Skip to main content
SpringerLink
Log in
Book cover

Chromatin Dynamics in Cellular Function pp 25–46Cite as

The Generation and Recognition of Histone Methylation

  • Chapter
  • First Online:

Part of the book series: Results and Problems in Cell Differentiation ((RESULTS,volume 41))

Abstract

The posttranslational modification of histone proteins via methylation has important functions in gene activation, transcriptional silencing, establishment of chromatin states, and likely many aspects of DNA metabolism. The identification of numerous effector protein domains with the capability of binding methylated histones has significantly advanced our understanding of how such histone modifications may exert their biological effects. Here, we summarize aspects of the generation of arginine and lysine methylation marks on core histones, the characterization of the protein modules that interact with them, and how histone methylation cross-talks with other modifications.

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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA 51:786–794

    Article  CAS  PubMed  Google Scholar 

  2. Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410:120–124

    Article  CAS  PubMed  Google Scholar 

  3. Bannister AJ, Schneider R, Kouzarides T (2002) Histone methylation: dynamic or static? Cell 109:801–806

    Article  CAS  PubMed  Google Scholar 

  4. Bateman A, Birney E (2000) Searching databases to find protein domain organization. Adv Protein Chem 54:137–157

    Article  CAS  PubMed  Google Scholar 

  5. Baxter CS, Byvoet P (1975) CMR studies of protein modification. Progressive decrease in charge density at the epsilon-amino function of lysine with increasing methyl substitution. Biochem Biophys Res Commun 64:514–518

    Article  CAS  PubMed  Google Scholar 

  6. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, Gingeras TR, Schreiber SL, Lander ES (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120:169–181

    Article  CAS  PubMed  Google Scholar 

  7. Boggs BA, Cheung P, Heard E, Spector DL, Chinault AC, Allis CD (2002) Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat Genet 30:73–76

    Article  CAS  PubMed  Google Scholar 

  8. Brahms H, Meheus L, de Brabandere V, Fischer U, Luhrmann R (2001) Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B′and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA 7:1531–1542

    Article  CAS  PubMed  Google Scholar 

  9. Briggs SD, Bryk M, Strahl BD, Cheung WL, Davie JK, Dent SY, Winston F, Allis CD (2001) Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev 15:3286–3295

    Article  CAS  PubMed  Google Scholar 

  10. Briggs SD, Xiao T, Sun ZW, Caldwell JA, Shabanowitz J, Hunt DF, Allis CD, Strahl BD (2002) Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418:498

    Article  CAS  PubMed  Google Scholar 

  11. Bryk M, Banerjee M, Murphy M, Knudsen KE, Garfinkel DJ, Curcio MJ (1997) Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev 11:255–269

    Article  CAS  PubMed  Google Scholar 

  12. Bryk M, Briggs SD, Strahl BD, Curcio MJ, Allis CD, Winston F (2002) Evidence that Set1, a factor required for methylation of histone H3, regulates rDNA silencing in S. cerevisae by a Sir2-independent mechanism. Curr Biol 12:165–170

    Article  CAS  PubMed  Google Scholar 

  13. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298:1039–1043

    Article  CAS  PubMed  Google Scholar 

  14. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123:581–592

    Article  CAS  PubMed  Google Scholar 

  15. Cary PD, Crane-Robinson C, Bradbury EM, Dixon GH (1982) Effect of acetylation on the binding of N-terminal peptides of histone H4 to DNA. Eur J Biochem 127:137–143

    Article  CAS  PubMed  Google Scholar 

  16. Chen D, Ma H, Hong H, Koh SS, Huang SM, Schurter BT, Aswad DW, Stallcup MR (1999) Regulation of transcription by a protein methyltransferase. Science 284:2174–2177

    Article  CAS  PubMed  Google Scholar 

  17. Cosgrove MS, Boeke JD, Wolberger C (2004) Regulated nucleosome mobility and the histone code. Nat Struct Mol Biol 11:1037–1043

    Article  CAS  PubMed  Google Scholar 

  18. Cuthbert GL, Daujat S, Snowden AW, Erdjument-Bromage H, Hagiwara T, Yamada M, Schneider R, Gregory PD, Tempst P, Bannister AJ, Kouzarides T (2004) Histone deimination antagonizes arginine methylation. Cell 118:545–553

    Article  CAS  PubMed  Google Scholar 

  19. Czermin B, Melfi R, McCabe D, Seitz V, Imhof A, Pirrotta V (2002) Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111:185–196

    Article  CAS  PubMed  Google Scholar 

  20. Daniel JA, Torok MS, Sun ZW, Schieltz D, Allis CD, Yates JR 3rd, Grant PA (2004) Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem 279:1867–1871

    Article  CAS  PubMed  Google Scholar 

  21. Daniel JA, Pray-Grant MG, Grant PA (2005) Effector proteins for methylated histones: an expanding family. Cell Cycle 4:919–926

    Article  CAS  PubMed  Google Scholar 

  22. Davie JR, Murphy LC (1990) Level of ubiquitinated histone H2B in chromatin is coupled to ongoing transcription. Biochemistry 29:4752–4757

    Article  CAS  PubMed  Google Scholar 

  23. Dou Y, Milne TA, Tackett AJ, Smith ER, Fukuda A, Wysocka J, Allis CD, Chait BT, Hess JL, Roeder RG (2005) Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF. Cell 121:873–885

    Article  CAS  PubMed  Google Scholar 

  24. Dover J, Schneider J, Tawiah-Boateng MA, Wood A, Dean K, Johnston M, Shilatifard A (2002) Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem 277:28368–28371

    Article  CAS  PubMed  Google Scholar 

  25. Emre NC, Ingvarsdottir K, Wyce A, Wood A, Krogan NJ, Henry KW, Li K, Marmorstein R, Greenblatt JF, Shilatifard A, Berger SL (2005) Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing. Mol Cell 17:585–594

    Article  CAS  PubMed  Google Scholar 

  26. Felsenfeld G, Groudine M (2003) Controlling the double helix. Nature 421:448–453

    Article  PubMed  CAS  Google Scholar 

  27. Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S (2003) Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev 17:1870–1881

    Article  CAS  PubMed  Google Scholar 

  28. Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA, Shabanowitz J, Hunt DF, Funabiki H, Allis CD (2005) Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438:1116–1122

    Article  CAS  PubMed  Google Scholar 

  29. Friesen WJ, Massenet S, Paushkin S, Wyce A, Dreyfuss G (2001) SMN, the product of the spinal muscular atrophy gene, binds preferentially to dimethylarginine-containing protein targets. Mol Cell 7:1111–1117

    Article  CAS  PubMed  Google Scholar 

  30. Game JC, Williamson MS, Baccari C (2005) X-ray survival characteristics and genetic analysis for nine Saccharomyces deletion mutants that show altered radiation sensitivity. Genetics 169:51–63

    Article  CAS  PubMed  Google Scholar 

  31. Garcia-Ramirez M, Dong F, Ausio J (1992) Role of the histone tails in the folding of oligonucleosomes depleted of histone H1. J Biol Chem 267:19587–19595

    CAS  PubMed  Google Scholar 

  32. Garcia-Ramirez M, Rocchini C, Ausio J (1995) Modulation of chromatin folding by histone acetylation. J Biol Chem 270:17923–17928

    Article  CAS  PubMed  Google Scholar 

  33. Gardner RG, Nelson ZW, Gottschling DE (2005) Ubp10/Dot4p regulates the persistence of ubiquitinated histone H2B: distinct roles in telomeric silencing and general chromatin. Mol Cell Biol 25:6123–6139

    Article  CAS  PubMed  Google Scholar 

  34. Gottschling DE, Aparicio OM, Billington BL, Zakian VA (1990) Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63:751–762

    Article  CAS  PubMed  Google Scholar 

  35. Guarente L (1999) Diverse and dynamic functions of the Sir silencing complex. Nat Genet 23:281–285

    Article  CAS  PubMed  Google Scholar 

  36. Henikoff S (2000) Heterochromatin function in complex genomes. Biochim Biophys Acta 1470:1–8

    Google Scholar 

  37. Henry KW, Wyce A, Lo WS, Duggan LJ, Emre NC, Kao CF, Pillus L, Shilatifard A, Osley MA, Berger SL (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev 17:2648–2663

    Article  CAS  PubMed  Google Scholar 

  38. Hirota T, Lipp JJ, Toh BH, Peters JM (2005) Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin. Nature 438:1176–1180

    Article  CAS  PubMed  Google Scholar 

  39. Hochstrasser M (1996) Ubiquitin-dependent protein degradation. Annu Rev Genet 30:405–439

    Article  CAS  PubMed  Google Scholar 

  40. Huang L, Zhang W, Roth SY (1997) Amino termini of histones H3 and H4 are required for a1-alpha2 repression in yeast. Mol Cell Biol 17:6555–6562

    CAS  PubMed  Google Scholar 

  41. Huyen Y, Zgheib O, Ditullio RA Jr, Gorgoulis VG, Zacharatos P, Petty TJ, Sheston EA, Mellert HS, Stavridi ES, Halazonetis TD (2004) Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432:406–411

    Article  CAS  PubMed  Google Scholar 

  42. Hwang WW, Venkatasubrahmanyam S, Ianculescu AG, Tong A, Boone C, Madhani HD (2003) A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. Mol Cell 11:261–266

    Article  CAS  PubMed  Google Scholar 

  43. Jacobs SA, Khorasanizadeh S (2002) Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295:2080–2083

    Article  CAS  PubMed  Google Scholar 

  44. Jentsch S, McGrath JP, Varshavsky A (1987) The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme. Nature 329:131–134

    Article  CAS  PubMed  Google Scholar 

  45. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080

    Article  CAS  PubMed  Google Scholar 

  46. Karachentsev D, Sarma K, Reinberg D, Steward R (2005) PR-Set7-dependent methylation of histone H4 Lys 20 functions in repression of gene expression and is essential for mitosis. Genes Dev 19:431–435

    Article  CAS  PubMed  Google Scholar 

  47. Karpen GH, Allshire RC (1997) The case for epigenetic effects on centromere identity and function. Trends Genet 13:489–496

    Article  CAS  PubMed  Google Scholar 

  48. Katan-Khaykovich Y, Struhl K (2005) Heterochromatin formation involves changes in histone modifications over multiple cell generations. Embo J 24:2138–2149

    Article  CAS  PubMed  Google Scholar 

  49. Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123:593–605

    Article  CAS  PubMed  Google Scholar 

  50. Krogan NJ, Kim M, Ahn SH, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF (2002) RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol 22:6979–6992

    Article  CAS  PubMed  Google Scholar 

  51. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C et al (2003) Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 23:4207–4218

    Article  CAS  PubMed  Google Scholar 

  52. Kuriyan J, Cowburn D (1997) Modular peptide recognition domains in eukaryotic signaling. Annu Rev Biophys Biomol Struct 26:259–288

    Article  CAS  PubMed  Google Scholar 

  53. Kuzmichev A, Nishioka K, Erdjument-Bromage H, Tempst P, Reinberg D (2002) Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev 16:2893–2905

    Article  CAS  PubMed  Google Scholar 

  54. Lachner M, Jenuwein T (2002) The many faces of histone lysine methylation. Curr Opin Cell Biol 14:286–298

    Article  CAS  PubMed  Google Scholar 

  55. Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410:116–120

    Article  CAS  PubMed  Google Scholar 

  56. Lacoste N, Utley RT, Hunter JM, Poirier GG, Cote J (2002) Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J Biol Chem 277:30421–30424

    Article  CAS  PubMed  Google Scholar 

  57. Lanzotti DJ, Kaygun H, Yang X, Duronio RJ, Marzluff WF (2002) Developmental control of histone mRNA and dSLBP synthesis during Drosophila embryogenesis and the role of dSLBP in histone mRNA 3′end processing in vivo. Mol Cell Biol 22:2267–2282

    Article  CAS  PubMed  Google Scholar 

  58. Lee DY, Teyssier C, Strahl BD, Stallcup MR (2005a) Role of protein methylation in regulation of transcription. Endocr Rev 26:147–170

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  60. Li B, Howe L, Anderson S, Yates JR III, Workman JL (2003) The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II J Biol Chem 278:8897–8903

    CAS  Google Scholar 

  61. Li J, Lin Q, Yoon HG, Huang ZQ, Strahl BD, Allis CD, Wong J (2002) Involvement of histone methylation and phosphorylation in regulation of transcription by thyroid hormone receptor. Mol Cell Biol 22:5688–5697

    Article  CAS  PubMed  Google Scholar 

  62. Litt MD, Simpson M, Gaszner M, Allis CD, Felsenfeld G (2001) Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science 293:2453–2455

    Article  CAS  PubMed  Google Scholar 

  63. Loo S, Rine J (1995) Silencing and heritable domains of gene expression. Annu Rev Cell Dev Biol 11:519–548

    Article  CAS  PubMed  Google Scholar 

  64. Lowell JE, Pillus L (1998) Telomere tales: chromatin, telomerase and telomere function in Saccharomyces cerevisiae. Cell Mol Life Sci 54:32–49

    Article  CAS  PubMed  Google Scholar 

  65. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260

    Article  CAS  PubMed  Google Scholar 

  66. Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP (2003) The Tudor domain royal family: Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem Sci 28:69–74

    Article  CAS  PubMed  Google Scholar 

  67. 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

    CAS  PubMed  Google Scholar 

  68. Miller T, Krogan NJ, Dover J, Erdjument-Bromage H, Tempst P, Johnston M, Greenblatt JF, Shilatifard A (2001) COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Proc Natl Acad Sci USA 98:12902–12907

    Article  CAS  PubMed  Google Scholar 

  69. Milne TA, Briggs SD, Brock HW, Martin ME, Gibbs D, Allis CD, Hess JL (2002) MLL targets SET domain methyltransferase activity to Hox gene promoters. Mol Cell 10:1107–1117

    Article  CAS  PubMed  Google Scholar 

  70. Morris SA, Shibata Y, Noma K, Tsukamoto Y, Warren E, Temple B, Grewal SI, Strahl BD (2005) Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe. Eukaryot Cell 4:1446–1454

    Article  CAS  PubMed  Google Scholar 

  71. Murray K (1964) The occurrence of ε-N-methyl lysine in histones. Biochemistry 3:10–15

    Article  CAS  PubMed  Google Scholar 

  72. Nagy PL, Griesenbeck J, Kornberg RD, Cleary ML (2002) A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3. Proc Natl Acad Sci USA 99:90–94

    Article  CAS  PubMed  Google Scholar 

  73. Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SI (2001) Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292:110–113

    Article  CAS  PubMed  Google Scholar 

  74. Ng HH, Xu RM, Zhang Y, Struhl K (2002) Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J Biol Chem 277:34655–34657

    Article  CAS  PubMed  Google Scholar 

  75. Ng HH, Ciccone DN, Morshead KB, Oettinger MA, Struhl K (2003a). Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc Natl Acad Sci USA 100:1820–1825

    Article  CAS  PubMed  Google Scholar 

  76. Ng HH, Robert F, Young RA, Struhl K (2003b). Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11:709–719

    Article  CAS  PubMed  Google Scholar 

  77. Nickel BE, Allis CD, Davie JR (1989) Ubiquitinated histone H2B is preferentially located in transcriptionally active chromatin. Biochemistry 28:958–963

    Article  CAS  PubMed  Google Scholar 

  78. Nielsen PR, Nietlispach D, Mott HR, Callaghan J, Bannister A, Kouzarides T, Murzin AG, Murzina NV, Laue ED (2002) Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 416:103–107

    Article  CAS  PubMed  Google Scholar 

  79. Nishioka K, Rice JC, Sarma K, Erdjument-Bromage H, Werner J, Wang Y, Chuikov S, Valenzuela P, Tempst P, Steward R et al (2002) PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell 9:1201–1213

    Article  CAS  PubMed  Google Scholar 

  80. Noma K, Allis CD, Grewal SI (2001) Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293:1150–1155

    Article  CAS  PubMed  Google Scholar 

  81. Pal S, Vishwanath SN, Erdjument-Bromage H, Tempst P, Sif S (2004) Human SWI/SNF-associated PRMT5 methylates histone H3 arginine 8 and negatively regulates expression of ST7 and NM23 tumor suppressor genes. Mol Cell Biol 24:9630–9645

    Article  CAS  PubMed  Google Scholar 

  82. Pawson T, Nash P (2000) Protein–protein interactions define specificity in signal transduction. Genes Dev 14:1027–1047

    CAS  PubMed  Google Scholar 

  83. Peters AH, Mermoud JE, O'Carroll D, Pagani M, Schweizer D, Brockdorff N, Jenuwein T (2002) Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nat Genet 30:77–80

    Article  CAS  PubMed  Google Scholar 

  84. Peterson CL, Laniel MA (2004) Histones and histone modifications. Curr Biol 14:R546–R551

    Article  CAS  PubMed  Google Scholar 

  85. Pray-Grant MG, Daniel JA, Schieltz D, Yates JR III, Grant PA (2005) Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433:434–438

    Article  CAS  PubMed  Google Scholar 

  86. Rea S, Eisenhaber F, O'Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, Jenuwein T (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406:593–599

    Article  CAS  PubMed  Google Scholar 

  87. Rice JC, Allis CD (2001) Histone methylation versus histone acetylation: new insights into epigenetic regulation. Curr Opin Cell Biol 13:263–273

    Article  CAS  PubMed  Google Scholar 

  88. Rice JC, Nishioka K, Sarma K, Steward R, Reinberg D, Allis CD (2002) Mitotic-specific methylation of histone H4 Lys 20 follows increased PR-Set7 expression and its localization to mitotic chromosomes. Genes Dev 16:2225–2230

    Article  CAS  PubMed  Google Scholar 

  89. Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, Hunt DF, Shinkai Y, Allis CD (2003) Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell 12:1591–1598

    Article  CAS  PubMed  Google Scholar 

  90. Ringrose L, Ehret H, Paro R (2004) Distinct contributions of histone H3 lysine 9 and 27 methylation to locus-specific stability of polycomb complexes. Mol Cell 16:641–653

    Article  CAS  PubMed  Google Scholar 

  91. Robzyk K, Recht J, Osley MA (2000) Rad6-dependent ubiquitination of histone H2B in yeast. Science 287:501–504

    Article  CAS  PubMed  Google Scholar 

  92. Roguev A, Schaft D, Shevchenko A, Aasland R, Stewart AF (2003) High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation in budding and fission yeasts. J Biol Chem 278:8487–8493

    Article  CAS  PubMed  Google Scholar 

  93. Sanders SL, Portoso M, Mata J, Bahler J, Allshire RC, Kouzarides T (2004) Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell 119:603–614

    Article  CAS  PubMed  Google Scholar 

  94. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor J, Kouzarides T (2002) Active genes are tri-methylated at K4 of histone H3. Nature 419:407–411

    Article  CAS  PubMed  Google Scholar 

  95. Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, Schreiber SL, Mellor J, Kouzarides T (2003) Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol Cell 12:1325–1332

    Article  CAS  PubMed  Google Scholar 

  96. Santos-Rosa H, Bannister AJ, Dehe PM, Geli V, Kouzarides T (2004) Methylation of H3 lysine 4 at euchromatin promotes Sir3p association with heterochromatin. J Biol Chem 279:47506–47512

    Article  CAS  PubMed  Google Scholar 

  97. Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, Neugebauer KM, Stewart AF (2003) The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res 31:2475–2482

    Article  CAS  PubMed  Google Scholar 

  98. Schlichter A, Cairns BR (2005) Histone trimethylation by Set1 is coordinated by the RRM, autoinhibitory, and catalytic domains. Embo J 24:1222–1231

    Article  CAS  PubMed  Google Scholar 

  99. Schotta G, Ebert A, Dorn R, Reuter G (2003) Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin Cell Dev Biol 14:67–75

    Article  CAS  PubMed  Google Scholar 

  100. Schotta G, Lachner M, Sarma K, Ebert A, Sengupta R, Reuter G, Reinberg D, Jenuwein T (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev 18:1251–1262

    Article  CAS  PubMed  Google Scholar 

  101. Schurter BT, Koh SS, Chen D, Bunick GJ, Harp JM, Hanson BL, Henschen-Edman A, Mackay DR, Stallcup MR, Aswad DW (2001) Methylation of histone H3 by coactivator-associated arginine methyltransferase 1. Biochemistry 40:5747–5756

    Article  CAS  PubMed  Google Scholar 

  102. Selenko P, Sprangers R, Stier G, Buhler D, Fischer U, Sattler M (2001) SMN tudor domain structure and its interaction with the Sm proteins. Nat Struct Biol 8:27–31

    Article  CAS  PubMed  Google Scholar 

  103. Shahbazian MD, Zhang K, Grunstein M (2005) Histone H2B ubiquitylation controls processive methylation but not monomethylation by Dot1 and Set1. Mol Cell 19:271–277

    Article  CAS  PubMed  Google Scholar 

  104. Sharon G, Raboy B, Parag HA, Dimitrovsky D, Kulka RG (1991) RAD6 gene product of Saccharomyces cerevisiae requires a putative ubiquitin protein ligase (E3) for the ubiquitination of certain proteins. J Biol Chem 266:15890–15894

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  106. Shiio Y, Eisenman RN (2003) Histone sumoylation is associated with transcriptional repression. Proc Natl Acad Sci USA 100:13225–13230

    Article  CAS  PubMed  Google Scholar 

  107. Simic R, Lindstrom DL, Tran HG, Roinick KL, Costa PJ, Johnson AD, Hartzog GA, Arndt KM (2003) Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. Embo J 22:1846–1856

    Article  CAS  PubMed  Google Scholar 

  108. Sims RJ, Nishioka K, Reinberg D (2003) Histone lysine methylation: a signature for chromatin function. Trends Genet 19:629–639

    Article  CAS  PubMed  Google Scholar 

  109. Sims RJ, Chen CF, Santos-Rosa H, Kouzarides T, Patel SS, Reinberg D (2005) Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains. J Biol Chem 280:41789–41792

    Article  CAS  PubMed  Google Scholar 

  110. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45

    Article  CAS  PubMed  Google Scholar 

  111. Strahl BD, Ohba R, Cook RG, Allis CD (1999) Methylation of histone H3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in Tetrahymena. Proc Natl Acad Sci USA 96:14967–14972

    Article  CAS  PubMed  Google Scholar 

  112. Strahl BD, Briggs SD, Brame CJ, Caldwell JA, Koh SS, Ma H, Cook RG, Shabanowitz J, Hunt DF, Stallcup MR, Allis CD (2001) Methylation of histone H4 at arginine 3 occurs in vivo and is mediated by the nuclear receptor coactivator PRMT1. Curr Biol 11:996–1000

    Article  CAS  PubMed  Google Scholar 

  113. Strahl BD, Grant PA, Briggs SD, Sun ZW, Bone JR, Caldwell JA, Mollah S, Cook RG, Shabanowitz J, Hunt DF, Allis CD (2002) Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol 22:1298–1306

    Article  CAS  PubMed  Google Scholar 

  114. Sun ZW, Allis CD (2002) Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418:104–108

    Article  CAS  PubMed  Google Scholar 

  115. Sung P, Prakash S, Prakash L (1988) The RAD6 protein of Saccharomyces cerevisiae polyubiquitinates histones, and its acidic domain mediates this activity. Genes Dev 2:1476–1485

    Article  CAS  PubMed  Google Scholar 

  116. Tachibana M, Sugimoto K, Fukushima T, Shinkai Y (2001) Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem 276:25309–25317

    Article  CAS  PubMed  Google Scholar 

  117. Thiru A, Nietlispach D, Mott HR, Okuwaki M, Lyon D, Nielsen PR, Hirshberg M, Verreault A, Murzina NV, Laue ED (2004) Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin. Embo J 23:489–499

    Article  CAS  PubMed  Google Scholar 

  118. Torok MS, Grant PA (2004) Histone acetyltransferase proteins contribute to transcriptional processes at multiple levels. Adv Protein Chem 67:181–199

    Article  CAS  PubMed  Google Scholar 

  119. Tran HG, Steger DJ, Iyer VR, Johnson AD (2000) The chromo domain protein chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. Embo J 19:2323–2331

    Article  CAS  PubMed  Google Scholar 

  120. Tsukada YI, 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  CAS  PubMed  Google Scholar 

  121. Turner BM (1993) Decoding the nucleosome. Cell 75:5–8

    Article  CAS  PubMed  Google Scholar 

  122. Turner BM (2000) Histone acetylation and an epigenetic code. Bioessays 22:836–845

    Article  CAS  PubMed  Google Scholar 

  123. Turner BM (2002) Cellular memory and the histone code. Cell 111:285–291

    Article  CAS  PubMed  Google Scholar 

  124. Vakoc CR, Mandat SA, Olenchock BA, Blobel GA (2005) Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol Cell 19:381–391

    Article  CAS  PubMed  Google Scholar 

  125. van Leeuwen F, Gafken PR, Gottschling DE (2002) Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109:745–756

    Article  PubMed  Google Scholar 

  126. Wallrath LL, Elgin SC (1995) Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev 9:1263–1277

    Article  CAS  PubMed  Google Scholar 

  127. Wang H, Cao R, Xia L, Erdjument-Bromage H, Borchers C, Tempst P, Zhang Y (2001) Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase. Mol Cell 8:1207–1217

    Article  CAS  PubMed  Google Scholar 

  128. Wang H, An W, Cao R, Xia L, Erdjument-Bromage H, Chatton B, Tempst P, Roeder RG, Zhang Y (2003) mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression. Mol Cell 12:475–487

    Article  CAS  PubMed  Google Scholar 

  129. Wang Y, Fischle W, Cheung W, Jacobs S, Khorasanizadeh S, Allis CD (2004a) Beyond the double helix: writing and reading the histone code. Novartis Found Symp 259:3–17; discussion 17–21, pp 163–169

    Article  CAS  PubMed  Google Scholar 

  130. 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 (2004b). Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306:279–283

    Article  CAS  PubMed  Google Scholar 

  131. West MH, Bonner WM (1980) Histone 2B can be modified by the attachment of ubiquitin. Nucleic Acids Res 8:4671–4680

    Article  CAS  PubMed  Google Scholar 

  132. White CL, Suto RK, Luger K (2001) Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. Embo J 20:5207–5218

    Article  CAS  PubMed  Google Scholar 

  133. Wood A, Krogan NJ, Dover J, Schneider J, Heidt J, Boateng MA, Dean K, Golshani A, Zhang Y, Greenblatt JF et al (2003) Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol Cell 11:267–274

    Article  CAS  PubMed  Google Scholar 

  134. Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, Roeder RG, Brivanlou AH, Allis CD (2005) WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121:859–872

    Article  CAS  PubMed  Google Scholar 

  135. Xiao T, Kao CF, Krogan NJ, Sun ZW, Greenblatt JF, Osley MA, Strahl BD (2005) Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol Cell Biol 25:637–651

    Article  CAS  PubMed  Google Scholar 

  136. Zhang L, Schroeder S, Fong N, Bentley DL (2005) Altered nucleosome occupancy and histone H3K4 methylation in response to transcriptional stress. Embo J 24:2379–2390

    Article  CAS  PubMed  Google Scholar 

  137. Zhang Y (2003) Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev 17:2733–2740

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 22908, Charlottesville, VA, USA

    Michael S. Torok & Patrick A. Grant

Authors
  1. Michael S. Torok
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Patrick A. Grant
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Patrick A. Grant .

Editor information

Brehon C. Laurent

Rights and permissions

Reprints and permissions

About this chapter

Cite this chapter

Torok, M.S., Grant, P.A. The Generation and Recognition of Histone Methylation. In: Laurent, B.C. (eds) Chromatin Dynamics in Cellular Function. Results and Problems in Cell Differentiation, vol 41. Springer, Berlin, Heidelberg. https://doi.org/10.1007/400_016

Download citation

Publish with us

Policies and ethics

Search

Navigation