Hormonal gene regulation through DNA methylation and demethylation

Epigenomics

Volumn 2, Issue 6, 2010, Pages 765-774

  Kouzmenko, Alexander ^a,b   Ohtake, Fumiaki ^a   Fujiki, Ryoji ^a   Kato, Shigeaki ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b ALFAISAL UNIVERSITY   (Saudi Arabia)

Author keywords

active DNA demethylation; CYP27B1; derepression; DNA methylation; DNMT1; DNMT3B; MBD4; PTH; transcriptional silencing; VDR

Indexed keywords

CYTOCHROME P450; CYTOCHROME P450 27B1; DNA; PARATHYROID HORMONE; UNCLASSIFIED DRUG; VITAMIN D RECEPTOR;

CHROMATIN; DEMETHYLATION; DNA METHYLATION; DNA MODIFICATION; E BOX ELEMENT; EPIGENETICS; GENE ACTIVATION; GENE ACTIVITY; GENE CONTROL; GENE LOCUS; GENE STRUCTURE; GENOMICS; PRIORITY JOURNAL; REVIEW;

25-HYDROXYVITAMIN D3 1-ALPHA-HYDROXYLASE; CHROMATIN; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; HUMANS; MODELS, BIOLOGICAL; PARATHYROID HORMONE; PROMOTER REGIONS, GENETIC; RECEPTORS, CALCITRIOL; SIGNAL TRANSDUCTION;

EID: 78650447193     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.10.58     Document Type: Review

References (60)

1. Kong A, Steinthorsdottir V, Masson G et al.: Parental origin of sequence variants associated with complex diseases. Nature 462, 868-874 (2009)
2. Ooi SKT, ODonnell AH, Bestor TH: Mammalian cytosine methylation at a glance. J. Cell Sci. 122, 2787-2791 (2009).
3. Bender J: DNA methylation and epigenetics. Annu. Rev. Plant Biol. 55, 41-68 (2004).
4. Bartolomei MS: Genomic imprinting: employing and avoiding epigenetic processes. Genes Dev. 23, 2124-2133 (2009).
5. Guibert S, Forne T, Weber M: Dynamic regulation of DNA methylation during mammalian development. Epigenomics 1, 81-98 (2009).
6. Mohn F, Schubeler D: Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends Genet. 25, 129-36 (2009).
7. Law JA, Jacobsen SE: Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204-220 (2010).
8. Aravin AA, Bourchis D: Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev. 22, 970-975 (2008).
9. Zhu JK: Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 43, 143-66 (2009).
10. Huh JH, Bauer MJ, Hsieh TF, Fischer RL: Cellular programming of plant gene imprinting. Cell 132, 735-744 (2008).
11. Chotalia M, Smallwood SA, Ruf N et al.: Transcription is required for establishment of germline methylation marks at imprinted genes. Genes Dev. 23, 105-117 (2009).
12. Gehring M, Reik W, Henikoff S: DNA demethylation by DNA repair. Trends Genet. 25, 82-90 (2009).
13. Reid G, Gallais R, Métivier R: Marking time: the dynamic role of chromatin and covalent modification in transcription. Int. J. Biochem. Cell Biol. 41, 155-63 (2009).
14. Métivier R, Gallais R, Tiffoche C et al.: Cyclical DNA methylation of a transcriptionally active promoter. Nature 452, 45-50 (2008). nn Together with the [14], presents first evidence of cyclical DNA methylation and demethylation at constitutively active gene promoter.
15. Kangaspeska S, Stride B, Métivier R et al.: Transient cyclical methylation of promoter DNA. Nature 452, 112-115 (2008). n Back-to-back paper with the previous reference to report transient DNA methylation/demethylation of several actively transcribed mammalian genes.
16. Laird PW: Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet. 11, 191-203 (2010).
17. Cheng X, Blumenthal RM: Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochemistry 49, 2999-3008 (2010).
18. Kato S: Genetic mutation in the human 25-hydroxyvitamin D3 1a-hydroxylase gene causes vitamin D-dependent rickets type I. Mol. Cell. Endocrinol. 156, 7-12 (1999).
19. Kato S, Yoshizazawa T, Kitanaka S, Murayama A, Takeyama K: Molecular genetics of vitamin D- dependent hereditary rickets. Horm. Res. 57, 73-78 (2002).
20. Takeyama K, Kitanaka S, Sato T, Kobori M, Yanagisawa J, Kato S: 25-hydroxyvitamin D3 1a-hydroxylase and vitamin D synthesis. Science 277, 1827-1830 (1997).
21. Mangelsdorf DJ, Thummel C, Beato M et al.: The nuclear receptor superfamily: the second decade. Cell 83, 835-839 (1995).
22. Yoshizawa T, Handa Y, Uematsu Y et al.: Mice lacking the vitamin D receptor exhibit impaired bone formation, uterine hypoplasia and growth retardation after weaning. Nat. Genet. 16, 391-396 (1997).
23. Bouillon R, Carmeliet G, Verlinden L et al.: Vitamin D and human health: lessons from vitamin D receptor null mice. Endocr. Rev. 29, 726-776 (2008).
24. McCullough ML, Bostick RM, Mayo TL: Vitamin D gene pathway polymorphisms and risk of colorectal, breast, and prostate cancer. Annu. Rev. Nutr. 29, 111-132 (2009).
25. Haussler MR, Haussler CA, Bartik L et al.: Vitamin D receptor: molecular signaling and actions of nutritional ligands in disease prevention. Nutr. Rev. 66(Suppl. 2), S98-S112 (2008)
26. Rachez C, Lemon D, Suldan Z et al.: Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex. Nature 398, 824-828 (1999).
27. Glass CK, Rosenfeld MG: The coregulator exchange in transcriptional functions of nuclear receptors. Genes Dev. 14, 121-141 (2000).
28. Kitagawa H, Fujiki R, Yoshimura K et al.: The chromatin remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams Syndrome. Cell 113, 1-13 (2003).
29. Murayama A, Kim MS, Yanagisawa J, Takeyama K, Kato S: Transrepression by a liganded nuclear receptor via a bHLH activator through co-regulator switching. EMBO J. 23, 1598-1608 (2004).
30. DeLuca HF: Overview of general physiologic features and functions of vitamin D. Am. J. Clin. Nutr. 80(Suppl.), 1689S-1696S (2004).
31. Meyer MB, Watanuki M, Kim S, Shevde NK, Pike JW: The human transient receptor potential vanilloid type 6 distal promoter contains multiple vitamin D receptor binding sites that mediate activation by 1,25-dihydroxyvitamin D3 in intestinal cells. Mol. Endocrinol. 20, 1447-1461 (2006).
32. Dusso AS, Brown AJ, Slatopolsky E: Vitamin D. Am. J. Physiol. Renal. Physiol. 289, F8-F28 (2005).
33. Alroy I, Towers TL, Freedman LP: Transcriptional repression of the interleukin-2 gene by vitamin D3: direct inhibition of NFATp/AP-1 complex formation by a nuclear hormone receptor. Mol. Cell. Biol. 15, 5789-5799 (1995).
34. Demay MB, Kiernan MS, DeLuca HF, Kronenberg HM: Sequences in the human parathyroid hormone gene that bind the 1,25-dihydroxyvitamin D3 receptor and mediate transcriptional repression in response to 1,25-dihydroxyvitamin D3. Proc. Natl. Acad. Sci. USA 89, 8097-8101 (1992).
35. Falzon M: DNA sequences in the rat parathyroid hormone related peptide gene responsible for 1,25-dihydroxyvitamin D3-mediated transcriptional repression. Mol. Endocrinol. 10, 672-681 (1996).
36. Russell J, Ashok S, Koszewski NJ: Vitamin D receptor interactions with the rat parathyroid hormone gene: synergistic effects between two negative vitamin D response elements. J. Bone Miner. Res. 14, 1828-1837 (1999). (Pubitemid 29521777)
37. Kim MS, Fujiki R, Murayama A et al.: 1a,25(OH)2D3-induced transrepression by vitamin D receptor through E-box-type elements in the human parathyroid hormone gene promoter. Mol. Endocrinol. 21, 334-342 (2007).
38. Henry HL: Parathyroid hormone modulation of 25-hydroxyvitamin D3 metabolism by cultured chick kidney cells is mimicked and enhanced by forskolin. Endocrinology 116, 503-510 (1985).
39. Fujiki R, Kim MS, Sasaki Y, Yoshimura K, Kitagawa H, Kato S: Ligand-induced transrepression by VDR through association of WSTF with acetylated histones. EMBO J. 24, 3881-3894 (2005).
40. Xu W, Chen H, Du K et al.: A transcriptional switch mediated by cofactor methylation. Science 294, 2507-2511 (2001).
41. Kato S, Fujiki R, Kitagawa H: Vitamin D receptor (VDR) promoter targeting through a novel chromatin remodeling complex. J. Steroid Biochem. Mol. Biol. 89-90, 173-178 (2004).
42. Kim MS, Kondo T, Takada I et al.: DNA demethylation in hormone-induced transcriptional derepression. Nature 461, 1007-1012 (2009).
43. Okano M, Bell DW, Haber DA, Li E: DNA methyltransferases DNMT3A and DNMT3B are essential for de novo methylation and mammalian development. Cell 99, 247-257 (1999).
44. Howell CY, Bestor TH, Ding F et al.: Genomic imprinting disrupted by a maternal effect mutation in the DNMT1 gene. Cell 104, 829-838 (2001).
45. Rhee I, Bachman KE, Park BH et al.: DNMT1 and DNMT3B cooperate to silence genes in human cancer cells. Nature 416, 552-556 (2002).
46. Maison C, Almouzni G: HP1 and the dynamics of heterochromatin maintenance. Nat. Rev. Mol. Cell Biol. 5, 296-304 (2004).
47. Probst AV, Dunleavy E, Almouzni G: Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol. 10, 192-206 (2009).
48. Lee M, Partridge NC: Parathyroid hormone signaling in bone and kidney. Curr. Opin. Nephrol. Hypertens. 18, 298-302 (2009).
49. Simonsson S, Gurdon J: DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nat. Cell Biol. 6, 984-990 (2004).
50. Moss TJ, Wallrath LL: Connections between epigenetic gene silencing and human disease. Mutat. Res. 618, 163-174 (2007).
51. Hendrich B, Bird A: Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol. 18, 6538-6547 (1998).
52. Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A: The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401, 301-304 (1999).
53. Kondo E, Gu Z, Horii A, Fukushige S: The thymine DNA glycosylase MBD4 represses transcription and is associated with methylated p16(INK4a) and hMLH1 genes. Mol. Cell. Biol. 25, 4388-4396 (2005).
54. Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR: DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and Gadd45. Cell 135, 1201-1212 (2008).
55. Demple B, Sung JS: Molecular and biological roles of Ape1 protein in mammalian base excision repair. DNA Repair 4, 1442-1449 (2005).
56. David SS, OShea VL, Kundu S: Baseexcision repair of oxidative DNA damage. Nature 447, 941-945 (2007).
57. Métivier R, Penot G, Hübner MR et al.: Estrogen receptor-a directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751-763 (2003).
58. Métivier R, Huet G, Gallais R et al.: Dynamics of estrogen receptor-mediated transcriptional activation of responsive genes in vivo: apprehending transcription in four dimensions. Adv. Exp. Med. Biol. 617, 129-138 (2008).
59. Kriaucionis S, Heintz N: The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929-930 (2009).
60. Tahiliani M, Koh KP, Shen Y et al.: Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935 (2009).