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229 Genes related to vitamin D - Aug 2010

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


see the wiki for review and link to the PDF: http://www.vitamindwiki.com/tiki-index.php?page_id=794

From the PDF: Significance analysis of genomic overlap

In order to assess if there is a significant overlap between two sets of genomic features we followed the procedure described in Gentleman et al. (2004). In brief, the percentage base overlap between a query set of genomic intervals is tested against a reference set of genomic intervals and the overlap is recorded. The expected overlap is then computed by randomizing the locations of the query set of intervals. The procedure accounts for compositional biases by requiring that the randomized location of a segment remains on the same chromosome and preserves the local G+C content. From 10,000 randomizations the procedure computes the expected overlap and an empirical P-value. The reported fold enrichment is the ratio of the observed overlap and the expected overlap. By aggregating the randomizations from multiple reference sets, an empirical FDR is computed. Only results with an FDR of <1% are reported. For analysis of enrichment of VDR binding sites in relation to DNase I hypersensitivity, CTCF binding, and histone modifications, ENCODE data generated for the unstimulated lymphoblastoid cell line GM12878 were used. We tested disease and selection intervals from data available at www.t1dbase.org, the NHGRI GWAS database (http://www.genome.gov/26525384), and data from (Voight et al. 2006; Barrett et al. 2008; De Jager et al. 2009; Gandhi et al. 2010) (interval defined as 150 kb on either side of main disease-associated SNP, or 100 kb on either side of a gene shown to be differentially expressed) for

  • acute myeloid leukemia,
  • BMI, aging,
  • alcohol dependence,
  • Alzheimer's disease,
  • amyotrophic lateral sclerosis,
  • ankylosing spondylitis,
  • asthma,
  • atrial fibrillation,
  • attention deficit hyperactivity disorder,
  • bipolar disorder,
  • blood pressure,
  • bone mineral density,
  • breast cancer,
  • celiac disease,
  • cholesterol,
  • chronic lymphocytic
  • leukemia,
  • colorectal cancer,
  • coronary artery disease,
  • Crohn's disease,
  • fasting glucose,
  • hair color,
  • HDL cholesterol,
  • height,
  • LDL cholesterol,
  • leprosy, lung cancer,
  • melanoma,
  • multiple sclerosis,
  • myocardial infarction,
  • pancreatic cancer,
  • Parkinson's disease,
  • primary biliary cirrhosis,
  • prostate cancer,
  • psoriasis,
  • QT interval,
  • restless legs syndrome,
  • rheumatoid arthritis,
  • schizophrenia,
  • stroke,
  • systemic lupus erythematosus,
  • tanning,
  • triglycerides,
  • type 2 diabetes
  • ulcerative colitis.

4393 glucocorticoid receptor binding sites as described in Reddy et al. (2009) were also used to test for enrichment in disease intervals.

See also VitaminDWiki

The following are a few of the many reports on this breakthru

Genetic effects of vitamin D studied - NHS August 24 2010

The skin produces vitamin D when exposed to sunlight
“Stocking up on vitamin D supplements and enjoying the summer sun could cut the risk of a host of diseases,” reported the Daily Mail.
This news story is based on a study that investigated how vitamin D might influence the risk of certain diseases by affecting the activity of genes. It found that vitamin D binds directly to genes associated with several common autoimmune diseases, including multiple sclerosis, type 1 diabetes, rheumatoid arthritis and colorectal cancer.

Studies of this kind add to our knowledge of the function of vitamin D, and will be used to assess the guidelines for recommended vitamin D intake.

On its own, this study does not provide definitive evidence that lack of vitamin D causes any of these diseases, or that a certain intake of vitamin D will prevent them. It also did not look at how much vitamin D is best for health and whether supplements are as good as natural sources such as diet and the sun.

It is important to get some sunlight for an adequate intake of vitamin D, but this needs to be balanced with the fact that excessive exposure to UV rays increases the risk of skin cancer. Vitamin D can also be found in oily fish, eggs and some fortified foods such as cereals.

Where did the story come from?

The study was carried out by researchers from the University of Oxford, the Simon Fraser University in Canada, the University of London, and Barts and the London School of Medicine and Dentistry. It was funded by the Multiple Sclerosis Society of Canada, the Multiple Sclerosis Society of Great Britain and Northern Ireland, the Medical Research Council and the Wellcome Trust. The study was published as an advance online article in the peer-reviewed journal Genome Research.

The study was reported widely and, for the most part, accurately in the media. The Independent explained in detail that the study identified a possible mechanism by which vitamin D binds directly to genes known to be linked to various genetic disorders. The Mail’s report implied that the study shows that boosting levels of vitamin D, potentially through taking supplements, could keep illnesses at bay. However, the study did not look at how differing levels of vitamin D might affect health outcomes, and a clinical trial would be needed for this.

What kind of research was this?

The researchers say that a billion people worldwide have vitamin D deficiency due to insufficient sun exposure or inadequate dietary intake. This deficiency has been associated with a greater risk of several diseases including multiple sclerosis, rheumatoid arthritis and type 1 diabetes. How vitamin D might affect the risk of these diseases is not fully understood.

They suggest that one way vitamin D might have an impact on the risk of disease is through altering the activity of certain genes. At the cellular level, vitamin D binds to a protein called vitamin D receptor (VDR), and the resulting combination (called a vitamin D complex) can then bind to specific sites in the DNA called ‘vitamin D response elements’. This can affect the activity of nearby genes.

In this laboratory study, the researchers set out to identify genes that change their activity in response to vitamin D, and where in the DNA the vitamin D complex binds. Their aim was to investigate how vitamin D might affect processes at the cellular level.

What did the research involve?

In the laboratory, human cells were exposed to calcitriol, the active form of vitamin D. A technique called ChIP-seq was then used to analyse how the cells had been stimulated at the genetic level.

The researchers isolated and sequenced the fragments of DNA that bound to VDR. These fragments were then mapped to their location in the genome (all the genetic information encoded in the DNA). The researchers were interested in the genes that were near to these sites and that could, potentially, be affected by VDR binding. To identify potential genetic links between vitamin D and disease, the researchers also looked at whether these VDR binding sites were more common (were “enriched”) in areas that contained genetic variations that had been linked to diseases in previous genetic research. These diseases included type I diabetes, Crohn’s disease, multiple sclerosis and other conditions.

The researchers also carried out experiments to determine which genes showed significant changes in their level of activity when the cells were treated with calcitriol.

What were the basic results?

The researchers identified 2,776 sites in the DNA that were related to VDR binding, and 229 genes that showed significant changes in their activity in response to vitamin D.

They found that VDR binding sites were more common near genes that have been associated with several common autoimmune diseases. These were:

  • multiple sclerosis (2.2 times more common)
  • type I diabetes (2.9 times more common)
  • Crohn’s disease (3.5 times more common)
  • systemic lupus erythematosus (5.1 times more common)
  • rheumatoid arthritis (2.8 times more common)
  • chronic lymphocytic leukaemia (8.3 times more common)
  • colorectal cancer (4 times more common)

How did the researchers interpret the results?

The researchers say their study provides a comprehensive map of VDR binding throughout the human genome. VDR was found to bind to a number of genes associated with autoimmune disease and cancer. Their data, they say, provide “new evidence supporting a role for vitamin D in susceptibility to autoimmune disease through effects on a substantial number of associated genes”.


This is a valuable addition to our knowledge of the effects of vitamin D in the cells and how it might affect our risk of certain diseases.

In isolation, this study cannot tell us for certain if lack of vitamin D causes any of the diseases in question, or if a certain intake of vitamin D will prevent them. It also did not look at how much vitamin D is best for health. The question of whether vitamin supplements affect health in the same way as vitamin D from natural sources such as the sun and diet also needs to be addressed.

The effect of vitamin D on health and disease is currently an area of great interest and ongoing research. Studies of this kind add to our knowledge of the function of vitamin D, and will be used to assess the guidelines for recommended vitamin D intake.

It is important to get some sunlight for an adequate intake of vitamin D, but this needs to be balanced with the fact that excessive exposure to UV rays increases the risk of skin cancer. Vitamin D can also be found in oily fish, eggs and some fortified foods such as cereals.

Press Release: Vitamin D linked to autoimmune and cancer disease genes, underscoring risks of deficiency

August 24, 2010 – Vitamin D insufficiency is a risk factor for a number of diseases and thus, is a growing concern worldwide, as approximately one billion people may be vitamin D deficient. However, the biological basis for vitamin D deficiency predisposing to disease is poorly understood. In a report published online today in Genome Research (www.genome.org), scientists have mapped the molecular interactions of the vitamin D receptor genome-wide, finding novel connections of vitamin D with genes related to autoimmune disease and cancer.

Vitamin D deficiency, resulting from either lack of sun exposure or poor dietary intake, is increasingly being recognized as a risk factor for a number of serious illnesses, and has been linked with autoimmune conditions such as multiple sclerosis, type 1 diabetes, and rheumatoid arthritis. Yet exactly how vitamin D is involved in disease is largely unknown. Researchers suspect that genetics could be contributing to the connection.

Vitamin D exerts its effects on genes through the vitamin D receptor (VDR), which binds to specific locations of the genome to influence gene expression. An international team of researchers from the United Kingdom and Canada have now mapped sites of VDR binding, information they can then use to identify disease-related genes that vitamin D might influence.

Employing a technique called ChIP-seq, Dr. Sreeram Ramagopalan, of the Wellcome Trust Centre for Human Genetics at Oxford University, and colleagues isolated fragments of genomic DNA bound to the VDR before and after treatment of cells with calcitriol, the active form of vitamin D, and then sequenced the DNA fragments. By mapping the sequences back to the genome, they identified more than 2,700 sites of VDR binding, a number that Ramagopalan noted "shows just how important vitamin D is to humans, and the wide variety of biological pathways that vitamin D plays a role in."

In recent years, genome-wide association studies (GWAS) have uncovered numerous genomic regions harboring genetic variants that confer increased risk to disease. To identify potential genetic links between vitamin D and disease, the group analyzed known disease-associated regions of the genome looking for enrichment of VDR binding in these intervals.

They found that VDR binding is significantly enriched in genomic regions associated with several common autoimmune diseases, such as multiple sclerosis, type 1 diabetes, and Crohn's disease. Importantly, the analysis revealed a novel role for vitamin D at several disease genes, information that will be crucial for future investigations. VDR binding was also enriched in regions associated with cancers such as leukemia and colorectal cancer, and even common traits such as tanning, height, and hair color.

Ramagopalan explained that their findings lend significant support to the hypothesis that vitamin D interacts with genes in the pathogenesis of these diseases, and underscores the serious risks of vitamin D deficiency, especially for individuals who may be genetically predisposed to be sensitive to insufficiency. "Considerations of vitamin D supplementation as a preventative measure for these diseases are strongly warranted," Ramagopalan added.

Scientists from the University of Oxford (Oxford, UK), Barts and The London School of Medicine and Dentistry (London, UK), and Simon Fraser University (Burnaby, Canada) contributed to this study.

This work was supported by the Multiple Sclerosis Society of Canada Scientific Research Foundation, the Multiple Sclerosis Society of Great Britain and Northern Ireland, the Medical Research Council (UK), and the Wellcome Trust (UK).

Media contacts: Sreeram Ramagopalan, PhD (sreeramr@well.ox.ac.uk; +44 7915 490 167) and Craig Brierley, Senior Media Officer for the Wellcome Trust, (C.Brierley@wellcome.ac.uk; +44 20 7611 7329), are available for more information.

Interested reporters may obtain copies of the manuscript from Peggy Calicchia, Editorial Secretary, Genome Research (calicchi@cshl.edu; +1-516-422-4012).

About the article: The manuscript will be published online ahead of print on August 24, 2010. Its full citation is as follows: Ramagopalan SV, Heger A, Berlanga AJ, Maugeri NJ, Lincoln MR, Burrell A, Handunnetthi L, Handel AE, Disanto G, Orton S, Watson CT, Morahan JM, Giovannoni G, Ponting CP, Ebers GC, Knight JC. A ChIP-seq-defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution. Genome Res doi:10.1101/gr.107920.110.

About Genome Research:

Launched in 1995, Genome Research (www.genome.org) is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies.

About Cold Spring Harbor Laboratory Press:

Cold Spring Harbor Laboratory is a private, nonprofit institution in New York that conducts research in cancer and other life sciences and has a variety of educational programs. Its Press, originating in 1933, is the largest of the Laboratory's five education divisions and is a publisher of books, journals, and electronic media for scientists, students, and the general public.

Genome Research issues press releases to highlight significant research studies that are published in the journal.

The extent to which vitamin D deficiency may increase susceptibility to a wide range of diseases is dramatically highlighted in research published today. Scientists have mapped the points at which vitamin D interacts with our DNA - and identified over two hundred genes that it directly influences. The results are published today in the journal Genome Research.

It is estimated that one billion people worldwide do not have sufficient vitamin D. This deficiency is thought to be largely due to insufficient exposure to the sun and in some cases to poor diet. As well as being a well-known risk factor for rickets, there is a growing body of evidence that vitamin D deficiency also increases an individual's susceptibility to autoimmune conditions such as multiple sclerosis (MS), rheumatoid arthritis and type 1 diabetes, as well as certain cancers and even dementia.

Now, in a study whose funders include the Medical Research Council (MRC), the MS Society, the Wellcome Trust and the MS Society of Canada, researchers at the University of Oxford have shown the extent to which vitamin D interacts with our DNA. They used new DNA sequencing technology to create a map of vitamin D receptor binding across the genome. The vitamin D receptor is a protein activated by vitamin D, which attaches itself to DNA and thus influences what proteins are made from our genetic code.

The researchers found 2,776 binding sites for the vitamin D receptor along the length of the genome. These were unusually concentrated near a number of genes associated with susceptibility to autoimmune conditions such as MS, Crohn's disease, systemic lupus erythematosus (or 'lupus') and rheumatoid arthritis, and to cancers such as chronic lymphocytic leukaemia and colorectal cancer.

They also showed that vitamin D had a significant effect on the activity of 229 genes including IRF8, previously associated with MS, and PTPN2, associated with Crohn's disease and type 1 diabetes.

"Our study shows quite dramatically the wide-ranging influence that vitamin D exerts over our health," says Dr Andreas Heger from the MRC Functional Genomics Unit at Oxford, one of the lead authors of the study.

The first author of the paper, Dr Sreeram Ramagopalan from the Wellcome Trust Centre for Human Genetics, adds: "There is now evidence supporting a role for vitamin D in susceptibility to a host of diseases. Vitamin D supplements during pregnancy and the early years could have a beneficial effect on a child's health in later life. Some countries such as France have instituted this as a routine public health measure."

The main source of vitamin D in the body comes from exposing the skin to sunlight, although a diet of oily fish can provide some of the vitamin. Research has previously suggested that lighter skin colour and hair colour evolved in populations moving to parts of the globe with less sun to optimise production of vitamin D in the body. A lack of vitamin D can affect bone development, leading to rickets; in pregnant mothers, poor bone health can be fatal to both mother and child at birth, hence there are selective pressures in favour of people who are able to produce adequate vitamin D.

This new study supports this hypothesis, having found a significant number of vitamin D receptor binding sites in regions of the genome with genetic changes more commonly found in people of European and Asian descent. It is probable that skin lightening as we migrated out of Africa resulted from the necessity to be able to make more vitamin D and prevent rickets: vitamin D deficiency led to pelvic contraction resulting in increased risk of fatality of both mother and unborn child, effectively ending maternal lineages unable to find ways of increasing availability of the vitamin.

"Vitamin D status is potentially one of the most powerful selective pressures on the genome in relatively recent times," says Professor George Ebers, Action Medical Research Professor of Clinical Neurology and one of the senior authors of the paper. "Our study appears to support this interpretation and it may be we have not had enough time to make all the adaptations we have needed to cope with our northern circumstances."

WebMD included the following

"Many experts, including Ramagopalan, say 2,000 IU of the vitamin may be optimal for preventing disease."

Summary of the paper by Dr David Grimes (Updated Sept 20, 2010)

He is the author of VITAMIN D and cholesterol - The importance of the sun

His web site is http://www.vitamin-d-deficiency.co.uk/

Vitamin D is a pre-hormone, synthesised in the skin by the action of the sun, and also obtained from diet, especially from fish. It is converted in the body to calcidiol and then to calcitriol, its active form and the real hormone. A hormone is a chemical messenger that transmits a signal from one part of the body to another, to target cells, which contain specific receptors. When it reaches the target cells by circulation in the blood, calcitriol binds to its vitamin D receptor (VDR), and it is the VDR that is responsible for actions within the cells. VDRs are complex proteins that are inherited and are therefore found within the genome, the intra-nuclear DNA. The VDR inside the target cells then combines with retinoid X receptor (RXR) to form a “hetero-dimer”. This in turn binds with vitamin D responsive elements (VDREs), which influence gene transcription and which activate genes.

The laboratory method used in this study is that of “ChIP-seq” (chromatin immuno-precipitation with massively parallel sequencing). It used lymphoblastoid cells.

The study confirmed VDR binding with specific genes, including the VDR gene itself.

The research paper confirms VDR binding sites on the genome, but of great importance it identified that calcitriol enriches the genome VDR binding sites.
This demonstrates a very important role for vitamin D.

2776 VDR binding sites were identified.

Many genes were influenced by vitamin D as calcitriol: 226 genes were significantly up-regulated and three were significantly down-regulated by calcitriol stimulation.

The genes significantly enriched were those associated with immune functions.

The action of VDR is of major importance as a gene transcription factor activated by calcitriol (a “ligand”, a chemical messenger from outside a cell that activates processes within the cell).

The study illustrates how specific genetic and environmental risk factors may interact. Given the very rapid recent increase in knowledge of genes (strictly “genomic loci”) that are important in common diseases, the study sought to determine whether VDR binding sites preferentially occur within specific disease genomic intervals.

The genomic intervals studied included those for Type 1 Diabetes (T1D), Crohn’s disease (CD) and multiple sclerosis (MS), together with 44 other common conditions.

Strikingly significant enrichment for VDR binding was found in the genomic intervals for MS, T1D, CD, systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), chronic lymphocytic leukaemia (CLL), colorectal cancer, hair colour, tanning, and height.

This analysis highlighted a number of gene loci in which roles for vitamin D in gene regulation had not previously been proposed. For example, VDR binding sites involving IRF8, which is associated with MS, and in PTPN2, a gene locus strongly implicated in both Crohns disease and T1D. Both genes showed increased expression after calcitriol, and similarly gene loci such as PTPN22 and CD226, which have been strongly associated with autoimmune disease.

Also observed was significant enrichment of VDR binding by calcitriol in genes that are expressed in all MS forms, compared with controls.