Chromatin Accessibility and Gene Expression Dynamics Suggest Immune-Modulatory Effects of Vitamin D3 In Vivo [ATAC-seq]
Vitamin D3 is a key micronutrient known to support innate immunity and modulate adaptive responses, with in vitro studies suggesting involvement of epigenetic mechanisms. However, in vivo evidence for such regulation remains limited. In this proof-of-principle study, we investigated genome-wide epigenomic and transcriptomic responses to vitamin D3 in a high responder (n=1) from the VitDHiD intervention trial. The participant received monthly oral boluses of 80,000 IU vitamin D3 over three months. Peripheral blood mononuclear cells were collected at baseline (day 0) and at 24 and 48 hours post-supplementation (days 1 and 2) for ATAC-seq and RNA-seq profiling. ATAC-seq revealed over 3,500 regions with increased chromatin accessibility, mainly at gene promoters, indicating a strong epigenomic response. Motif enrichment analysis identified immune-regulatory transcription factors, but not VDR (vitamin D receptor) motifs, suggesting indirect or cooperative regulation. RNA-seq identified 380 vitamin D target genes with time-dependent expression changes, including DUSP6 and FOS. Functional enrichment highlighted pathways related to innate immunity and interferon signaling. Integrative analysis linked 306 differentially expressed genes to nearby vitamin D-sensitive chromatin regions, including both promoters and enhancers. Many of these overlapped with VDR binding sites and promoters of neighboring non-target genes, indicating potential long-range regulatory interactions. Redundancies in regulatory elements were observed among closely located genes sharing enhancers and promoters. These findings provide in vivo evidence that vitamin D3 modulates chromatin accessibility and gene expression, supporting its role as an epigenetic regulator of immune function and highlighting its potential in personalized nutrition and immune health. Overall design: ATAC-seq libraries of PBMCs obtained from a healthy individual before (day 0) as well as 24 hour (day 1) and 48 hours (day 2) after taking a vitamin D3 bolus (80.000 IU) in three biological repeats