Trilogies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 69, Issue , 2004, Pages 209-218

  Lachner, M ^a   Sengupta, R ^a   Schotta, G ^a   Jenuwein, T ^a  

^a RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; LYSINE; SCHIZOSACCHAROMYCES POMBE PROTEIN; HISTONE H3; HISTONE H4;

AMINO ACID SEQUENCE; CHROMATIN; CONFERENCE PAPER; EPIGENETICS; EUKARYOTE; GENE CONTROL; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENE SILENCING; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC MARKER; GENETIC REGULATION; GENOME; GENOME ANALYSIS; HETEROCHROMATIN; METHYLATION; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN METHYLATION; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ANALYSIS; X CHROMOSOME; ARTICLE; DROSOPHILA MELANOGASTER; EUKARYOTIC CELL; GENOME SIZE; HISTONE METHYLATION; NUCLEOSOME; SACCHAROMYCES CEREVISIAE; SPECIES COMPARISON;

ANIMALS; CHROMATIN; DROSOPHILA MELANOGASTER; EPIGENESIS, GENETIC; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENE SILENCING; GENOME; HETEROCHROMATIN; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; LYSINE; METHYLATION; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES;

EUKARYOTA; SCHIZOSACCHAROMYCES POMBE;

EID: 23044475091     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2004.69.209     Document Type: Conference Paper

References (81)

1. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C., Rogers Y.H., Blazej R.G., Champe M., Pfeiffer B.D., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185.
2. Allfrey V.G., Faulkner R., and Mirsky A.E. 1964. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl. Acad. Sci. 51: 786.
3. Bastow R., Mylne J.S., Lister C., Lippman Z., Martienssen R.A., and Dean C. 2004. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427: 164.
4. Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev. 16: 6.
5. Brasher S.V., Smith B.O., Fogh R.H., Nietlispach D., Thiru A., Nielsen P.R., Broadhurst R.W., Ball L.J., Murzina N.V., and Laue E.D. 2000. The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer. EMBO J. 19: 1587.
6. Briggs S.D., Bryk M., Strahl B.D., Cheung W.L., Davie J.K., Dent S.Y., Winston F., and Allis C.D. 2001. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15: 3286.
7. Cao R., Wang L., Wang H., Xia L., Erdjument-Bromage H., Tempst P., Jones R.S., and Zhang Y. 2002. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298: 1039.
8. Chadwick B.P. and Willard H.F. 2003. Chromatin of the Barr body: Histone and non-histone proteins associated with or excluded from the inactive X chromosome. Hum. Mol. Genet. 12: 2167.
9. Czermin B., Melfi R., McCabe D., Seitz V., Imhof A., and Pirrotta V. 2002. Drosophila Enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111: 185.
10. DeLange R.J. and Smith E.L. 1973. Histone 3. I. Isolation and sequences of the tryptic peptides from the maleylated calf thymus protein. J. Biol. Chem. 248: 3248.
11. Fang J., Feng Q., Ketel C.S., Wang H., Cao R., Xia L., Erdjument-Bromage H., Tempst P., Simon J.A., and Zhang Y. 2002. Purification and functional characterization of SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase. Curr. Biol. 12: 1086.
12. Feng Q., Wang H., Ng H.H., Erdjument-Bromage H., Tempst P., Struhl K., and Zhang Y. 2002. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12: 1052.
13. Fischle W., Wang Y., and Allis C.D. 2003a. Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 15: 172.
14. _. 2003b. Binary switches and modification cassettes in histone biology and beyond. Nature 425: 475.
15. Fischle W., Wang Y., Jacobs S.A., Kim Y., Allis C.D., and Khorasanizadeh S. 2003c. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17: 1870.
16. Gasser S.M. and Cockell M.M. 2001. The molecular biology of the SIR proteins. Gene 279: 1.
17. Grunstein M. 1997. Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell Biol. 9: 383.
18. Han J.S., Szak S.T., and Boeke J.D. 2004. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429: 268.
19. Jackson J.P., Johnson L., Jasencakova Z., Zhang X., PerezBurgos L., Singh P.B., Cheng X., Schubert I., Jenuwein T., and Jacobsen S.E. 2004. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112: 308.
20. Jacobs S.A. and Khorasanizadeh S. 2002. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295: 2080.
21. Jaenisch R. and Bird A. 2003. Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nat. Genet. 33: 245.
22. Jasencakova Z., Soppe W.J., Meister A., Gernand D., Turner B.M., and Schubert I. 2003. Histone modifications in Arabidopsis- high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J. 33: 471.
23. Jenuwein T. 2001. Re-SET-ting heterochromatin by histone methyltransferases. Trends Cell Biol. 11: 266.
24. Jenuwein T. and Allis C.D. 2001. Translating the histone code. Science 293: 1074.
25. Jones P.A. and Baylin S.B. 2002. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3: 415.
26. Kazazian H.H., Jr. 2004. Mobile elements: Drivers of genome evolution. Science 303: 1626.
27. Klochendler-Yeivin A., Muchardt C., and Yaniv M. 2002. SWI/SNF chromatin remodeling and cancer. Curr. Opin. Genet. Dev. 12: 73.
28. Kohlmaier A., Savarese F., Lachner M., Martens J.H., Jenuwein T., and Wutz A. 2004. A chromosomal memory triggered by Xist regulates histone methylation in X inactivation. PloS Biol. 2: 991.
29. Kouzarides T. 2002. Histone methylation in transcriptional control. Curr. Opin. Genet. Dev. 12: 198.
30. Kuzmichev A., Jenuwein T., Tempst P., and Reinberg D. 2004. Different EZH2-containing complexes target methylation of histone H1 or nucleosomal histone H3. Mol. Cell 14: 183.
31. Kuzmichev A., Nishioka K., Erdjument-Bromage H., Tempst P., and Reinberg D. 2002. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16: 2893.
32. Lachner M., O'Sullivan R.J., and Jenuwein T. 2003. An epigenetic road map for histone lysine methylation. J. Cell Sci. 116: 2117.
33. Luger K. 2003. Structure and dynamic behavior of nucleosomes. Curr. Opin. Genet. Dev. 13: 127.
34. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389: 251.
35. Maison C., Bailly D., Peters A.H., Quivy J.P., Roche D., Taddei A., Lachner M., Jenuwein T., and Almouzni G. 2002. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat. Genet. 30: 329.
36. Mateescu B., England P., Halgand F., Yaniv M., and Muchardt C. 2004. Tethering of HP1 proteins to chromatin is relieved by phosphoacetylation of histone H3. EMBO Rep. 5: 490.
37. Meehan R.R., Kao C.F., and Pennings S. 2003. HP1 binding to native chromatin in vitro is determined by the hinge region and not by the chromodomain. EMBO J. 22: 3164.
38. Min J., Zhang Y., and Xu R.M. 2003. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev. 17: 1823.
39. Muchardt C., Guilleme M., Seeler J.S., Trouche D., Dejean A., and Yaniv M. 2002. Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1alpha. EMBO Rep. 3: 975.
40. Müller J., Hart C.M., Francis N.J., Vargas M.L., Sengupta A., Wild B., Miller E.L., O'Connor M.B., Kingston R.E., and Simon J.A. 2002. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111: 197.
41. Nakayama J., Rice J.C., Strahl B.D., Allis C.D., and Grewal S.I. 2001. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292: 110.
42. Narlikar G.J., Fan H.Y., and Kingston R.E. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108: 475.
43. Nielsen A.L., Oulad-Abdelghani M., Ortiz J.A., Remboutsika E., Chambon P., and Losson R. 2001. Heterochromatin formation in mammalian cells: Interaction between histones and HP1 proteins. Mol. Cell 7: 729.
44. Nielsen P.R., Nietlispach D., Mott H.R., Callaghan J., Bannister A., Kouzarides T., Murzin A.G., Murzina N.V., and Laue E.D. 2002. Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 416: 103.
45. Nishioka K., Rice J.C., Sarma K., Erdjument-Bromage H., Werner J., Wang Y., Chuikov S., Valenzuela P., Tempst P., Steward R., Lis T.J., Allis C.D., and Reinberg D. 2002. PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol. Cell 9: 1201.
46. Noma K. and Grewal S.I. 2002. Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast. Proc. Natl. Acad. Sci. 99: 16438.
47. Noma K., Allis C.D., and Grewal S.I. 2001. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293: 1150.
48. O'Carroll D., Scherthan H., Peters A.H., Opravil S., Haynes A.R., Laible G., Rea S., Schmid M., Lebersorger A., Jerratsch M., Sattler L., Mattei M.G., Denny P., Brown S.D., Schweizer D., and Jenuwein T. 2000. Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression. Mol. Cell. Biol. 20: 9423.
49. Ogawa H., Ishiguro K., Gaubatz S., Livingston D.M., and Nakatani Y. 2002. A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. Science 296: 1132.
50. Okamoto I., Otte A.P., Allis C.D., Reinberg D., and Heard E. 2004. Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303: 644.
51. Paik W.K. and Kim S. 1971. Protein methylation. Science 174: 114.
52. Perez-Burgos L., Peters A.H., Opravil S., Kauer M., Mechtler K., and Jenuwein T. 2004. Generation and characterization of methyl-lysine histone antibodies. Methods Enzymol. 376: 234.
53. Peters A.H., Kubicek S., Mechtler K., O'Sullivan R.J., Derijck A.A., Perez-Burgos L., Kohlmaier A., Opravil S., Tachibana M., Shinkai Y., Martens J.H., and Jenuwein T. 2003. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12: 1577.
54. Plath K., Fang J., Mlynarczyk-Evans S.K., Cao R., Worringer K.A., Wang H., de la Cruz C.C., Otte A.P., Panning B., and Zhang Y. 2003. Role of histone H3 lysine 27 methylation in X inactivation. Science 300: 131.
55. Rea S., Eisenhaber F., O'Carroll D., Strahl B.D., Sun Z.W., Schmid M., Opravil S., Mechtler K., Ponting C.P., Allis C.D., and Jenuwein T. 2000. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406: 593.
56. Rice J.C., Nishioka K., Sarma K., Steward R., Reinberg D., and Allis C.D. 2002. Mitotic-specific methylation of histone H4 Lys 20 follows increased PR-Set7 expression and its localization to mitotic chromosomes. Genes Dev. 16: 2225.
57. Rice J.C., Briggs S.D., Ueberheide B., Barber C.M., Shabanowitz J., Hunt D.F., Shinkai Y., and Allis C.D. 2003. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 12: 1591.
58. Santos F., Zakhartchenko V., Stojkovic M., Peters A., Jenuwein T., Wolf E., Reik W., and Dean W. 2003. Epigenetic marking correlates with developmental potential in cloned bovine preimplantation embryos. Curr. Biol. 13: 1116.
59. Santos-Rosa H., Schneider R., Bannister A.J., Sherriff J., Bernstein B.E., Emre N.C., Schreiber S.L., Mellor J., and Kouzarides T. 2002. Active genes are tri-methylated at K4 of histone H3. Nature 419: 407.
60. Schneider R., Bannister A.J., and Kouzarides T. 2002. Unsafe SETs: Histone lysine methyltransferases and cancer. Trends Biochem. Sci. 27: 396.
61. Schotta G., Lachner M., Sarma K., Ebert A., Sengupta R., Reuter G., Reinberg D., and Jenuwein T. 2004. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 18: 1251.
62. Silva J., Mak W., Zvetkova I., Appanah R., Nesterova T.B., Webster Z., Peters A.H., Jenuwein T., Otte A.P., and Brockdorff N. 2003. Establishment of histone H3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. Dev. Cell 4: 481.
63. Strahl B.D. and Allis C.D. 2000. The language of covalent histone modifications. Nature 403: 41.
64. Strahl B.D., Grant P.A., Briggs S.D., Sun Z.W., Bone J.R., Caldwell J.A., Mollah S., Cook R.G., Shabanowitz J., Hunt D.F., and Allis C.D. 2002. Set2 is a nucleosomal histone H3-specific methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22: 1298.
65. Sung S. and Amasino R.M. 2004. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427: 159.
66. Tachibana M., Sugimoto K., Nozaki M., Ueda J., Ohta T., Ohki M., Fukuda M., Takeda N., Niida H., Kato H., and Shinkai Y. 2002. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 16: 1779.
67. Tamaru H., Zhang X., McMillen D., Singh P.B., Nakayama J., Grewal S.I., Allis C.D., Cheng X., and Selker E.U. 2003. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat. Genet. 34: 75.
68. Turner B.M. 2000. Histone acetylation and an epigenetic code. Bioessays 22: 836.
69. van Holde K.E. 1988. Chromatin. Springer Verlag, New York.
70. van Leeuwen F., Gafken P.R., and Gottschling D.E. 2002. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109: 745.
71. Volpe T., Schramke V., Hamilton G.L., White S.A., Teng G., Martienssen R.A., and Allshire R.C. 2003. RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11: 137.
72. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., Antonarakis S.E., Attwood J., Baertsch R., Bailey J., Barlow K., Beck S., Berry E., Birren B., Bloom T., Bork P., Botcherby M., Bray N., Brent M.R., Brown D.G., and Brown S.D., et al. (Mouse Genome Sequencing Consortium). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520.
73. Watson J.D. (Interview). 2003. Celebrating the genetic jubilee: A conversation with James D. Watson. Sci. Am. (April issue) 2003: 67.
74. Wood V., Gwilliam R., Rajandream M.A., Lyne M., Lyne R., Stewart A., Sgouros J., Peat N., Hayles J., Baker S., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C., Collins M., Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., and Goble A., et al. 2002. The genome sequence of Schizosaccharomyces pombe. Nature 415: 871.
75. Xiao B., Jing C., Wilson J.R., Walker P.A., Vasisht N., Kelly G., Howell S., Taylor I.A., Blackburn G.M., and Gamblin S.J. 2003. Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature 421: 652.
76. Xiao T., Hall H., Kizer K.O., Shibata Y., Hall M.C., Borchers C.H., and Strahl B.D. 2003. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev. 17: 654.
77. Yang L., Xia L., Wu D.Y., Wang H., Chansky H.A., Schubach W.H., Hickstein D.D., and Zhang Y. 2002. Molecular cloning of ESET, a novel histone H3-specific methyltransferase that interacts with ERG transcription factor. Oncogene 21: 148.
78. Yeast Genome Directory. 1997. The yeast genome directory. Nature (suppl. 6632) 387: 5.
79. Zhang L., Eugeni E.E., Parthun M.R., and Freitas M.A. 2003. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma 112: 77.
80. Zhang X., Yang Z., Khan S.I., Horton J.R., Tamaru H., Selker E.U., and Cheng X. 2003. Structural basis for the product specificity of histone lysine methyltransferases. Mol. Cell 12: 177.
81. Zhang Y. and Reinberg D. 2001. Transcription regulation by histone methylation: Interplay between different covalent modifications of the core histone tails. Genes Dev. 15: 2343.