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Updated: May 14, 2026
Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)
Published on: April 19, 2013
Molecular network of chromatin immunoprecipitation followed by deep sequencing-based vitamin D receptor target genes
Jun-ichi Satoh1, Hiroko Tabunoki
1Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan. satoj@my-pharm.ac.jp
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.
Insights
Vitamin D receptor target genes (VDRTGs) in immune cells were identified. A network of these genes is linked to immune regulation, suggesting vitamin D deficiency may trigger autoimmune responses like multiple sclerosis (MS).
Area of Science:
- Immunology
- Molecular Biology
- Genetics
Background:
- Vitamin D is crucial for calcium metabolism and gene regulation via the vitamin D receptor (VDR).
- Vitamin D deficiency is linked to an increased risk of multiple sclerosis (MS).
Purpose of the Study:
- To investigate the protective role of vitamin D in MS by characterizing the global network of VDR target genes (VDRTGs) in immune cells.
Main Methods:
- Genome-wide VDRTGs were identified using chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) on B cells and monocytes.
- Next-generation sequencing (NGS) data was processed using Bowtie, MACS, and a novel genome viewer, GenomeJack.
Main Results:
- 2997 VDR-binding sites were identified on protein-coding genes.
- Transcriptome data confirmed calcitriol-induced upregulation of a subset of VDRTGs.
- A network of 1541 calcitriol-responsive VDRTGs was associated with leukocyte migration, phagocytosis, and VDR transcriptional regulation, indicating a role in immune regulation.
Conclusions:
- The study proposes a hypothesis that persistent vitamin D deficiency may disrupt the VDRTG network in immune cells.
- This disruption could lead to autoimmune responses, potentially causing MS.
