Difference and Similarity of DNA Sequence Recognized by VDR Homodimer and VDR/RXR Heterodimer

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1994 Aug 11

PMID 8065900

Citations 14

Authors

J Nishikawa

M Kitaura

M Matsumoto

M Imagawa

T Nishihara

Affiliations

Soon will be listed here.

Abstract

Nuclear receptors for the thyroid hormone and vitamin A and D cooperate with the retinoid X receptor (RXR) in activating the transcription. Although the hormone response elements for these receptors have been proposed in which spacing of the direct repeated motifs determine the specificity (so called 3-4-5 rule), vitamin D response elements (VDREs) in the natural context consist of often imperfect direct repeats. Vitamin D receptor (VDR) alone can bind to the mouse osteopontin (mSPP-1) VDRE, which contains a direct repeat separated by 3 nucleotides, but not to the rat osteocalcin (rOST) VDRE having inexact direct repeat. The presence of RXR not only allows the VDR to bind to the rOST VDRE, but also increases the binding affinity for the mSPP-1 VDRE. The RXR/VDR heterodimer exhibits the similar affinity constants for the mSPP-1 VDRE and the rOST VDRE, in spite of the apparently different affinities for two VDREs of the VDR homodimer. A random oligonucleotide selection procedure revealed that the consensus sequence selected by the RXR homodimer is the direct repeat spaced by one A residue. In contrast, the sequences preferentially selected by the VDR homodimer and the VDR/RXR heterodimer are similar, which are the direct repeats spaced by 3 nucleotides. The difference and similarity of DNA sequence recognition are discussed.

Citing Articles

Vitamin D Receptor Regulates Liver Regeneration After Partial Hepatectomy in Male Mice.

Elangovan H, Stokes R, Keane J, Chahal S, Samer C, Agoncillo M Endocrinology. 2024; 165(8).

PMID: 38963813 PMC: 11250209. DOI: 10.1210/endocr/bqae077.

A Review: Highlighting the Links between Epigenetics, COVID-19 Infection, and Vitamin D.

Foolchand A, Mazaleni S, Ghazi T, Chuturgoon A Int J Mol Sci. 2022; 23(20).

PMID: 36293144 PMC: 9603374. DOI: 10.3390/ijms232012292.

HOTAIR but not ANRIL long non-coding RNA contributes to the pathogenesis of multiple sclerosis.

Pahlevan Kakhki M, Nikravesh A, Shirvani Farsani Z, Sahraian M, Behmanesh M Immunology. 2017; 153(4):479-487.

PMID: 29030863 PMC: 5838425. DOI: 10.1111/imm.12850.

The regulatory role of miRNAs on VDR in breast cancer.

Singh T, Adams B Transcription. 2017; 8(4):232-241.

PMID: 28598255 PMC: 5574530. DOI: 10.1080/21541264.2017.1317695.

Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes.

Singh P, van den Berg P, Long M, Vreugdenhil A, Grieshober L, Ochs-Balcom H BMC Genomics. 2017; 18(1):132.

PMID: 28166722 PMC: 5294817. DOI: 10.1186/s12864-017-3481-4.

References

Green S, Walter P, Kumar V, Krust A, Bornert J, Argos P . Human oestrogen receptor cDNA: sequence, expression and homology to v-erb-A. Nature. 1986; 320(6058):134-9. DOI: 10.1038/320134a0. View

Ross T, Moss V, Prahl J, DeLuca H . A nuclear protein essential for binding of rat 1,25-dihydroxyvitamin D3 receptor to its response elements. Proc Natl Acad Sci U S A. 1992; 89(1):256-60. PMC: 48215. DOI: 10.1073/pnas.89.1.256. View

Studier F, Moffatt B . Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 1986; 189(1):113-30. DOI: 10.1016/0022-2836(86)90385-2. View

Weinberger C, Thompson C, Ong E, Lebo R, Gruol D, Evans R . The c-erb-A gene encodes a thyroid hormone receptor. Nature. 1986; 324(6098):641-6. DOI: 10.1038/324641a0. View

Kerner S, Scott R, Pike J . Sequence elements in the human osteocalcin gene confer basal activation and inducible response to hormonal vitamin D3. Proc Natl Acad Sci U S A. 1989; 86(12):4455-9. PMC: 287288. DOI: 10.1073/pnas.86.12.4455. View

Demay M, Gerardi J, DeLuca H, Kronenberg H . DNA sequences in the rat osteocalcin gene that bind the 1,25-dihydroxyvitamin D3 receptor and confer responsiveness to 1,25-dihydroxyvitamin D3. Proc Natl Acad Sci U S A. 1990; 87(1):369-73. PMC: 53265. DOI: 10.1073/pnas.87.1.369. View

Darwish H, DeLuca H . Identification of a 1,25-dihydroxyvitamin D3-response element in the 5'-flanking region of the rat calbindin D-9k gene. Proc Natl Acad Sci U S A. 1992; 89(2):603-7. PMC: 48287. DOI: 10.1073/pnas.89.2.603. View

Leid M, Kastner P, Lyons R, Nakshatri H, Saunders M, Zacharewski T . Purification, cloning, and RXR identity of the HeLa cell factor with which RAR or TR heterodimerizes to bind target sequences efficiently. Cell. 1992; 68(2):377-95. DOI: 10.1016/0092-8674(92)90478-u. View

Freedman L, Towers T . DNA binding properties of the vitamin D3 receptor zinc finger region. Mol Endocrinol. 1991; 5(12):1815-26. DOI: 10.1210/mend-5-12-1815. View

10.

Bugge T, Pohl J, Lonnoy O, Stunnenberg H . RXR alpha, a promiscuous partner of retinoic acid and thyroid hormone receptors. EMBO J. 1992; 11(4):1409-18. PMC: 556590. DOI: 10.1002/j.1460-2075.1992.tb05186.x. View

11.

Marks M, Hallenbeck P, Nagata T, Segars J, Appella E, Nikodem V . H-2RIIBP (RXR beta) heterodimerization provides a mechanism for combinatorial diversity in the regulation of retinoic acid and thyroid hormone responsive genes. EMBO J. 1992; 11(4):1419-35. PMC: 556591. DOI: 10.1002/j.1460-2075.1992.tb05187.x. View

12.

Zhang X, Lehmann J, Hoffmann B, Dawson M, Cameron J, Graupner G . Homodimer formation of retinoid X receptor induced by 9-cis retinoic acid. Nature. 1992; 358(6387):587-91. DOI: 10.1038/358587a0. View

13.

Kliewer S, Umesono K, Noonan D, HEYMAN R, Evans R . Convergence of 9-cis retinoic acid and peroxisome proliferator signalling pathways through heterodimer formation of their receptors. Nature. 1992; 358(6389):771-4. PMC: 6159883. DOI: 10.1038/358771a0. View

14.

Towers T, Luisi B, Asianov A, Freedman L . DNA target selectivity by the vitamin D3 receptor: mechanism of dimer binding to an asymmetric repeat element. Proc Natl Acad Sci U S A. 1993; 90(13):6310-4. PMC: 46918. DOI: 10.1073/pnas.90.13.6310. View

15.

Perlmann T, Rangarajan P, Umesono K, Evans R . Determinants for selective RAR and TR recognition of direct repeat HREs. Genes Dev. 1993; 7(7B):1411-22. DOI: 10.1101/gad.7.7b.1411. View

16.

Nishikawa J, Matsumoto M, Sakoda K, Kitaura M, Imagawa M, Nishihara T . Vitamin D receptor zinc finger region binds to a direct repeat as a dimer and discriminates the spacing number between each half-site. J Biol Chem. 1993; 268(26):19739-43. View

17.

Mader S, Chen J, Chen Z, White J, Chambon P, Gronemeyer H . The patterns of binding of RAR, RXR and TR homo- and heterodimers to direct repeats are dictated by the binding specificites of the DNA binding domains. EMBO J. 1993; 12(13):5029-41. PMC: 413763. DOI: 10.1002/j.1460-2075.1993.tb06196.x. View

18.

Cao X, Ross F, Zhang L, MacDonald P, Chappel J, Teitelbaum S . Cloning of the promoter for the avian integrin beta 3 subunit gene and its regulation by 1,25-dihydroxyvitamin D3. J Biol Chem. 1993; 268(36):27371-80. View

19.

Zierold C, Darwish H, DeLuca H . Identification of a vitamin D-response element in the rat calcidiol (25-hydroxyvitamin D3) 24-hydroxylase gene. Proc Natl Acad Sci U S A. 1994; 91(3):900-2. PMC: 521420. DOI: 10.1073/pnas.91.3.900. View

20.

DeLuca H, Schnoes H . Vitamin D: recent advances. Annu Rev Biochem. 1983; 52:411-39. DOI: 10.1146/annurev.bi.52.070183.002211. View