Reading, writing and editing methylated lysines on histone tails: New insights from recent structural studies

Current Opinion in Structural Biology

Volumn 20, Issue 6, 2010, Pages 730-738

  Justin, Neil ^a   De Marco, Valeria ^a   Aasland, Rein ^b   Gamblin, Steven J ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^b UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

AMINE OXIDASE (FLAVIN CONTAINING); HISTONE H3; HISTONE H3 LYSINE 27; HISTONE H3 LYSINE 4; LYSINE SPECIFIC DEMETHYLASE 1; MIXED LINEAGE LEUKEMIA 1 PROTEIN; MIXED LINEAGE LEUKEMIA PROTEIN; OXIDOREDUCTASE; POLYCOMB GROUP PROTEIN; POLYCOMB REPRESSIVE COMPLEX 1; POLYCOMB REPRESSIVE COMPLEX 2; PROTEIN KIAA1718; PROTEIN PHF8; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; CARBOXY TERMINAL SEQUENCE; CHROMATIN STRUCTURE; COMPLEX FORMATION; CRYSTAL STRUCTURE; DEMETHYLATION; DNA METHYLATION; DNA MODIFICATION; DNA PROTEIN COMPLEX; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; ENZYME ACTIVE SITE; GENETIC EPIGENESIS; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; REVIEW; RNA EDITING; RNA TRANSCRIPTION; STRUCTURE ANALYSIS; TRANSCRIPTION INITIATION;

ANIMALS; EPISTASIS, GENETIC; HISTONES; HUMANS; JUMONJI DOMAIN-CONTAINING HISTONE DEMETHYLASES; LYSINE; METHYLATION;

EID: 78649682494     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2010.09.012     Document Type: Review

References (60)

1. Cavalli G., Paro R. Epigenetic inheritance of active chromatin after removal of the main transactivator. Science 1999, 286:955-958.
2. Muramoto T., Müller I., Thomas G., Melvin A., Chubb J.R. Methylation of H3K4 Is required for inheritance of active transcriptional states. Curr Biol 2010, 20:397-406.
3. Ringrose L., Paro R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 2004, 38:413-443.
4. Simon J.A., Kingston R.E. Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 2009, 10:697-708.
5. Eissenberg J.C., Shilatifard A. Histone H3 lysine 4 (H3K4) methylation in development and differentiation. Dev Biol 2010, 339:240-249.
6. Ruthenburg A.J., Li H., Patel D.J., Allis C.D. Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol 2007, 8:983-994.
7. Shilatifard A. Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Curr Opin Cell Biol 2008, 20:341-348.
8. Briggs S.D., Bryk M., Strahl B.D., Cheung W.L., Davie J.K., Dent S.Y., Winston F., Allis C.D. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev 2001, 15:3286-3295.
9. Miller T., Krogan N.J., Dover J., Erdjument-Bromage H., Tempst P., Johnston M., Greenblatt J.F., Shilatifard A. COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Proc Natl Acad Sci USA 2001, 98:12902-12907.
10. Roguev A., Schaft D., Shevchenko A., Pijnappel W.W., Wilm M., Aasland R., Stewart A.F. The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4. EMBO J 2001, 20:7137-7148.
11. Glaser S., Schaft J., Lubitz S., Vintersten K., van der Hoeven F., Tufteland K.R., Aasland R., Anastassiadis K., Ang S.-L., Stewart A.F. Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development. Development 2006, 133:1423-1432.
12. Guenther M.G., Jenner R.G., Chevalier B., Nakamura T., Croce C.M., Canaani E., Young R.A. Global and Hox-specific roles for the MLL1 methyltransferase. Proc Natl Acad Sci USA 2005, 102:8603-8608.
13. Yu B.D., Hess J.L., Horning S.E., Brown G.A., Korsmeyer S.J. Altered Hox expression and segmental identity in Mll-mutant mice. Nature 1995, 378:505-508.
14. Cosgrove M.S., Patel A. Mixed lineage leukemia: a structure-function perspective of the MLL1 protein. FEBS J 2010, 277:1832-1842.
15. Meyer C., Schneider B., Jakob S., Strehl S., Attarbaschi A., Schnittger S., Schoch C., Jansen M.W.J.C., van Dongen J.J.M., den Boer M.L., et al. The MLL recombinome of acute leukemias. Leukemia 2006, 20:777-784.
16. Hess J.L. MLL: a histone methyltransferase disrupted in leukemia. Trends Mol Med 2004, 10:500-507.
17. Dou Y., Milne T.A., Ruthenburg A.J., Lee S., Lee J.W., Verdine G.L., Allis C.D., Roeder R.G. Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nat Struct Mol Biol 2006, 13:713-719.
18. Southall S.M., Wong P.-S., Odho Z., Roe S.M., Wilson J.R. Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks. Mol Cell 2009, 33:181-191.
19. Couture J.-F., Collazo E., Trievel R.C. Molecular recognition of histone H3 by the WD40 protein WDR5. Nat Struct Mol Biol 2006, 13:698-703.
20. Han Z., Guo L., Wang H., Shen Y., Deng X.W., Chai J. Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell 2006, 22:137-144.
21. Ruthenburg A.J., Wang W., Graybosch D.M., Li H., Allis C.D., Patel D.J., Verdine G.L. Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat Struct Mol Biol 2006, 13:704-712.
22. Schuetz A., Allali-Hassani A., Martín F., Loppnau P., Vedadi M., Bochkarev A., Plotnikov A.N., Arrowsmith C.H., Min J. Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO J 2006, 25:4245-4252.
23. Wysocka J., Swigut T., Milne T.A., Dou Y., Zhang X., Burlingame A.L., Roeder R.G., Brivanlou A.H., Allis C.D. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 2005, 121:859-872.
24. Patel A., Dharmarajan V., Cosgrove M.S. Structure of WDR5 bound to mixed lineage leukemia protein-1 peptide. J Biol Chem 2008, 283:32158-32161.
25. Patel A., Vought V.E., Dharmarajan V., Cosgrove M.S. A conserved arginine-containing motif crucial for the assembly and enzymatic activity of the mixed lineage leukemia protein-1 core complex. J Biol Chem 2008, 283:32162-32175.
26. Wang Z., Song J., Milne T.A., Wang G.G., Li H., Allis C.D., Patel D.J. Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression. Cell 2010, 141:1183-1194.
27. Byvoet P., Shepherd G.R., Hardin J.M., Noland B.J. The distribution and turnover of labeled methyl groups in histone fractions of cultured mammalian cells. Arch Biochem Biophys 1972, 148:558-567.
28. Thomas G., Lange H.W., Hempel K. 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 1972, 353:1423-1428.
29. Shi Y., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., Casero R.A., Shi Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004, 119:941-953.
30. Klose R.J., Kallin E.M., Zhang Y. JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 2006, 7:715-727.
31. Lee M.G., Wynder C., Cooch N., Shiekhattar R. An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 2005, 437:432-435.
32. Stavropoulos P., Blobel G., Hoelz A. Crystal structure and mechanism of human lysine-specific demethylase-1. Nat Struct Mol Biol 2006, 13:626-632.
33. Yang M., Gocke C.B., Luo X., Borek D., Tomchick D.R., Machius M., Otwinowski Z., Yu H. Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Mol Cell 2006, 23:377-387.
34. Yang M., Culhane J.C., Szewczuk L.M., Gocke C.B., Brautigam C.A., Tomchick D.R., Machius M., Cole P.A., Yu H. Structural basis of histone demethylation by LSD1 revealed by suicide inactivation. Nat Struct Mol Biol 2007, 14:535-539.
35. Metzger E., Wissmann M., Yin N., Müller J.M., Schneider R., Peters A.H.F.M., Günther T., Buettner R., Schüle R. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 2005, 437:436-439.
36. Metzger E., Imhof A., Patel D., Kahl P., Hoffmeyer K., Friedrichs N., Müller J.M., Greschik H., Kirfel J., Ji S., et al. Phosphorylation of histone H3T6 by PKCbeta(I) controls demethylation at histone H3K4. Nature 2010, 464:792-796.
37. Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., Levine S.S., Wernig M., Tajonar A., Ray M.K., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006, 441:349-353.
38. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., Chevalier B., Johnstone S.E., Cole M.F., Isono K., et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006, 125:301-313.
39. Schuettengruber B., Ganapathi M., Leblanc B., Portoso M., Jaschek R., Tolhuis B., van Lohuizen M., Tanay A., Cavalli G. Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol 2009, 7:e13.
40. Schwartz Y.B., Kahn T.G., Nix D.A., Li X.Y., Bourgon R., Biggin M., Pirrotta V. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 2006, 38:700-705.
41. Muller J., Verrijzer P. Biochemical mechanisms of gene regulation by polycomb group protein complexes. Curr Opin Genet Dev 2009, 19:150-158.
42. 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 2002, 16:2893-2905.
43. Muller J., Hart C.M., Francis N.J., Vargas M.L., Sengupta A., Wild B., Miller E.L., O'Connor M.B., Kingston R.E., Simon J.A. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 2002, 111:197-208.
44. Margueron R., Justin N., Ohno K., Sharpe M.L., Son J., Drury W.J., Voigt P., Martin S.R., Taylor W.R., De Marco V., et al. Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 2009, 461:762-767.
45. Murzina N.V., Pei X.Y., Zhang W., Sparkes M., Vicente-Garcia J., Pratap J.V., McLaughlin S.H., Ben-Shahar T.R., Verreault A., Luisi B.F., et al. Structural basis for the recognition of histone H4 by the histone-chaperone RbAp46. Structure 2008, 16:1077-1085.
46. Song J.J., Garlick J.D., Kingston R.E. Structural basis of histone H4 recognition by p55. Genes Dev 2008, 22:1313-1318.
47. Zhang X., Tamaru H., Khan S.I., Horton J.R., Keefe L.J., Selker E.U., Cheng X. Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell 2002, 111:117-127.
48. Hansen K.H., Bracken A.P., Pasini D., Dietrich N., Gehani S.S., Monrad A., Rappsilber J., Lerdrup M., Helin K. A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 2008, 10:1291-1300.
49. Huang Y., Fang J., Bedford M.T., Zhang Y., Xu R.M. Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science 2006, 312:748-751.
50. Li H., Ilin S., Wang W., Duncan E.M., Wysocka J., Allis C.D., Patel D.J. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 2006, 442:91-95.
51. Pena P.V., Davrazou F., Shi X., Walter K.L., Verkhusha V.V., Gozani O., Zhao R., Kutateladze T.G. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 2006, 442:100-103.
52. Han Z., Xing X., Hu M., Zhang Y., Liu P., Chai J. Structural basis of EZH2 recognition by EED. Structure 2007, 15:1306-1315.
53. Ketel C.S., Andersen E.F., Vargas M.L., Suh J., Strome S., Simon J.A. Subunit contributions to histone methyltransferase activities of fly and worm polycomb group complexes. Mol Cell Biol 2005, 25:6857-6868.
54. Cao R., Wang H., He J., Erdjument-Bromage H., Tempst P., Zhang Y. Role of hPHF1 in H3K27 methylation and Hox gene silencing. Mol Cell Biol 2008, 28:1862-1872.
55. Sarma K., Margueron R., Ivanov A., Pirrotta V., Reinberg D. Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo. Mol Cell Biol 2008, 28:2718-2731.
56. Li G., Margueron R., Ku M., Chambon P., Bernstein B.E., Reinberg D. Jarid2 and PRC2, partners in regulating gene expression. Genes Dev 2010, 24:368-380.
57. Pasini D., Cloos P.A., Walfridsson J., Olsson L., Bukowski J.P., Johansen J.V., Bak M., Tommerup N., Rappsilber J., Helin K. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature 2010, 464:306-310.
58. Peng J.C., Valouev A., Swigut T., Zhang J., Zhao Y., Sidow A., Wysocka J. Jarid2/JmjC coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 2009, 139:1290-1302.
59. Shen X., Kim W., Fujiwara Y., Simon M.D., Liu Y., Mysliwiec M.R., Yuan G.C., Lee Y., Orkin S.H. JmjC modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell 2009, 139:1303-1314.
60. Horton J.R., Upadhyay A.K., Qi H.H., Zhang X., Shi Y., Cheng X. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol 2010, 17:38-43.