scholarly journals A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution

2010 ◽  
Vol 20 (10) ◽  
pp. 1352-1360 ◽  
Author(s):  
S. V. Ramagopalan ◽  
A. Heger ◽  
A. J. Berlanga ◽  
N. J. Maugeri ◽  
M. R. Lincoln ◽  
...  
Keyword(s):  
Vitamin D ◽  
Vitamin D Receptor ◽  
Receptor Binding ◽  
Genome Wide

Molecular network of chromatin immunoprecipitation followed by deep sequencing-based vitamin D receptor target genes

2013 ◽  
Vol 19 (8) ◽  
pp. 1035-1045 ◽  
Author(s):  
Jun-ichi Satoh ◽  
Hiroko Tabunoki
Keyword(s):  
Multiple Sclerosis ◽  
Vitamin D ◽  
Vitamin D Receptor ◽  
Deep Sequencing ◽  
Immune Cells ◽  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Molecular Network ◽  
Genome Wide

Background: Vitamin D is a liposoluble vitamin essential for calcium metabolism. The ligand-bound vitamin D receptor (VDR), heterodimerized with retinoid X receptor, interacts with vitamin D response elements (VDREs) to regulate gene expression. Vitamin D deficiency due to insufficient sunlight exposure confers an increased risk for multiple sclerosis (MS). Objective: To study a protective role of vitamin D in multiple sclerosis (MS), it is important to characterize the global molecular network of VDR target genes (VDRTGs) in immune cells. Methods: We identified genome-wide VDRTGs collectively from two distinct chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) datasets of VDR-binding sites derived from calcitriol-treated human cells of B cell and monocyte origins. We mapped short reads of next generation sequencing (NGS) data on hg19 with Bowtie, detected the peaks with Model-based Analysis of ChIP-Seq (MACS), and identified genomic locations by GenomeJack, a novel genome viewer for NGS platforms. Results: We found 2997 stringent peaks distributed on protein-coding genes, chiefly located in the promoter and the intron on VDRE DR3 sequences. However, the corresponding transcriptome data verified calcitriol-induced upregulation of only a small set of VDRTGs. The molecular network of 1541 calcitriol-responsive VDRTGs showed a significant relationship with leukocyte transendothelial migration, Fcγ receptor-mediated phagocytosis, and transcriptional regulation by VDR, suggesting a pivotal role of genome-wide VDRTGs in immune regulation. Conclusion: These results suggest the working hypothesis that persistent deficiency of vitamin D might perturb the complex network of VDRTGs in immune cells, being responsible for induction of an autoimmune response causative for MS.

Genome-Wide Perspectives on Vitamin D Receptor–Mediated Control of Gene Expression in Target Cells

Vitamin D ◽  
2018 ◽  
pp. 141-174
Author(s):  
J. Wesley Pike ◽  
Mark B. Meyer ◽  
Seong M. Lee ◽  
Melda Onal ◽  
Nancy A. Benkusky
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Vitamin D Receptor ◽  
Target Cells ◽  
Control Of Gene Expression ◽  
Genome Wide

scholarly journals Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease

2017 ◽  
Vol 26 (11) ◽  
pp. 2164-2176 ◽  
Author(s):  
Giuseppe Gallone ◽  
Wilfried Haerty ◽  
Giulio Disanto ◽  
Sreeram V. Ramagopalan ◽  
Chris P. Ponting ◽  
...  
Keyword(s):  
Vitamin D ◽  
Autoimmune Disease ◽  
Vitamin D Receptor ◽  
Receptor Binding ◽  
Genetic Variants

scholarly journals Recombinant Expression, Isotope Labeling and Purification of the Vitamin D Receptor Binding Peptide

2011 ◽  
Vol 32 (12) ◽  
pp. 4337-4340
Author(s):  
Young-Kee Chae ◽  
Kiran Singarapu ◽  
W. Milo Westler ◽  
John L. Markley
Keyword(s):  
Vitamin D ◽  
Vitamin D Receptor ◽  
Receptor Binding ◽  
Isotope Labeling ◽  
Recombinant Expression ◽  
Binding Peptide

scholarly journals Characterization of Genomic Vitamin D Receptor Binding Sites through Chromatin Looping and Opening

PLoS ONE ◽  
2014 ◽  
Vol 9 (4) ◽  
pp. e96184 ◽  
Author(s):  
Sabine Seuter ◽  
Antonio Neme ◽  
Carsten Carlberg
Keyword(s):  
Vitamin D ◽  
Vitamin D Receptor ◽  
Receptor Binding ◽  
Binding Sites ◽  
Chromatin Looping

scholarly journals Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota

2016 ◽  
Vol 48 (11) ◽  
pp. 1396-1406 ◽  
Author(s):  
Jun Wang ◽  
Louise B Thingholm ◽  
Jurgita Skiecevičienė ◽  
Philipp Rausch ◽  
Martin Kummen ◽  
...  
Keyword(s):  
Vitamin D ◽  
Gut Microbiota ◽  
Association Analysis ◽  
Vitamin D Receptor ◽  
Host Factors ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Factors Influencing ◽  
Genome Wide

Vitamin D receptor binding and biological effects of cholecalciferol analogues in rat thyroid cells

1994 ◽  
Vol 50 (3-4) ◽  
pp. 145-150 ◽  
Author(s):  
Jens P. Berg ◽  
Kjellaug M. Liane ◽  
Siri B. Bjørhovde ◽  
Trine Bjøro ◽  
Peter A. Torjesen ◽  
...  
Keyword(s):  
Vitamin D ◽  
Vitamin D Receptor ◽  
Receptor Binding ◽  
Biological Effects ◽  
Thyroid Cells ◽  
Rat Thyroid

Controlling the chromatin organization of vitamin D target genes by multiple vitamin D receptor binding sites

2007 ◽  
Vol 103 (3-5) ◽  
pp. 338-343 ◽  
Author(s):  
Carsten Carlberg ◽  
Thomas W. Dunlop ◽  
Anna Saramäki ◽  
Lasse Sinkkonen ◽  
Merja Matilainen ◽  
...  
Keyword(s):  
Vitamin D ◽  
Vitamin D Receptor ◽  
Receptor Binding ◽  
Binding Sites ◽  
Target Genes ◽  
Chromatin Organization
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