29","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1182\/blood-2011-02-339911","article-title":"Role of C-MYC in Alternative Activation of Human Macrophages and Tumor-Associated Macrophage Biology","volume":"119","author":"Pello","year":"2012","journal-title":"Blood"},{"key":"B30","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1016\/j.imbio.2010.05.018","article-title":"The Novel RUNX3\/p33 Isoform Is Induced upon Monocyte-Derived Dendritic Cell Maturation and Downregulates IL-8 Expression","volume":"215","author":"Puig-Kr\u00f6ger","year":"2010","journal-title":"Immunobiology"},{"key":"B31","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/ng.513","article-title":"Genome-wide Association Study of Ankylosing Spondylitis Identifies Non-MHC Susceptibility Loci","volume":"42","author":"Reveille","year":"2010","journal-title":"Nat. Genet."},{"key":"B32","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1016\/j.berh.2018.08.012","article-title":"Gut Inflammation in Spondyloarthritis","volume":"31","author":"Rizzo","year":"2017","journal-title":"Best Pract. Res. Clin. Rheumatol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1038\/gene.2015.49","article-title":"The Genetic Associations of Acute Anterior Uveitis and Their Overlap with the Genetics of Ankylosing Spondylitis","volume":"17","author":"Robinson","year":"2016","journal-title":"Genes Immun."},{"key":"B34","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1007\/s00412-016-0593-6","article-title":"Chromosome Conformation Capture Technologies and Their Impact in Understanding Genome Function","volume":"126","author":"Sati","year":"2017","journal-title":"Chromosoma"},{"key":"B35","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1056\/nejm197304052881403","article-title":"High Association of an HL-A Antigen, W27, with Ankylosing Spondylitis","volume":"288","author":"Schlosstein","year":"1973","journal-title":"N. Engl. J. Med."},{"key":"B36","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 Years of Image Analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"B37","doi-asserted-by":"publisher","first-page":"2219","DOI":"10.1038\/leu.2017.40","article-title":"RUNX3 Is Oncogenic in Natural killer\/T-Cell Lymphoma and Is Transcriptionally Regulated by MYC","volume":"31","author":"Selvarajan","year":"2017","journal-title":"Leukemia"},{"key":"B38","doi-asserted-by":"publisher","first-page":"6540","DOI":"10.1038\/s41467-021-26750-6","article-title":"Targeting Chondrocytes for Arresting Bony Fusion in Ankylosing Spondylitis","volume":"12","author":"Shao","year":"2021","journal-title":"Nat. Commun."},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1016\/j.jid.2021.01.015","article-title":"Chromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits","author":"Shi","year":"2021","journal-title":"J. Invest. Dermatol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"3137","DOI":"10.1093\/rheumatology\/keaa283","article-title":"Using Functional Genomics to advance the Understanding of Psoriatic Arthritis","volume":"59","author":"Shi","year":"2020","journal-title":"Rheumatology (Oxford)"},{"key":"B41","doi-asserted-by":"publisher","first-page":"3625","DOI":"10.1093\/bioinformatics\/btaa202","article-title":"HiChIP-Peaks: a HiChIP Peak Calling Algorithm","volume":"36","author":"Shi","year":"2020","journal-title":"Bioinformatics"},{"key":"B42","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1136\/annrheumdis-2013-203582","article-title":"Prevalence of Extra-articular Manifestations in Patients with Ankylosing Spondylitis: a Systematic Review and Meta-Analysis","volume":"74","author":"Stolwijk","year":"2015","journal-title":"Ann. Rheum. Dis."},{"key":"B43","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1002\/art.41628","article-title":"Functional Genomic Analysis of a RUNX3 Polymorphism Associated with Ankylosing Spondylitis","volume":"73","author":"Vecellio","year":"2021","journal-title":"Arthritis Rheumatol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"e000628","DOI":"10.1136\/rmdopen-2017-000628","article-title":"Evidence for a Second Ankylosing Spondylitis-Associated RUNX3 Regulatory Polymorphism","volume":"4","author":"Vecellio","year":"2018","journal-title":"RMD open"},{"key":"B45","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1136\/annrheumdis-2015-207490","article-title":"The Genetic Association ofRUNX3with Ankylosing Spondylitis Can Be Explained by Allele-specific Effects on IRF4 Recruitment that Alter Gene Expression","volume":"75","author":"Vecellio","year":"2016","journal-title":"Ann. Rheum. Dis."},{"key":"B46","doi-asserted-by":"publisher","first-page":"2778","DOI":"10.1101\/gad.251694.114","article-title":"Spatial Genome Organization: Contrasting Views from Chromosome Conformation Capture and Fluorescence In Situ Hybridization","volume":"28","author":"Williamson","year":"2014","journal-title":"Genes Dev."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2021.741867\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,7]],"date-time":"2022-01-07T00:29:06Z","timestamp":1641515346000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2021.741867\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,7]]},"references-count":46,"alternative-id":["10.3389\/fgene.2021.741867"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2021.741867","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.09.07.459234","asserted-by":"object"}]},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,7]]},"article-number":"741867"}}