Histone lysine demethylases: Emerging roles in development, physiology and disease

Nature Reviews Genetics

Volumn 8, Issue 11, 2007, Pages 829-833

  Shi, Yang ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE LYSINE METHYLTRANSFERASE; HISTONE METHYLTRANSFERASE;

CANCER; CHROMATIN; DISEASE ASSOCIATION; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME SPECIFICITY; EPIGENETICS; EUKARYOTIC CELL; GENE CONTROL; GENE MUTATION; GENE OVEREXPRESSION; GENETIC REGULATION; GENOME; HUMAN; MOLECULAR DYNAMICS; NEUROLOGIC DISEASE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN METHYLATION; REVIEW;

AMINO ACID SEQUENCE; ANIMALS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; HUMANS; LYSINE; METHYLATION; MOLECULAR SEQUENCE DATA; NEOPLASMS; NERVOUS SYSTEM DISEASES;

EUKARYOTA;

EID: 35349006314     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2218     Document Type: Review

References (64)

1. Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41-45 (2000).
2. Zhang, Y. & Reinberg, D. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev. 15, 2343-2360 (2001).
3. Margueron, R., Trojer, P. & Reinberg, D. The key to development: interpreting the histone code? Curr. Opin. Genet. Dev. 15, 163-176 (2005).
4. Sanders, S. L. et al. Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell 119, 603-614 (2004).
5. Shi, Y. & Whetstine, J. R. Dynamic regulation of histone lysine methylation by demethylases. Mol. Cell 25, 1-14 (2007).
6. Klose, R. J., Kallin, E. M. & Zhang, Y. JmjC-domain-containing proteins and histone demethylation. Nature Rev. Genet. 7, 715-727 (2006).
7. Lee, M. G. et al. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 30 August 2007 (doi:10.1126/science.1149042).
8. Agger, K. et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 22 August 2007 (doi:10.1038/nature06145).
9. De Santa, F. et al. The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 5 September 2007 (doi:10.1016/j.cell.2007.08.019).
10. Lan, F. et al. A histone H3 lysine 27 demthylase regulates animal posterior development. Nature 12 September 2007 (epub ahead of print).
11. Wang, J. et al. Opposing LSD1 complexes function in developmental gene activation and repression programmes. Nature 446, 882-887 (2007).
12. Di Stefano, L., Ji, J. Y., Moon, N. S., Herr, A. & Dyson, N. Mutation of Drosophila Lsd1 disrupts H3-K4 methylation, resulting in tissue-specific defects during development. Curr. Biol. 17, 808-812 (2007).
13. He, Y., Michaels, S. D. & Amasino, R. M. Regulation of flowering time by histone acetylation in Arabidopsis. Science 302, 1751-1754 (2003).
14. Eimer, S., Lakowski, B., Donhauser, R. & Baumeister, R. Loss of spr-5 bypasses the requirement for the C.elegans presenilin sel-12 by derepressing hop-1. EMBO J. 21, 5787-5796 (2002).
15. Jarriault, S. & Greenwald, I. Suppressors of the egg-laying defective phenotype of sel-12 presenilin mutants implicate the CoREST co-repressor complex in LIN-12/Notch signalling in C. elegans. Genes Dev. 16, 2713-2728 (2002).
16. Saleque, S., Kim, J., Rooke, H. M. & Orkin, S. H. Epigenetic regulation of haematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1. Mol. Cell 27, 562-572 (2007).
17. Garcia-Bassets, I. et al. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell 128, 505-518 (2007).
18. Godmann, M. et al. Dynamic regulation of histone H3 methylation at lysine 4 in mammalian spermatogenesis. Biol. Reprod. 18 July 2007 (doi:10.1095/biolreprod.107.062265).
19. Gildea, J. J., Lopez, R. & Shearn, A. A screen for new trithorax group genes identified little imaginal discs, the Drosophila melanogaster homologue of human retinoblastoma binding protein 2. Genetics 156, 645-663 (2000).
20. Secombe, J., Li, L., Carlos, L. & Eisenman, R. N. The Trithorax group protein LID is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth. Genes Dev. 21, 537-551 (2007).
21. Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039-1043 (2002).
22. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893-2905 (2002).
23. Czermin, B. et al. Drosophila Enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111, 185-196 (2002).
24. Muller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197-208 (2002).
25. Trojer, P. & Reinberg, D. Histone lysine demethylases and their impact on epigenetics. Cell 125, 213-217 (2006).
26. Lan, F. et al. S. pombe LSD1 homologues regulate heterochromatin propagation and euchromatic gene transcription. Mol. Cell 26, 89-101 (2007).
27. Opel, M. et al. Genome-wide studies of histone demethylation catalysed by the fission yeast homologues of mammalian LSD1. PLoS ONE 2, e386 (2007).
28. Gordon, M. et al. Genome?wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol. Cell. Biol. 27, 4058-4069 (2007).
29. Metzger, E. et al. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437, 436-439 (2005).
30. Rudolph, T. et al. Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homologue SU(VAR)3-3. Mol. Cell 26, 103-115 (2007).
31. Yamane, K. et al. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125, 483-495 (2006).
32. Wissmann, M. et al. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nature Cell Biol. 9, 347-353 (2007).
33. Heery, D. M., Kalkhoven, E., Hoare, S. & Parker, M. G. A signature motif in transcriptinal co-activators mediates binding to nuclear receptors. Nature 387, 733-736 (1997).
34. Yamane, K. et al. PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol. Cell 25, 801-812 (2007).
35. Lee, J. W., Choi, H. S., Gyuris, J., Brent, R. & Moore, D. D. Two classes of proteins dependent on either the presence or absence of thyroid hormone for interaction with the thyroid hormone receptor. Mol. Endocrinol. 9, 243-254 (1995).
36. Schneider, R., Bannister, A. J. & Kouzarides, T. Unsafe SETs: histone lysine methyltransferases and cancer. Trends Biochem. Sci. 27, 396-402 (2002).
37. Fraga, M. F. et al. Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nature Genet. 37, 391-400 (2005).
38. Kahl, P. et al. Androgen receptor co-activators lysine-specific histone demethylase 1 and four and a half LIM domain protein 2 predict risk of prostate cancer recurrence. Cancer Res. 66, 11341-11347 (2006).
39. Scoumanne, A. & Chen, X. The lysine-specific demethylase 1 is required for cell proliferation in both p53-dependent and -independent manners. J. Biol. Chem. 282, 15471-15475 (2007).
40. Bradley, C. et al. Carcinogen-induced histone alteration in normal human mammary epithelial cells. Carcinogenesis 29 April 2007 (doi:10.1093/carcin/bgm100).
41. Lee, M. G., Wynder, C., Schmidt, D. M., McCafferty, D. G. & Shiekhattar, R. Histone H3 lysine 4 demethylation is a target of nonselective antidepressive medications. Chem. Biol. 13, 563-567 (2006).
42. Huang, Y. et al. Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes. Proc. Natl Acad. Sci. USA 104, 8023-8028 (2007).
43. Lu, P. J. et al. A novel gene (PLU-1) containing highly conserved putative DNA/chromatin binding motifs is specifically upregulated in breast cancer. J. Biol. Chem. 274, 15633-15645 (1999).
44. Barrett, A. et al. PLU-1 nuclear protein, which is upregulated in breast cancer, shows restricted expression in normal human adult tissues: a new cancer/testis antigen? Int. J. Cancer 101, 581-588 (2002).
45. Yang, Z. Q. et al. Identification of a novel gene, GASC1, within an amplicon at 9p23-24 frequently detected in esophageal cancer cell lines. Cancer Res. 60, 4735-4739 (2000).
46. Klose, R. J. et al. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128, 889-900 (2007).
47. Christensen, J. et al. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 128, 1063-1076 (2007).
48. Fattaey, A. R. et al. Characterization of the retinoblastoma binding proteins RBP1 and RBP2. Oncogene 8, 3149-3156 (1993).
49. Cloos, P. A. et al. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442, 307-311 (2006).
50. Tsuneoka, M., Koda, Y., Soejima, M., Teye, K. & Kimura, H. A novel MYC target gene, Mina53, that is involved in cell proliferation. J. Biol. Chem. 277, 35450-35459 (2002).
51. Tsuneoka, M. et al. MINA53 as a potential prognostic factor for esophageal squamous cell carcinoma. Clin. Cancer Res. 10, 7347-7356 (2004).
52. Teye, K. et al. Increased expression of a MYC target gene MINA53 in human colon cancer. Am. J. Pathol. 164, 205-216 (2004).
53. Suzuki, C. et al. Identification of MYC-associated protein with JmjC domain as a novel therapeutic target oncogene for lung cancer. Mol. Cancer Ther. 6, 542-551 (2007).
54. Suzuki, T., Minehata, K., Akagi, K., Jenkins, N. A. & Copeland, N. G. Tumour suppressor gene identification using retroviral insertional mutagenesis in Blm-deficient mice. Embo J. 25, 3422-3431 (2006).
55. Whetstine, J. R. et al. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125, 467-481 (2006).
56. Jensen, L. R. et al. Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am. J. Hum. Genet. 76, 227-236 (2005).
57. Tzschach, A. et al. Novel JARID1C/SMCX mutations in patients with X-linked mental retardation. Hum. Mutat. 27, 389 (2006).
58. Iwase, S. et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128, 1077-1088 (2007).
59. Tahiliani, M. et al. The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. Nature (2007).
60. Abidi, F., Miano, M., Murray, J. & Schwartz, C. A novel mutation in the PHF8 gene is associated with X-linked mental retardation with cleft lip/cleft palate. Clin. Genet. 72, 19-22 (2007).
61. Laumonnier, F. et al. Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate. J. Med. Genet. 42, 780-786 (2005).
62. Koivisto, A. M. et al. Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate. Clin. Genet. 72, 145-149 (2007).
63. Fiala, J. C., Spacek, J. & Harris, K. M. Dendritic spine pathology: cause or consequence of neurological disorders? Brain Res. Brain Res. Rev. 39, 29-54 (2002).
64. Ropers, H. H. & Hamel, B. C. X-linked mental retardation. Nature Rev. Genet. 6, 46-57 (2005).