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Biochim Biophys Acta. 2013 Dec;1829(12):1266-75. doi: 10.1016/j.bbagrm.2013.10.003. Epub 2013 Nov 1.

Dynamics of 1α,25-dihydroxyvitamin D3-dependent chromatin accessibility of early vitamin D receptor target genes.

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School of Medicine, Institute of Biomedicine, University of Eastern Finland, FIN-70211 Kuopio, Finland.


The signaling cascade of the transcription factor vitamin D receptor (VDR) is triggered by its specific ligand 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3). In this study we demonstrate that in THP-1 human monocytic leukemia cells 87.4% of the 1034 most prominent genome-wide VDR binding sites co-localize with loci of open chromatin. At 165 of them 1α,25(OH)2D3 strongly increases chromatin accessibility and has at further 217 sites weaker effects. Interestingly, VDR binding sites in 1α,25(OH)2D3-responsive chromatin regions are far more often composed of direct repeats with 3 intervening nucleotides (DR3s) than those in ligand insensitive regions. DR3-containing VDR sites are enriched in the neighborhood of genes that are involved in controling cellular growth, while non-DR3 VDR binding is often found close to genes related to immunity. At the example of six early VDR target genes we show that the slope of their 1α,25(OH)2D3-induced transcription correlates with the basal chromatin accessibility of their major VDR binding regions. However, the chromatin loci controlling these genes are indistinguishable in their VDR association kinetics. Taken together, ligand responsive chromatin loci represent dynamically regulated contact points of VDR with the genome, from where it controls early 1α,25(OH)2D3 target genes.


1α,25(OH)(2)D(3) or 1,25D; 1α,25-dihydroxyvitamin D(3); B2M; CAMP; CD14; ChIP; ChIP sequencing; ChIP-seq; DR3; FAIRE; FAIRE sequencing; FAIRE-seq; FANCE; FBP1; FCS; FDR; Fanconi anemia, complementation group E; GAPDH; GEO; GREAT; Gene Expression Omnibus; Genomic Regions Enrichment of Annotations Tool; H3K27ac; HBB; HBEGF; HDAC; HDAC inhibitor; HPRTI; IGV; Integrative Genomics Viewer; MB; NFKBIA; NINJ1; Open chromatin; PDCD1LG2; PPARGC1B; PSMA6; SAHA; SCTR; SEMA6B; TMEM37; TSS; TsA; VDR; VPA; Vitamin D; beta-2-microglobulin; cathelicidin antimicrobial peptide; chromatin immunoprecipitation; cluster of differentiation 14 molecule; direct repeat spaced by 3 nucleotides; false discovery rate; fetal calf serum; formaldehyde-assisted isolation of regulatory elements; fructose-1,6-bisphosphatase 1; gylcerinaldehyde-3-phosphate-dehydrogenase; hemoglobin, beta; heparin-binding EGF-like growth factor; histone 3 acetylation at lysine 27; histone deacetylase; hypoxanthine phosphoribosyltransferase 1; myoglobin; ninjurin 1; nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha; peroxisome proliferator-activated receptor γ, co-activator 1β; programmed cell death 1 ligand 2; proteasome subunit, alpha type, 6; qPCR; real-time quantitative polymerase chain reaction; secretin receptor; semaphorin 6B; suberoylanilide hydroxamic acid; transcription start site; transmembrane protein 37; trichostatin A; valproic acid; vitamin D receptor

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