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Large-Scale in Silico and Microarray-Based Identification of Direct 1,25-Dihydroxyvitamin D₃ Target Genes

Departments of Physiology (T.T.W., E.L., Y.N., N.B.M., R.Z., V.B., A.K., B.L. J.H.W.) and Medicine (L.E.T.-M., S.M., J.H.W.), McGill University and Genome Quebec Innovation Centre (Y.N.), Centre for Nonlinear Dynamics in Physiology and Medicine (E.L., Y.N.), McGill University, Montréal, Québec H3G 1Y6, Canada; and Département de Biochimie (D.L., V.B., S.M.), Université de Montréal, Montréal, Québec H3A 1A4, Canada

Address all correspondence and requests for reprints to: John H. White, Department of Physiology, McIntyre Building, Room 1128, McGill University, 3655 Drummond Street, Montreal, Quebec H3G 1Y6, Canada. E-mail: john.white{at}mcgill.ca.

1,25-Dihydroxyvitamin D₃ [1,25(OH)₂D₃] regulates calcium homeostasis and controls cellular differentiation and proliferation. The vitamin D receptor (VDR) is a ligand-regulated transcription factor that recognizes cognate vitamin D response elements (VDREs) formed by direct or everted repeats of PuG(G/T)TCA motifs separated by 3 or 6 bp (DR3 or ER6). Here, we have identified direct 1,25(OH)₂D₃ target genes by combining 35,000+ gene microarrays and genome-wide screens for consensus DR3 and ER6 elements, and DR3 elements containing single nucleotide substitutions. We find that the effect of a nucleotide substitution on VDR binding in vitro does not predict VDRE function in vivo, because substitutions that disrupted binding in vitro were found in several functional elements. Hu133A microarray analyses, performed with RNA from human SCC25 cells treated with 1,25(OH)₂D₃ and protein synthesis inhibitor cycloheximide, identified more than 900 regulated genes. VDREs lying within –10 to +5 kb of 5'-ends were assigned to 65% of these genes, and VDR binding was confirmed to several elements in vivo. A screen of the mouse genome identified more than 3000 conserved VDREs, and 158 human genes containing conserved elements were 1,25(OH₂)D₃-regulated on Hu133A microarrays. These experiments also revealed 16 VDREs in 11 of 12 genes induced more than 10-fold in our previous microarray study, five elements in the human gene encoding the epithelial calcium channel TRPV6, as well as novel 1,25(OH₂)D₃ target genes implicated in regulation of cell cycle progression. The combined approaches used here thus provide numerous insights into the direct target genes underlying the broad physiological actions of 1,25(OH)₂D₃.

NURSA Molecule Pages Link:

Nuclear Receptors:   VDR  |  RXRα

Ligands:   Calcitriol

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