{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T01:09:05Z","timestamp":1770512945631,"version":"3.49.0"},"reference-count":52,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2014,4,24]],"date-time":"2014-04-24T00:00:00Z","timestamp":1398297600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0096184","type":"journal-article","created":{"date-parts":[[2014,4,24]],"date-time":"2014-04-24T21:02:17Z","timestamp":1398373337000},"page":"e96184","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":30,"title":["Characterization of Genomic Vitamin D Receptor Binding Sites through Chromatin Looping and Opening"],"prefix":"10.1371","volume":"9","author":[{"given":"Sabine","family":"Seuter","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio","family":"Neme","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carsten","family":"Carlberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2014,4,24]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/nrm1680","article-title":"Controlling nuclear receptors: the circular logic of cofactor cycles","volume":"6","author":"V Perissi","year":"2005","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"528","DOI":"10.2174\/156802612799436623","article-title":"Current status of vitamin D signaling and its therapeutic applications","volume":"12","author":"C Carlberg","year":"2012","journal-title":"Curr Top Med Chem"},{"key":"ref3","first-page":"1689S","article-title":"Overview of general physiologic features and functions of vitamin D. Am J Clin Nutr","volume":"80","author":"HF DeLuca","year":"2004"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1185\/030079907X253519","article-title":"Molecular basis of the potential of vitamin D to prevent cancer","volume":"24","author":"BA Ingraham","year":"2008","journal-title":"Curr Med Res Opin"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/ki.2010.17","article-title":"Vitamin D: a pleiotropic hormone","volume":"78","author":"A Verstuyf","year":"2010","journal-title":"Kidney Int"},{"key":"ref6","first-page":"337","article-title":"Antibacterial effects of vitamin D. Nat Rev Endocrinol","volume":"7","author":"M Hewison","year":"2011"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"9181","DOI":"10.1093\/nar\/gkr654","article-title":"Nuclear hormone 1\u03b1,25-dihydroxyvitamin D<sub>3<\/sub> elicits a genome-wide shift in the locations of VDR chromatin occupancy","volume":"39","author":"S Heikkinen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1016\/j.bbamcr.2011.01.037","article-title":"Mechanism of 1\u03b1,25-dihydroxyvitamin D<sub>3<\/sub>-dependent repression of interleukin-12B","volume":"1813","author":"P Gynther","year":"2011","journal-title":"Biochim Biophys Acta"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.bbamcr.2010.07.009","article-title":"Primary effect of 1\u03b1,25(OH)<sub>2<\/sub>D<sub>3<\/sub> on IL-10 expression in monocytes is short-term down-regulation","volume":"1803","author":"JM Matilainen","year":"2010","journal-title":"Biochim Biophys Acta"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/ng.375","article-title":"The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line","volume":"41","author":"H FANTOM-Consortium, Suzuki","year":"2009","journal-title":"Nat Genet"},{"key":"ref11","first-page":"271","article-title":"The first genome-wide view of vitamin D receptor locations and their mechanistic implications","volume":"32","author":"C Carlberg","year":"2012","journal-title":"Anticancer Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1016\/0092-8674(91)90020-Y","article-title":"Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D<sub>3<\/sub> receptors","volume":"65","author":"K Umesono","year":"1991","journal-title":"Cell"},{"key":"ref13","first-page":"657","article-title":"Two nuclear signalling pathways for vitamin D. Nature","volume":"361","author":"C Carlberg","year":"1993"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1007\/s00412-010-0283-8","article-title":"Dynamics of nuclear receptor target gene regulation","volume":"119","author":"C Carlberg","year":"2010","journal-title":"Chromosoma"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1093\/embo-reports\/kvf053","article-title":"Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics","volume":"3","author":"A Eberharter","year":"2002","journal-title":"EMBO Rep"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1101\/gr.5533506","article-title":"FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin","volume":"17","author":"PG Giresi","year":"2007","journal-title":"Genome Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.ymeth.2009.03.003","article-title":"Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)","volume":"48","author":"PG Giresi","year":"2009","journal-title":"Methods"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1101\/gr.121541.111","article-title":"Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity","volume":"21","author":"L Song","year":"2011","journal-title":"Genome Res"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1096\/fj.14.10.1455","article-title":"VDR-Alien: a novel, DNA-selective vitamin D<sub>3<\/sub> receptor-corepressor partnership","volume":"14","author":"P Polly","year":"2000","journal-title":"Faseb J"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1093\/nar\/gkm913","article-title":"Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to trichostatin A and 1\u03b1,25-dihydroxyvitamin D<sub>3<\/sub>","volume":"36","author":"M Malinen","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1038\/nrd1551","article-title":"Principles for modulation of the nuclear receptor superfamily","volume":"3","author":"H Gronemeyer","year":"2004","journal-title":"Nat Rev Drug Discov"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1016\/j.molcel.2013.02.011","article-title":"The hierarchy of the 3D genome","volume":"49","author":"JH Gibcus","year":"2013","journal-title":"Mol Cell"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.steroids.2012.10.019","article-title":"Vitamin D receptor signaling mechanisms: Integrated actions of a well-defined transcription factor","volume":"78","author":"C Carlberg","year":"2013","journal-title":"Steroids"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1038\/nrg2641","article-title":"ChIP-seq: advantages and challenges of a maturing technology","volume":"10","author":"PJ Park","year":"2009","journal-title":"Nat Rev Genet"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1101\/gr.107920.110","article-title":"A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution","volume":"20","author":"SV Ramagopalan","year":"2010","journal-title":"Genome Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1210\/me.2011-1109","article-title":"VDR\/RXR and TCF4\/beta-catenin cistromes in colonic cells of colorectal tumor origin: impact on c-FOS and c-MYC gene expression","volume":"26","author":"MB Meyer","year":"2012","journal-title":"Mol Endocrinol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/j.cell.2013.03.028","article-title":"A vitamin D receptor\/SMAD genomic circuit gates hepatic fibrotic response","volume":"153","author":"N Ding","year":"2013","journal-title":"Cell"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1186\/1741-7015-11-163","article-title":"Vitamin D receptor ChIP-seq in primary CD4<sup>+<\/sup> cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease","volume":"11","author":"AE Handel","year":"2013","journal-title":"BMC Med"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.bbagrm.2008.07.002","article-title":"Chromatin loops in gene regulation","volume":"1789","author":"S Kadauke","year":"2009","journal-title":"Biochim Biophys Acta"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.cell.2009.06.001","article-title":"CTCF: master weaver of the genome","volume":"137","author":"JE Phillips","year":"2009","journal-title":"Cell"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.cell.2011.11.058","article-title":"Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages","volume":"148","author":"D Schmidt","year":"2012","journal-title":"Cell"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nature08497","article-title":"An oestrogen-receptor-alpha-bound human chromatin interactome","volume":"462","author":"MJ Fullwood","year":"2009","journal-title":"Nature"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","year":"2012","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1002\/ijc.2910260208","article-title":"Establishment and characterization of a human acute monocytic leukemia cell line (THP-1)","volume":"26","author":"S Tsuchiya","year":"1980","journal-title":"Int J Cancer"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1016\/j.bbagrm.2013.10.003","article-title":"Dynamics of 1\u03b1,25-dihydroxyvitamin D-dependent chromatin accessibility of early vitamin D receptor target genes","volume":"1829","author":"S Seuter","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"H Thorvaldsdottir","year":"2013","journal-title":"Brief Bioinform"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102. Article published online before print in May 2002","article-title":"The human genome browser at UCSC","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"S Heinz","year":"2010","journal-title":"Mol Cell"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"R34","DOI":"10.1186\/gb-2002-3-7-research0034","article-title":"Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes","volume":"3","author":"J Vandesompele","year":"2002","journal-title":"Genome Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1002\/ijc.2910180405","article-title":"Properties of the K562 cell line, derived from a patient with chronic myeloid leukemia","volume":"18","author":"E Klein","year":"1976","journal-title":"Int J Cancer"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"e53766","DOI":"10.1371\/journal.pone.0053766","article-title":"Vorinostat induces apoptosis and differentiation in myeloid malignancies: genetic and molecular mechanisms","volume":"8","author":"G Silva","year":"2013","journal-title":"PLoS One"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1093\/nar\/gks959","article-title":"Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1\u03b1,25-dihydroxyvitamin D<sub>3<\/sub> and histone deacetylase inhibitors on gene expression","volume":"41","author":"S Seuter","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/j.cell.2007.01.028","article-title":"Beyond the sequence: cellular organization of genome function","volume":"128","author":"T Misteli","year":"2007","journal-title":"Cell"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.cell.2011.12.014","article-title":"Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation","volume":"148","author":"G Li","year":"2012","journal-title":"Cell"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1038\/msb.2011.73","article-title":"Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics","volume":"7","author":"MA Mendoza-Parra","year":"2011","journal-title":"Mol Syst Biol"},{"key":"ref46","doi-asserted-by":"crossref","unstructured":"Jakobsen JS, Waage J, Rapin N, Bisgaard HC, Larsen FS, <etal>et al<\/etal>.. (2013) Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Res.","DOI":"10.1101\/gr.146399.112"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1615\/CritRevEukarGeneExpr.v8.i1.20","article-title":"Gene regulation by vitamin D<sub>3<\/sub>","volume":"8","author":"C Carlberg","year":"1998","journal-title":"Crit Rev Eukaryot Gene Expr"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"19185","DOI":"10.1016\/S0021-9258(17)30642-7","article-title":"A growth factor-inducible nuclear protein with a novel cysteine\/histidine repetitive sequence","volume":"265","author":"RN DuBois","year":"1990","journal-title":"J Biol Chem"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1126\/science.281.5379.1001","article-title":"Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin","volume":"281","author":"E Carballo","year":"1998","journal-title":"Science"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"e61551","DOI":"10.1371\/journal.pone.0061551","article-title":"Identification of a mitochondrial target of thiazolidinedione insulin sensitizers (mTOT)\u2013relationship to newly identified mitochondrial pyruvate carrier proteins","volume":"8","author":"JR Colca","year":"2013","journal-title":"PLoS One"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1042\/BJ20040455","article-title":"Phosphorylation of septin 3 on Ser-91 by cGMP-dependent protein kinase-I in nerve terminals","volume":"381","author":"J Xue","year":"2004","journal-title":"Biochem J"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"4338","DOI":"10.4049\/jimmunol.145.12.4338","article-title":"Isolation and characterization of cDNA encoding a human nuclear antigen predominantly recognized by autoantibodies from patients with primary biliary cirrhosis","volume":"145","author":"C Szostecki","year":"1990","journal-title":"J Immunol"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0096184","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T11:16:56Z","timestamp":1689160616000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0096184"}},"subtitle":[],"editor":[{"given":"Sreeram V.","family":"Ramagopalan","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2014,4,24]]},"references-count":52,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2014,4,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0096184","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,4,24]]}}}