The impact of the vitamin D-modulated epigenome on VDR target gene regulation
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, online 3 July 2018, https://doi.org/10.1016/j.bbagrm.2018.05.006
Veijo Nurminen 1 Antonio Neme 1 Sabine Seuter 2 Carsten Carlberg
- 2,776 vitamin D receptor binding sites - April 2014
- Multiple Sclerosis more likely if poor vitamin D genes - 22nd study – Aug 2017
- 5839 genes changed during pregnancy (many genes were related to Vitamin D) – Oct 2016
- Preeclampsia 3.5 times more likely if low vitamin D (affects 348 Vit. D genes) – RCT Nov 2016
- Genes which regulate active vitamin D worsen with age – Oct 2016
- 2 Genes make AMD 6X more likely if low vitamin D - Aug 2015
- Vitamin D insufficiency was 3.7 X more likely if CYP2R1 gene variation– June 2014
- Breast Cancer rate reduced 72 percent by vitamin D gene polymorphism CYP24A1 – Nov 2014
- Genetics category listing has
266 items and the follolwing chart which summarizes 7 genes Vitamin D blood test misses a lot
Extremely technical PDF is available free at Sci-Hub 10.1016/j.bbagrm.2018.05.006
Highlights
- In THP-1 cells 550 of 23,000 H3K4me3 marks are significantly (p < 0.05) modulated by 1,25(OH)2D3.
- From 45,500 H3K27ac histone marks representing active chromatin even 2473 are ligand sensitive.
- Vitamin D modulated histone markers are well suited to distinguish promoter and enhancer regulation.
- Ligand-dependent histone markers link the effects of vitamin D on the epigenome with transcriptome changes.
The micronutrient vitamin D significantly modulates the human epigenome via enhancing genome-wide the rate of accessible chromatin and vitamin D receptor (VDR) binding. This study focuses on histone marks of active chromatin at promoter and enhancer regions and investigates, whether these genomic loci are sensitive to vitamin D.
The epigenome of THP-1 human monocytes contains nearly 23,000 sites with H3K4me3 histone modifications, 550 of which sites are significantly (p < 0.05) modulated by stimulation with the VDR ligand 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3).
H3K27ac histone modifications mark active chromatin and 2473 of 45,500 sites are vitamin D sensitive. The two types of ligand-dependent histone marks allow to distinguish promoter and enhancer regulation by vitamin D, respectively.
Transcription start site overlap is the prime attribute of ligand-dependent H3K4me3 marks, while VDR co-location is the top ranking parameter describing 1,25(OH)2D3-sensitive H3K27ac marks at enhancers.
A categorization of 1,25(OH)2D3-sensitive histone marks by machine learning algorithms - using the attributes overall peak strength and ligand inducibility - highlights 260 and 287 regions with H3K4me3 and H3K27ac modifications, respectively.
These loci are found at the promoter regions of 59 vitamin D target genes and their associated enhancers.
In this way, ligand-dependent histone marks provide a link of the effects of 1,25(OH)2D3 on the epigenome with previously reported mRNA expression changes of vitamin D target genes. In conclusion, the human epigenome responds also on the level of histone modifications to 1,25(OH)2D3 stimulation. This allows a more detailed understanding of vitamin D target gene regulation.Vitamin D affects at least 3,023 DNA locations – July 2018Printer Friendly PDF this page! Follow this page for updates1003 visitors, last modified 03 Jul, 2018, This page is in the following categories (# of items in each category)