Skip to main content
Log in

The JMJD2 members of histone demethylase revisited

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

The study of histone lysine demethylases has become very hot recently. Many histone demethylases have been reported by different research groups with various techniques. However, how many histone lysine-methylation states can be removed by one specific demethylase and how many demethylases can remove one specific histone lysine-methylation state? It remains a daunting challenge to answer these questions to date. An in-depth discussion on recent results, three important points were provided: (1) Some demethylases can remove more histone lysine-methylation states; (2) Some prokaryotes might be endowed with histone lysine demethylases although they are devoid of histones; (3) Protein-protein interaction provides a valuable framework for a better understanding of the functions of the histone lysine demethylases. All of these will be beneficial to a better understanding of demethylases and suggest how future research can be improved.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Byvoet P, Shepherd GR, Hardin JM, Noland BJ (1972) The distribution and turnover of labeled methyl groups in histone fractions of cultured mammalian cells. Arch Biochem Biophys 148:558–567

    Article  PubMed  CAS  Google Scholar 

  2. Thomas G, Lange HW, Hempel K (1972) Relative stability of lysine-bound methyl groups in arginie-rich histones and their subfrations in Ehrlich ascites tumor cells in vitro. Hoppe-Seyler’s Z Physiol Chem 353:1423–1428

    PubMed  CAS  Google Scholar 

  3. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941–953

    Article  PubMed  CAS  Google Scholar 

  4. Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y (2005) Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell 19:857–864

    Article  PubMed  CAS  Google Scholar 

  5. Christensen J, Agger K, Cloos PA, Pasini D, Rose S, Sennels L, Rappsilber J, Hansen KH, Salcini AE, Helin K (2007) RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 128:1063–1076

    Article  PubMed  CAS  Google Scholar 

  6. Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y (2007) The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128:1077–1088

    Article  PubMed  CAS  Google Scholar 

  7. Seward DJ, Cubberley G, Kim S, Schonewald M, Zhang L, Tripet B, Bentley DL (2007) Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat Struct Mol Biol 14:240–242

    Article  PubMed  CAS  Google Scholar 

  8. Liang G, Klose RJ, Gardner KE, Zhang Y (2007) Yeast Jhd2p is a histone H3 Lys4 trimethyl demethylase. Nat Struct Mol Biol 14:243–245

    Article  PubMed  CAS  Google Scholar 

  9. Eissenberg JC, Lee MG, Schneider J, Ilvarsonn A, Shiekhattar R, Shilatifard A (2007) The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase. Nat Struct Mol Biol 14:344–346

    Article  PubMed  CAS  Google Scholar 

  10. Lee N, Zhang J, Klose RJ, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y (2007) The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase. Nat Struct Mol Biol 14:341–343

    Article  PubMed  CAS  Google Scholar 

  11. Secombe J, Li L, Carlos L, Eisenman RN (2007) The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth. Genes Dev 21:537–551

    Article  PubMed  CAS  Google Scholar 

  12. Klose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P, Gilliland DG, Zhang Y, Kaelin WG Jr (2007) The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128:889–900

    Article  PubMed  CAS  Google Scholar 

  13. Shin S, Janknecht R (2007) Diversity within the JMJD2 histone demethylase family. Biochem Biophys Res Commun 353:973–977

    Article  PubMed  CAS  Google Scholar 

  14. Cloos PA, Christensen J, Agger K, Maiolica A, Rappsilber J, Antal T, Hansen KH, Helin K (2006) The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442:307–311

    Article  PubMed  CAS  Google Scholar 

  15. Klose RJ, Yamane K, Bae Y, Zhang D, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y (2006) The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442:312–316

    Article  PubMed  CAS  Google Scholar 

  16. Yamane K, Toumazou C, Tsukada Y, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y (2006) JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125:483–495

    Article  PubMed  CAS  Google Scholar 

  17. Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y (2006) Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125:467–481

    Article  PubMed  CAS  Google Scholar 

  18. Fodor BD, Kubicek S, Yonezawa M, O’Sullivan RJ, Sengupta R, Perez-Burgos L, Opravil S, Mechtler K, Schotta G, Jenuwein T (2006) Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev 20:1557–1562

    Article  PubMed  CAS  Google Scholar 

  19. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y (2006) Histone demethylation by a family of JmjC domain-containing proteins. Nature 439:811–816

    Article  PubMed  CAS  Google Scholar 

  20. Gray SG, Iglesias AH, Lizcano F, Villanueva R, Camelo S, Jingu H, Teh BT, Koibuchi N, Chin WW, Kokkotou E, Dangond F (2005) Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein. J Biol Chem 280:28507–28518

    Article  PubMed  CAS  Google Scholar 

  21. Yoon HG, Chan DW, Huang ZQ, Li J, Fondell JD, Qin J, Wong J (2003) Purification and functional characterization of the human N-CoR complex: the roles of HDAC3, TBL1 and TBLR1. EMBO J 22:1336–1346

    Article  PubMed  CAS  Google Scholar 

  22. Zhang D, Yoon HG, Wong J (2005) JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol 25:6404–6414

    Article  PubMed  CAS  Google Scholar 

  23. Shin S, Janknecht R (2007) Activation of androgen receptor by histone demethylases JMJD2A and JMJD2D. Biochem Biophys Res Commun 359:742–746

    Article  PubMed  CAS  Google Scholar 

  24. Wissmann M, Yin N, Muller JM, Greschik H, Fodor BD, Jenuwein T, Vogler C, Schneider R, Gunther T, Buettner R, Metzger E, Schule R (2007) Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat Cell Biol 9:347–353

    Article  PubMed  CAS  Google Scholar 

  25. Katoh M, Katoh M (2004) Identification and characterization of JMJD2 family genes in silico. Int J Oncol 24:1623–1628

    PubMed  CAS  Google Scholar 

  26. Yang ZQ, Imoto I, Fukuda Y, Pimkhaokham A, Shimada Y, Imamura M, Sugano S, Nakamura Y, Inazawa J (2000) Identification of a novel gene, GASC1, within an amplicon at 9p23–24 frequently detected in esophageal cancer cell lines. Cancer Res 60:4735–4739

    PubMed  CAS  Google Scholar 

  27. Huang Y, Fang J, Bedford MT, Zhang Y, Xu RM (2006) Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science 312:748–751

    Article  PubMed  CAS  Google Scholar 

  28. Wang Y, Wysocka J, Sayegh J, Lee YH, Perlin JR, Leonelli L, Sonbuchner LS, McDonald CH, Cook RG, Dou Y, Roeder RG, Clarke S, Stallcup MR, Allis CD, Coonrod SA (2004) Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306:279–283 (New York, N.Y)

    Article  PubMed  CAS  Google Scholar 

  29. Lee MG, Wynder C, Cooch N, Shiekhattar R (2005) An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 437:432–435

    PubMed  CAS  Google Scholar 

  30. Metzger E, Wissmann M, Yin N, Muller JM, Schneider R, Peters AH, Gunther T, Buettner R, Schule R (2005) LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437:436–439

    PubMed  CAS  Google Scholar 

  31. Klose RJ, Zhang Y (2007) Regulation of histone methylation by demethylimination and demethylation. Nat Rev 8:307–318

    Article  CAS  Google Scholar 

  32. Marsh EN, Patwardhan A, Huhta MS (2004) S-adenosylmethionine radical enzymes. Bioorg Chem 32:326–340

    Article  PubMed  CAS  Google Scholar 

  33. Paraskevopoulou C, Fairhurst SA, Lowe DJ, Brick P, Onesti S (2006) The Elongator subunit Elp3 contains a Fe4S4 cluster and binds S-adenosylmethionine. Mol Microbiol 59:795–806

    Article  PubMed  CAS  Google Scholar 

  34. Chinenov Y (2002) A second catalytic domain in the Elp3 histone acetyltransferases: a candidate for histone demethylase activity? Trends Biochem Sci 27:115–117

    Article  PubMed  CAS  Google Scholar 

  35. Shi Y, Whetstine JR (2007) Dynamic regulation of histone lysine methylation by demethylases. Mol Cell 25:1–14

    Article  PubMed  CAS  Google Scholar 

  36. Tsukada Y, Zhang Y (2006) Purification of histone demethylases from HeLa cells. Methods 40:318–326

    Article  PubMed  CAS  Google Scholar 

  37. Caceres JF, Misteli T, Screaton GR, Spector DL, Krainer AR (1997) Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity. J Cell Biol 138:225–238

    Article  PubMed  CAS  Google Scholar 

  38. Furuyama S, Bruzik JP (2002) Multiple roles for SR proteins in trans splicing. Mol Cell Biol 22:5337–5346

    Article  PubMed  CAS  Google Scholar 

  39. Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, Kutateladze TG, Simpson M, Mao Q, Pan CH, Dai S, Hagman J, Hansen K, Shi Y, Zhang G (2006) Structural insights into histone demethylation by JMJD2 family members. Cell 125:691–702

    Article  PubMed  CAS  Google Scholar 

  40. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    Article  PubMed  CAS  Google Scholar 

  41. Tomchick DR, Turner RJ, Switzer RL, Smith JL (1998) Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase. Structure 6:337–350

    Article  PubMed  CAS  Google Scholar 

  42. Sanchez C, Sanchez I, Demmers JA, Rodriguez P, Strouboulis J, Vidal M (2007) Proteomic analysis of Ring1B/Rnf2 interactors identifies a novel complex with the Fbxl10/Jmjd1B histone demethylase and the BcoR corepressor. Mol Cell Proteomics

Download references

Acknowledgements

This work was supported by CAS “100 Talents” program. The authors also thank the anonymous reviewers for a number of suggestions that have improved the quality of the paper.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Haidong Tan.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tan, H., Wu, S., Wang, J. et al. The JMJD2 members of histone demethylase revisited. Mol Biol Rep 35, 551–556 (2008). https://doi.org/10.1007/s11033-007-9121-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-007-9121-3

Keywords

Navigation