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Histone Ubiquitylation and the Regulation of Transcription

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Book cover Chromatin Dynamics in Cellular Function

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

Abstract

The small (76 amino acids) and highly conserved ubiquitin protein plays key roles in the physiology of eukaryotic cells. Protein ubiquitylation has emerged as one of the most important intracellular signaling mechanisms, and in 2004 the Nobel Prize was awarded to Aaron Ciechanower, Avram Hersko, and Irwin Rose for their pioneering studies of the enzymology of ubiquitin attachment. One of the most common features of protein ubiquitylation is the attachment of polyubiquitin chains (four or more ubiquitin moieties attached to each other), which is a widely used mechanism to target proteins for degradation via the 26S proteosome. However, it is noteworthy that the first ubiquitylated protein to be identified was histone H2A, to which a single ubiquitin moiety is most commonly attached. Following this discovery, other histones (H2B, H3, H1, H2A.Z, macroH2A), as well as many nonhistone proteins, have been found to be monoubiquitylated. The role of monoubiquitylation is still elusive because a single ubiquitin moiety is not sufficient to target proteins for turnover, and has been hypothesized to control the assembly or disassembly of multiprotein complexes by providing a protein-binding site. Indeed, a number of ubiquitin-binding domains have now been identified in both polyubiquitylated and monoubiquitylated proteins. Despite the early discovery of ubiquitylated histones, it has only been in the last five or so years that we have begun to understand how histone ubiquitylation is regulated and what roles it plays in the cell. This review will discuss current research on the factors that regulate the attachment and removal of ubiquitin from histones, describe the relationship of histone ubiquitylation to histone methylation, and focus on the roles of ubiquitylated histones in gene expression.

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References

  1. Amar N, Messenguy F et al. (2000) ArgrII, a component of the Argr-Mcm1 complex involved in the control of arginine metabolism in Saccharomyces cerevisiae, is the sensor of arginine. Mol Cell Biol 20:2087–2097

    Article  CAS  PubMed  Google Scholar 

  2. Amerik AY, Li SJ et al. (2000) Analysis of the deubiquitinating enzymes of the yeast Saccharomyces cerevisiae. Biol Chem 381:981–992

    Article  CAS  PubMed  Google Scholar 

  3. Baarends WM, Hoogerbrugge JW et al. (1999) Histone ubiquitination and chromatin remodeling in mouse spermatogenesis. Dev Biol 207:322–333

    Article  CAS  PubMed  Google Scholar 

  4. Baarends WM, Wassenaar E et al. (2005) Silencing of unpaired chromatin and histone H2A ubiquitination in mammalian meiosis. Mol Cell Biol 25:1041–1053

    Article  CAS  PubMed  Google Scholar 

  5. Bailly V, Lauder S et al. (1997) Yeast DNA repair proteins Rad6 and Rad18 form a heterodimer that has ubiquitin conjugating, DNA binding, and ATP hydrolytic activities. J Biol Chem 272:23 360–23 365

    Google Scholar 

  6. Ballal NR, Kang YJ et al. (1975) Changes in nucleolar proteins and their phosphorylation patterns during liver regeneration. J Biol Chem 250:5921–5925

    CAS  PubMed  Google Scholar 

  7. Bannister AJ, Schneider R et al. (2005) Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J Biol Chem 280:17 732–17 736

    Google Scholar 

  8. Barsoum J, Varshavsky A (1985) Preferential localization of variant nucleosomes near the 5′-end of the mouse dihydrofolate reductase gene. J Biol Chem 260:7688–7697

    CAS  PubMed  Google Scholar 

  9. Bartel B, Wunning I et al. (1990) The recognition component of the n-end rule pathway. EMBO J 9:3179–3189

    CAS  PubMed  Google Scholar 

  10. Bernstein BE, Humphrey EL et al. (2002) Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci USA 99:8695–8700

    Article  CAS  PubMed  Google Scholar 

  11. Bhaumik SR, Green MR (2002) Differential requirement of SAGA components for recruitment of TATA-box-binding protein to promoters in vivo. Mol Cell Biol 22:7365–7371

    Article  CAS  PubMed  Google Scholar 

  12. Bohm L, Crane-Robinson C et al. (1980) Proteolytic digestion studies of chromatin core-histone structure. Identification of a limit peptide of histone H2A. Eur J Biochem 106:525–530

    Article  CAS  PubMed  Google Scholar 

  13. Bray S, Musisi H et al. (2005) Bre1 is required for notch signaling and histone modification. Dev Cell 8:279–286

    Article  CAS  PubMed  Google Scholar 

  14. Briggs SD, Xiao T et al. (2002) Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418:498

    Article  CAS  PubMed  Google Scholar 

  15. Broomfield S, Hryciw T et al. (2001) DNA postreplication repair and mutagenesis in Saccharomyces cerevisiae. Mutat Res 486:167–184

    CAS  PubMed  Google Scholar 

  16. Bryk M, Briggs SD et al. (2002) Evidence that Set1, a factor required for methylation of histone H3, regulates rDna silencing in S. cerevisiae by a Sir2-independent mechanism. Curr Biol 12:165–170

    Article  CAS  PubMed  Google Scholar 

  17. Buchberger A (2002) From Uba to Ubx: new words in the ubiquitin vocabulary. Trends Cell Biol 12:216–221

    Article  CAS  PubMed  Google Scholar 

  18. Cai SY, Babbitt RW et al. (1999) A mutant deubiquitinating enzyme (Ubp-m) associates with mitotic chromosomes and blocks cell division. Proc Natl Acad Sci USA 96:2828–2833

    Article  CAS  PubMed  Google Scholar 

  19. Cao R, Tsukuda YI, Zhang Y (2005) Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. Mol Cell 20:845–854

    Article  CAS  PubMed  Google Scholar 

  20. Cao R, Wang L et al. (2002) Role of histone H3 lysine 27 methylation in polycomb-group silencing. Science 298:1039–1043

    Article  CAS  PubMed  Google Scholar 

  21. Carvin CD, Kladde MP (2004) Effectors of lysine 4 methylation of histone H3 in Saccharomyces cerevisiae are negative regulators of Pho5 and Gal1-10. J Biol Chem 279:33 057–33 062

    Article  Google Scholar 

  22. Chadwick BP, Willard HF (2003) Chromatin of the barr body: histone and non-histone proteins associated with or excluded from the inactive X chromosome. Hum Mol Genet 12:2167–2178

    Article  CAS  PubMed  Google Scholar 

  23. Chang M, French-Cornay D et al. (1999) A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol Cell Biol 19:1056–1067

    CAS  PubMed  Google Scholar 

  24. Chen HY, Sun JM et al. (1998) Ubiquitination of histone H3 in elongating spermatids of rat testes. J Biol Chem 273:13 165–13 169

    Article  PubMed  Google Scholar 

  25. Cismowski MJ, Laff GM et al. (1995) Kin28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol Cell Biol 15:2983–2992

    CAS  PubMed  Google Scholar 

  26. Citterio E, Papait R et al. (2004) Np95 is a histone-binding protein endowed with ubiquitin ligase activity. Mol Cell Biol 24:2526–2535

    Article  CAS  PubMed  Google Scholar 

  27. Cohen HR, Royce-Tolland ME et al. (2005) Chromatin modifications on the inactive X chromosome. Prog Mol Subcell Biol 38:91–122

    CAS  PubMed  Google Scholar 

  28. Costa PJ, Arndt KM (2000) Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics 156:535–547

    CAS  Google Scholar 

  29. Daniel JA, Torok MS et al. (2004) Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem 279:1867–1871

    Article  CAS  PubMed  Google Scholar 

  30. Davie JR, Lin R et al. (1991) Timing of the appearance of ubiquitinated histones in developing new macronuclei of Tetrahymena thermophila. Biochem Cell Biol 69:66–71

    CAS  Google Scholar 

  31. Davies N, Lindsey GG (1994) Histone H2B (and H2A) ubiquitination allows normal histone octamer and core particle reconstitution. Biochim Biophys Acta 1218:187–193

    CAS  PubMed  Google Scholar 

  32. de Napoles M, Mermoud JE et al. (2004) Polycomb group proteins Ring1a/b link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev Cell 7:663–676

    Article  PubMed  Google Scholar 

  33. Dejardin J, Cavalli G (2005) Epigenetic inheritance of chromatin states mediated by Polycomb and Trithorax group proteins in Drosophila. Prog Mol Subcell Biol 38:31–63

    CAS  PubMed  Google Scholar 

  34. Dong L, Xu CW (2004) Carbohydrates induce mono-ubiquitination of H2B in yeast. J Biol Chem 279:1577–1580

    Article  CAS  PubMed  Google Scholar 

  35. Dor Y, Raboy B et al. (1996) Role of the conserved carboxy-terminal alpha-helix of Rad6p in ubiquitination and DNA repair. Mol Microbiol 21:1197–1206

    Article  CAS  PubMed  Google Scholar 

  36. Dou Y, Milne TA et al. (2005) Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase mof. Cell 121:873–885

    CAS  Google Scholar 

  37. Dover J, Schneider J et al. (2002) Methylation of histone H3 by compass requires ubiquitination of histone H2B by Rad6. J Biol Chem 277:28 368–28 371

    Article  CAS  Google Scholar 

  38. Dudley AM, Rougeulle C et al. (1999) The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. Genes Dev 13:2940–2945

    Article  CAS  PubMed  Google Scholar 

  39. Emre NC, Berger SL (2004) Histone H2B ubiquitylation and deubiquitylation in genomic regulation. Cold Spring Harb Symp Quant Biol 69:289–299

    Article  CAS  PubMed  Google Scholar 

  40. Emre NC, Ingvarsdottir K et al. (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 

  41. Ezhkova E, Tansey WP (2004) Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3. Mol Cell 13:435–442

    Article  CAS  PubMed  Google Scholar 

  42. Fang J, Chen T et al. (2004) Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J Biol Chem 279:52 812–52 815

    Google Scholar 

  43. Fischle W, Wang Y et al. (2003) Histone and chromatin cross-talk. Curr Opin Cell Biol 15:172–183

    Article  CAS  PubMed  Google Scholar 

  44. Francis NJ, Kingston RE et al. (2004) Chromatin compaction by a Polycomb group protein complex. Science 306:1574–1577

    Article  CAS  PubMed  Google Scholar 

  45. Francis NJ, Saurin AJ et al. (2001) Reconstitution of a functional core Polycomb repressive complex. Mol Cell 8:545–556

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  47. Gardner RG, Nelson ZW et al. (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 

  48. Gerber M, Shilatifard A (2003) Transcriptional elongation by RNA polymerase II and histone methylation. J Biol Chem 278:26 303–26 306

    Article  CAS  Google Scholar 

  49. Giannattasio M, Lazzaro F et al. (2005) The DNA damage checkpoint response requires histone H2B ubiquitination by Rad6-Bre1 and H3 methylation by Dot1. J Biol Chem 280:9879–9886

    Article  CAS  PubMed  Google Scholar 

  50. Goldknopf IL, Busch H (1977) Isopeptide linkage between nonhistone and histone 2A polypeptides of chromosomal conjugate-protein A24. Proc Natl Acad Sci USA 74:864–868

    CAS  PubMed  Google Scholar 

  51. Goldknopf IL, French MF et al. (1978) A reciprocal relationship between contents of free ubiquitin and protein A24, its conjugate with histone 2A, in chromatin fractions obtained by the DNase II, Mg++ procedure. Biochem Biophys Res Commun 84:786–793

    Article  CAS  PubMed  Google Scholar 

  52. Goldknopf IL, Sudhakar S et al. (1980) Timing of ubiquitin synthesis and conjugation into protein A24 during the Hela cell cycle. Biochem Biophys Res Commun 95:1253–1260

    Article  CAS  PubMed  Google Scholar 

  53. Goldknopf IL, Taylor CW et al. (1975) Isolation and characterization of protein A24, a histone-like non-histone chromosomal protein. J Biol Chem 250:7182–7187

    CAS  PubMed  Google Scholar 

  54. Greer SF, Zika E et al. (2003) Enhancement of CIITA transcriptional function by ubiquitin. Nat Immunol 4:1074–1082

    Article  CAS  PubMed  Google Scholar 

  55. Haglund K, Di Fiore PP et al. (2003) Distinct monoubiquitin signals in receptor endocytosis. Trends Biochem Sci 28:598–603

    Article  CAS  PubMed  Google Scholar 

  56. Hanson RD, Hess JL et al. (1999) Mammalian Trithorax and Polycomb-group homologues are antagonistic regulators of homeotic development. Proc Natl Acad Sci USA 96:14 372–14 377

    Article  Google Scholar 

  57. Henry KW, Berger SL (2002) Trans-tail histone modifications: wedge or bridge? Nat Struct Biol 9:565–566

    Article  CAS  PubMed  Google Scholar 

  58. Henry KW, Wyce A et al. (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 

  59. Hernandez-Munoz I, Lund AH et al. (2005) Stable X chromosome inactivation involves the PRC1 polycomb complex and requires histone macroH2A1 and the Cullin3/Spop ubiquitin E3 ligase. Proc Natl Acad Sci USA 102:7635–7640

    Article  CAS  PubMed  Google Scholar 

  60. Hicke L (2001) Protein regulation by monoubiquitin. Nat Rev Mol Cell Biol 2:195–201

    Article  CAS  PubMed  Google Scholar 

  61. Hicke L, Dunn R (2003) Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins. Annu Rev Cell Dev Biol 19:141–172

    Article  CAS  PubMed  Google Scholar 

  62. Hochstrasser M (1995) Ubiquitin, proteasomes, and the regulation of intracellular protein degradation. Curr Opin Cell Biol 7:215–223

    Article  CAS  PubMed  Google Scholar 

  63. Hoege C, Pfander B et al. (2002) Rad6-dependent DNA repair is linked to modification of PCNA by ubiquitin and sumo. Nature 419:135–141

    Article  CAS  PubMed  Google Scholar 

  64. Huang H, Kahana A et al. (1997) The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae. Mol Cell Biol 17:6693–6699

    CAS  PubMed  Google Scholar 

  65. Huyen Y, Zgheib O et al. (2004) Methylated lysine 79 of histone H3 targets 53bp1 to DNA double-strand breaks. Nature 432:406–411

    Article  CAS  PubMed  Google Scholar 

  66. Hwang WW, Venkatasubrahmanyam S et al. (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 

  67. Ingvarsdottir K, Krogan NJ et al. (2005) H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex. Mol Cell Biol 25:1162–1172

    Article  CAS  PubMed  Google Scholar 

  68. Jaenisch R, Beard C et al. (1998) Mammalian X chromosome inactivation. Novartis Found Symp 214:200–209; discussion 209–213, 228–232

    CAS  PubMed  Google Scholar 

  69. Jason LJ, Finn RM et al. (2005) Histone H2A ubiquitination does not preclude histone H1 binding, but it facilitates its association with the nucleosome. J Biol Chem 280:4975–4982

    Article  CAS  PubMed  Google Scholar 

  70. Jason LJ, Moore SC et al. (2001) Magnesium-dependent association and folding of oligonucleosomes reconstituted with ubiquitinated H2A. J Biol Chem 276:14597–14601

    Article  CAS  PubMed  Google Scholar 

  71. Jason LJ, Moore SC et al. (2002) Histone ubiquitination: a tagging tail unfolds? Bioessays 24:166–174

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  73. Joazeiro CA, Weissman AM (2000) Ring finger proteins: mediators of ubiquitin ligase activity. Cell 102:549–552

    Article  CAS  PubMed  Google Scholar 

  74. Kang RS, Daniels CM et al. (2003) Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding. Cell 113:621–630

    Article  CAS  PubMed  Google Scholar 

  75. Kao CF, Hillyer C et al. (2004) Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B. Genes Dev 18:184–195

    Article  CAS  PubMed  Google Scholar 

  76. Kaplan CD, Holland MJ et al. (2005) Interaction between transcription elongation factors and mRNA 3′-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. J Biol Chem 280:913–922

    Article  CAS  PubMed  Google Scholar 

  77. Koken M, Reynolds P et al. (1991) Dhr6, a Drosophila homolog of the yeast DNA-repair gene RAD6. Proc Natl Acad Sci USA 88:3832–3836

    CAS  PubMed  Google Scholar 

  78. Koken MH, Hoogerbrugge JW et al. (1996) Expression of the ubiquitin-conjugating DNA repair enzymes hHR6a and b suggests a role in spermatogenesis and chromatin modification. Dev Biol 173:119–132

    Article  CAS  PubMed  Google Scholar 

  79. Koken MH, Reynolds P et al. (1991) Structural and functional conservation of two human homologs of the yeast DNA repair gene RAD6. Proc Natl Acad Sci USA 88:8865–8869

    CAS  PubMed  Google Scholar 

  80. Kouzarides T (2002) Histone methylation in transcriptional control. Curr Opin Genet Dev 12:198–209

    Article  CAS  PubMed  Google Scholar 

  81. Krogan NJ, Dover J et al. (2003) The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell 11:721–729

    Article  CAS  PubMed  Google Scholar 

  82. Krogan NJ, Kim M et al. (2002) RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol 22:6979–6992

    Article  CAS  PubMed  Google Scholar 

  83. Krogan NJ, Kim M 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 

  84. Laribee RN, Krogan NJ et al. (2005) BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Curr Biol 15:1487–1493

    Article  CAS  PubMed  Google Scholar 

  85. Larschan E, Winston F (2001) The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev 15:1946–1956

    Article  CAS  PubMed  Google Scholar 

  86. Larschan E, Winston F (2005) The Saccharomyces cerevisiae Srb8-Srb11 complex functions with the SAGA complex during Gal4-activated transcription. Mol Cell Biol 25:114–123

    Article  CAS  PubMed  Google Scholar 

  87. Lee KK, Florens L et al. (2005) The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex. Mol Cell Biol 25:1173–1182

    Article  CAS  PubMed  Google Scholar 

  88. Levinger L, Varshavsky A (1982) Selective arrangement of ubiquitinated and d1 protein-containing nucleosomes within the Drosophila genome. Cell 28:375–385

    Article  CAS  PubMed  Google Scholar 

  89. Lo WS, Henry KW et al. (2004) Histone modification patterns during gene activation. Methods Enzymol 377:130–153

    Article  CAS  PubMed  Google Scholar 

  90. Milne TA, Briggs SD et al. (2002) MLL targets set domain methyltransferase activity to Hox gene promoters. Mol Cell 10:1107–1117

    Article  CAS  PubMed  Google Scholar 

  91. Mimnaugh EG, Kayastha G et al. (2001) Caspase-dependent deubiquitination of monoubiquitinated nucleosomal histone H2A induced by diverse apoptogenic stimuli. Cell Death Differ 8:1182–1196

    CAS  Google Scholar 

  92. Minsky N, Oren M (2004) The ring domain of Mdm2 mediates histone ubiquitylation and transcriptional repression. Mol Cell 16:631–639

    Article  CAS  PubMed  Google Scholar 

  93. Montelone BA, Prakash S et al. (1981) Recombination and mutagenesis in rad6 mutants of Saccharomyces cerevisiae: evidence for multiple functions of the RAD6 gene. Mol Gen Genet 184:410–415

    Article  CAS  PubMed  Google Scholar 

  94. Moore SC, Jason L et al. (2002) The elusive structural role of ubiquitinated histones. Biochem Cell Biol 80:311–319

    CAS  Google Scholar 

  95. Morrison A, Miller EJ et al. (1988) Domain structure and functional analysis of the carboxyl-terminal polyacidic sequence of the Rad6 protein of Saccharomyces cerevisiae. Mol Cell Biol 8:1179–1185

    CAS  PubMed  Google Scholar 

  96. Mueller RD, Yasuda H et al. (1985) Identification of ubiquitinated histones 2A and 2B in Physarum polycephalum. Disappearance of these proteins at metaphase and reappearance at anaphase. J Biol Chem 260:5147–5153

    CAS  PubMed  Google Scholar 

  97. Mueller TD, Feigon J (2002) Solution structures of UBA domains reveal a conserved hydrophobic surface for protein–protein interactions. J Mol Biol 319:1243–1255

    Article  CAS  PubMed  Google Scholar 

  98. Muller J, Hart CM et al. (2002) Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111:197–208

    Article  CAS  PubMed  Google Scholar 

  99. Ng HH, Ciccone DN et al. (2003) 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 

  100. Ng HH, Dole S et al. (2003) The Rtf1 component of the PAF1 transcriptional elongation complex is required for ubiquitination of histone H2B. J Biol Chem 278:33 625–33 628

    Google Scholar 

  101. Ng HH, Feng Q et al. (2002) Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev 16:1518–1527

    Article  CAS  PubMed  Google Scholar 

  102. Ng HH, Robert F et al. (2003) 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 

  103. Ng HH, Xu RM et al. (2002) Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J Biol Chem 277:34 655–34 657

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  105. Nickel BE, Roth SY et al. (1987) Changes in the histone H2A variant H2A.Z and polyubiquitinated histone species in developing trout testis. Biochemistry 26:4417–4421

    Article  CAS  PubMed  Google Scholar 

  106. Nislow C, Ray E et al. (1997) Set1, a yeast member of the Trithorax family, functions in transcriptional silencing and diverse cellular processes. Mol Biol Cell 8:2421–2436

    CAS  PubMed  Google Scholar 

  107. O'Brien T, Tjian R (2000) Different functional domains of TAFII250 modulate expression of distinct subsets of mammalian genes. Proc Natl Acad Sci USA 97:2456–2461

    Article  PubMed  Google Scholar 

  108. Oh S, Zhang H et al. (2004) A mechanism related to the yeast transcriptional regulator PAF1c is required for expression of the Arabidopsis Flc/Maf Mads box gene family. Plant Cell 16:2940–2953

    Article  CAS  PubMed  Google Scholar 

  109. Orlandi I, Bettiga M et al. (2004) Transcriptional profiling of ubp10 null mutant reveals altered subtelomeric gene expression and insurgence of oxidative stress response. J Biol Chem 279:6414–6425

    Article  CAS  PubMed  Google Scholar 

  110. Orphanides G, Reinberg D (2000) Rna polymerase II elongation through chromatin. Nature 407:471–475

    Article  CAS  PubMed  Google Scholar 

  111. Pham AD, Sauer F (2000) Ubiquitin-activating/conjugating activity of TAFII250, a mediator of activation of gene expression in Drosophila. Science 289:2357–2360

    Article  CAS  PubMed  Google Scholar 

  112. Pickart CM (1997) Targeting of substrates to the 26s proteasome. Faseb J 11:1055–1066

    CAS  PubMed  Google Scholar 

  113. Pickart CM (2001a) Mechanisms underlying ubiquitination. Annu Rev Biochem 70:503–533

    Google Scholar 

  114. Pickart CM (2001b) Ubiquitin enters the new millennium. Mol Cell 8:499–504

    Google Scholar 

  115. Pickart CM, Eddins MJ (2004) Ubiquitin: structures, functions, mechanisms. Biochim Biophys Acta 1695:55–72

    Article  CAS  PubMed  Google Scholar 

  116. Plath K, Fang J et al. (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131–135

    Article  CAS  PubMed  Google Scholar 

  117. Pokholok DK, Hannett NM et al. (2002) Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell 9:799–809

    Article  CAS  PubMed  Google Scholar 

  118. Pokholok DK, Harbison CT et al. (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122:517–527

    CAS  Google Scholar 

  119. Polo S, Sigismund S et al. (2002) A single motif responsible for ubiquitin recognition and monoubiquitination in endocytic proteins. Nature 416:451–455

    Article  CAS  PubMed  Google Scholar 

  120. Powell DW, Weaver CM et al. (2004) Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol 24:7249–7259

    Article  CAS  PubMed  Google Scholar 

  121. Prag G, Misra S et al. (2003) Mechanism of ubiquitin recognition by the CUE domain of Vps9p. Cell 113:609–620

    Article  CAS  PubMed  Google Scholar 

  122. Prakash L (1981) Characterization of postreplication repair in Saccharomyces cerevisiae and effects of rad6, rad18, rev3 and rad52 mutations. Mol Gen Genet 184:471–478

    Article  CAS  PubMed  Google Scholar 

  123. Pray-Grant MG, Daniel JA et al. (2005) Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433:434–438

    Article  CAS  PubMed  Google Scholar 

  124. Raasi S, Pickart CM (2005) Ubiquitin chain synthesis. Methods Mol Biol 301:47–55

    CAS  PubMed  Google Scholar 

  125. Raboy B, Kulka RG (1994) Role of the C-terminus of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in substrate and ubiquitin-protein-ligase (E3-r) interactions. Eur J Biochem 221:247–251

    Article  CAS  PubMed  Google Scholar 

  126. Rao B, Shibata Y, Strahl B, Lieb JD (2005) Dimethylation of histone H3 at lysine 30 demarcates regulatory and nonregulatory chromatin genome-wide. Mol Cell Biol 25:9447–9459

    Article  CAS  PubMed  Google Scholar 

  127. Reverol L, Chirinos M et al. (1997) Presence of an unusually high concentration of an ubiquitinated histone-like protein in Trypanosoma cruzi. J Cell Biochem 66:433–440

    Article  CAS  PubMed  Google Scholar 

  128. Reynolds P, Koken MH et al. (1990) The rhp6+ gene of Schizosaccharomyces pombe: a structural and functional homolog of the RAD6 gene from the distantly related yeast Saccharomyces cerevisiae. EMBO J 9:1423–1430

    CAS  PubMed  Google Scholar 

  129. Ricci AR, Genereaux J et al. (2002) Components of the SAGA histone acetyltransferase complex are required for repressed transcription of ARG1 in rich medium. Mol Cell Biol 22:4033–4042

    Article  CAS  PubMed  Google Scholar 

  130. Robzyk K, Recht J et al. (2000) RAD6-dependent ubiquitination of histone H2B in yeast. Science 287:501–504

    Article  CAS  PubMed  Google Scholar 

  131. Roest HP, Baarends WM et al. (2004) The ubiquitin-conjugating DNA repair enzyme HR6A is a maternal factor essential for early embryonic development in mice. Mol Cell Biol 24:5485–5495

    Article  CAS  PubMed  Google Scholar 

  132. Roest HP, van Klaveren J et al. (1996) Inactivation of the HR6B ubiquitin-conjugating DNA repair enzyme in mice causes male sterility associated with chromatin modification. Cell 86:799–810

    Article  CAS  PubMed  Google Scholar 

  133. Ruppert S, Wang EH et al. (1993) Cloning and expression of human TAFII250: a TBP-associated factor implicated in cell-cycle regulation. Nature 362:175–179

    Article  CAS  PubMed  Google Scholar 

  134. Rusche LN, Kirchmaier AL et al. (2003) The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72:481–516

    Article  CAS  PubMed  Google Scholar 

  135. San-Segundo PA, Roeder GS (2000) Role for the silencing protein Dot1 in meiotic checkpoint control. Mol Biol Cell 11:3601–3615

    CAS  PubMed  Google Scholar 

  136. Santos-Rosa H, Schneider R et al. (2002) Active genes are tri-methylated at K4 of histone H3. Nature 419:407–411

    Article  CAS  PubMed  Google Scholar 

  137. Schneider J, Wood A et al. (2005) Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression. Mol Cell 19:849–856

    Article  CAS  PubMed  Google Scholar 

  138. Seale RL (1981) Rapid turnover of the histone–ubiquitin conjugate, protein A24. Nucleic Acids Res 9:3151–3158

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  140. Shi X, Chang M et al. (1997) Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Mol Cell Biol 17:1160–1169

    CAS  PubMed  Google Scholar 

  141. Shi X, Finkelstein A et al. (1996) Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription. Mol Cell Biol 16:669–676

    CAS  PubMed  Google Scholar 

  142. Shih SC, Prag G et al. (2003) A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain. EMBO J 22:1273–1281

    Article  CAS  PubMed  Google Scholar 

  143. Sigismund S, Polo S et al. (2004) Signaling through monoubiquitination. Curr Top Microbiol Immunol 286:149–185

    CAS  PubMed  Google Scholar 

  144. Simic R, Lindstrom DL et al. (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 

  145. Singh J, Goel V et al. (1998) A novel function of the DNA repair gene rhp6 in mating-type silencing by chromatin remodeling in fission yeast. Mol Cell Biol 18:5511–5522

    CAS  PubMed  Google Scholar 

  146. Smith KP, Byron M et al. (2004) Ubiquitinated proteins including uH2A on the human and mouse inactive X chromosome: enrichment in gene rich bands. Chromosoma 113:324–335

    Article  CAS  PubMed  Google Scholar 

  147. Sollier J, Lin W et al. (2004) SET1 is required for meiotic s-phase onset, double-strand break formation and middle gene expression. EMBO J 23:1957–1967

    Article  CAS  PubMed  Google Scholar 

  148. Squazzo SL, Costa PJ et al. (2002) The PAF1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J 21:1764–1774

    Article  CAS  PubMed  Google Scholar 

  149. Stelter P, Ulrich HD (2003) Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 425:188–191

    Article  CAS  PubMed  Google Scholar 

  150. Sterner DE, Grant PA et al. (1999) Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TATA–binding protein interaction. Mol Cell Biol 19:86–98

    CAS  PubMed  Google Scholar 

  151. 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 

  152. Sung P, Prakash S et al. (1988) The Rad6 protein of Saccharomyces cerevisiae polyubiquitinates histones, and its acidic domain mediates this activity. Genes Dev 2:1476–1485

    CAS  PubMed  Google Scholar 

  153. Sung P, Prakash S et al. (1990) Mutation of cysteine-88 in the Saccharomyces cerevisiae RAD6 protein abolishes its ubiquitin-conjugating activity and its various biological functions. Proc Natl Acad Sci USA 87:2695–2699

    CAS  PubMed  Google Scholar 

  154. Swerdlow PS, Schuster T et al. (1990) A conserved sequence in histone H2A which is a ubiquitination site in higher eucaryotes is not required for growth in Saccharomyces cerevisiae. Mol Cell Biol 10:4905–4911

    CAS  PubMed  Google Scholar 

  155. Tasaki T, Mulder LC et al. (2005) A family of mammalian E3 ubiquitin ligases that contain the UBR box motif and recognize N-degrons. Mol Cell Biol 25:7120–7136

    Article  CAS  PubMed  Google Scholar 

  156. Thorne AW, Sautiere P et al. (1987) The structure of ubiquitinated histone H2B. EMBO J 6:1005–1010

    CAS  PubMed  Google Scholar 

  157. Turner SD, Ricci AR et al. (2002) The E2 ubiquitin conjugase rad6 is required for the ArgR/Mcm1 repression of ARG1 transcription. Mol Cell Biol 22:4011–4019

    Article  CAS  PubMed  Google Scholar 

  158. Ulrich HD (2004) How to activate a damage-tolerant polymerase: consequences of PCNA modifications by ubiquitin and SUMO. Cell Cycle 3:15–18

    CAS  PubMed  Google Scholar 

  159. Ulrich HD, Jentsch S (2000) Two ring finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair. EMBO J 19:3388–3397

    Article  CAS  PubMed  Google Scholar 

  160. van der Knaap JA, Kumar BR et al. (2005) Gmp synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer Usp7. Mol Cell 17:695–707

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  162. van Leeuwen F, Gottschling DE (2002) Genome-wide histone modifications: gaining specificity by preventing promiscuity. Curr Opin Cell Biol 14:756–762

    Article  PubMed  CAS  Google Scholar 

  163. Vassilev AP, Rasmussen HH et al. (1995) The levels of ubiquitinated histone H2A are highly upregulated in transformed human cells: partial colocalization of uH2A clusters and PCNA/cyclin foci in a fraction of cells in S-phase. J Cell Sci 108 (Part 3):1205–1215

    Google Scholar 

  164. Wang H, Wang L et al. (2004) Role of histone H2A ubiquitination in Polycomb silencing. Nature 431:873–878

    Article  CAS  PubMed  Google Scholar 

  165. Wang L, Brown JL et al. (2004) Hierarchical recruitment of Polycomb group silencing complexes. Mol Cell 14:637–646

    Article  CAS  PubMed  Google Scholar 

  166. Watkins JF, Sung P et al. (1993) The extremely conserved amino terminus of RAD6 ubiquitin-conjugating enzyme is essential for amino-end rule-dependent protein degradation. Genes Dev 7:250–261

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  168. Wilkinson KD (1997) Regulation of ubiquitin-dependent processes by deubiquitinating enzymes. Faseb J 11:1245–1256

    CAS  PubMed  Google Scholar 

  169. Wing SS, Jain P (1995) Molecular cloning, expression and characterization of a ubiquitin conjugation enzyme (E2(17)kb) highly expressed in rat testis. Biochem J 305 (Part 1):125–132

    Google Scholar 

  170. Wood A, Krogan NJ 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 

  171. Wood A, Schneider J et al. (2003) The PAF1 complex is essential for histone monoubiquitination by the Rad6/Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. J Biol Chem 278:34739–34742

    Article  CAS  PubMed  Google Scholar 

  172. Wood A, Schneider J et al. (2005) The Bur1/Bur2 complex is required for H2B monoubiquitination by Rad6/Bre and histone methylation by COMPASS. Mol Cell 20:589–599

    Article  CAS  PubMed  Google Scholar 

  173. Wu RS, Kohn KW et al. (1981) Metabolism of ubiquitinated histones. J Biol Chem 256:5916–5920

    CAS  PubMed  Google Scholar 

  174. Wysocka J, Swigut T et al. (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 

  175. Wysocki R, Javaheri A et al. (2005) Role of Dot1-dependent histone H3 methylation in G1 and S phase DNA damage checkpoint functions of Rad9. Mol Cell Biol 25:8430–8443

    Article  CAS  PubMed  Google Scholar 

  176. Xiao T, Hall H et al. (2003) Phosphorylation of RNA polymerase III CTD regulates H3 methylation in yeast. Genes Dev 17:654–663

    Article  CAS  PubMed  Google Scholar 

  177. Xiao T, Kao CF et al. (2005) Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol Cell Biol 25:637–651

    Article  CAS  PubMed  Google Scholar 

  178. Xie Y, Varshavsky A (1999) The E2-E3 interaction in the N-end rule pathway: the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain. EMBO J 18:6832–6844

    Article  CAS  PubMed  Google Scholar 

  179. Yamashita K, Shinohara M et al. (2004) Rad6-Bre1-mediated histone H2B ubiquitylation modulates the formation of double-strand breaks during meiosis. Proc Natl Acad Sci USA 101:11 380–11 385

    Article  Google Scholar 

  180. Yao S, Neiman A et al. (2000) BUR1 and BUR2 encode a divergent cyclin-dependent kinase–cyclin complex important for transcription in vivo. Mol Cell Biol 20:7080–7087

    Article  CAS  PubMed  Google Scholar 

  181. Ye J, Ai X et al. (2005) Histone H4 lysine 91 acetylation, a core domain modification associated with chromatin assembly. Mol Cell 18:123–130

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  183. Zhang Y, Cao R et al. (2004) Mechanism of Polycomb group gene silencing. Cold Spring Harb Symp Quant Biol 69:309–317

    Article  CAS  PubMed  Google Scholar 

  184. Zhu B, Mandal SS et al. (2005) The human PAF complex coordinates transcription with events downstream of RNA synthesis. Genes Dev 19:1668–1673

    Article  CAS  PubMed  Google Scholar 

  185. Zhu B, Zheng Y et al. (2005) Monoubiquitination of human histone H2B: the factors involved and their roles in Hox gene regulation. Mol Cell 20:601–611

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank Shelley Berger, Danny Reinberg, and Yi Zhao for generously sharing unpublished data. Work from the authors' laboratory is supported by a grant from the NIH (GM40118) to M.A.O. and a Leukemia and Lymphoma Society Special Fellow award to C.-F.K.

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Correspondence to Mary Ann Osley .

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Osley, M.A., Fleming, A.B., Kao, CF. Histone Ubiquitylation and the Regulation of Transcription. 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_006

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