Circadian Regulation of Vitamin D Target Genes Reveals a Network Shaped by Individual Responsiveness
Abstract
1. Introduction
2. Materials and Methods
2.1. Transcriptome Data Sources
2.2. Differential Gene Expression Analysis
2.3. Characterization of Target Genes
2.4. Analysis of Genomic Regions of Vitamin D Target Genes
2.5. Statistical Tests
3. Results
3.1. Circadian Expression Profile of In Vivo Vitamin D Target Genes
3.2. Characterization of Vitamin D Targets with Circadian Behavior
3.3. Individual-Specific Responses of Circadian Vitamin D Target Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
1,25(OH)2D3 | 1α,25-dihydroxyvitamin D3 |
AMIGO2 | adhesion molecule with Ig-like domain 2 |
AMPK | AMP-activated protein kinase |
AQP9 | aquaporin 9 |
ASCL1 | acyl-CoA synthetase long chain family member 1 |
BCL | BCL transcription coactivator |
C5AR1 | complement C5a receptor 1 |
CCR7 | C-C motif chemokine receptor 7 |
CD3G | CD3 gamma subunit of T-cell receptor complex |
CD93 | CD93 molecule |
ChIP-seq | chromatin immunoprecipitation sequencing |
CPM | counts per million |
CPPED1 | calcineurin-like phosphoesterase domain containing 1 |
CREB5 | CAMP responsive element binding protein 5 |
CRISPLD2 | cysteine-rich secretory protein LCCL domain containing 2 |
CSF2RB | colony stimulating factor 2 receptor subunit beta |
CSF3R | colony stimulating factor 3 receptor |
CSRNP1 | cysteine- and serine-rich nuclear protein 1 |
DYSF | dysferlin |
FAIRE-seq | formaldehyde-assisted isolation of regulatory elements followed by sequencing |
FC | fold change |
FCGR2A | Fc gamma receptor IIa |
FDR | false discovery rate |
FGR | FGR proto-oncogene, Src family tyrosine kinase |
FOSL2 | FOS-like 2, AP1 transcription factor subunit |
GADD45B | growth arrest and DNA damage inducible beta |
GAS7 | growth arrest specific 7 |
IRAK3 | interleukin 1 receptor-associated kinase 3 |
IRS2 | insulin receptor substrate 2 |
JDP2 | Jun dimerization protein 2 |
KLF11 | KLF transcription factor 11 |
MAP3K7CL | MAP3K7 C-terminal like |
MYC | MYC proto-oncogene, BHLH transcription factor |
NAMPT | nicotinamide phosphoribosyltransferase |
NDEL1 | NudE neurodevelopment protein 1 like 1 |
NINJ1 | ninjurin 1 |
NLRP12 | NLR family pyrin domain containing 12 |
PADI2 | peptidyl arginine deiminase |
PBMC | peripheral blood mononuclear cell |
PER1 | period circadian regulator 1 |
PFKFB3 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 |
PILRA | paired immunoglobin-like type 2 receptor alpha |
PRKAG2 | protein kinase AMP-activated non-catalytic subunit gamma 2 |
RARA | retinoic acid receptor alpha |
RNA-seq | RNA sequencing |
RNF19B | ring finger protein 19B |
SIK3 | SIK family kinase 3 |
SIPA1L2 | signal-induced proliferation-associated 1 like 2 |
SIRPB2 | signal regulatory protein beta 2 |
SLC | solute carrier family |
STX11 | syntaxin 11 |
TAD | topologically associating domain |
TIMP2 | TIMP metallopeptidase inhibitor 2 |
TOM1 | target of Myb1 membrane trafficking protein |
TPCN2 | two pore segment channel 2 |
TREM1 | triggering receptor expressed on myeloid cells 1 |
TSC22D3 | TSC22 domain family member 3 |
TSS | transcription start site |
VDR | vitamin D receptor |
WDFY3 | WD repeat and FYVE domain containing 3 |
ZNF | zinc finger protein |
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Maissan, P.; Carlberg, C. Circadian Regulation of Vitamin D Target Genes Reveals a Network Shaped by Individual Responsiveness. Nutrients 2025, 17, 1204. https://doi.org/10.3390/nu17071204
Maissan P, Carlberg C. Circadian Regulation of Vitamin D Target Genes Reveals a Network Shaped by Individual Responsiveness. Nutrients. 2025; 17(7):1204. https://doi.org/10.3390/nu17071204
Chicago/Turabian StyleMaissan, Parcival, and Carsten Carlberg. 2025. "Circadian Regulation of Vitamin D Target Genes Reveals a Network Shaped by Individual Responsiveness" Nutrients 17, no. 7: 1204. https://doi.org/10.3390/nu17071204
APA StyleMaissan, P., & Carlberg, C. (2025). Circadian Regulation of Vitamin D Target Genes Reveals a Network Shaped by Individual Responsiveness. Nutrients, 17(7), 1204. https://doi.org/10.3390/nu17071204