Gene Selectors Consisting of DNA-Binding Proteins, Histories, and Histone-Binding Proteins Regulate the Three Major Stages of Gene Expression

  • Shinsuke Muto
  • Masami Horikoshi 


Gene expression is the process whereby DNA sequence information is converted into a functional transmitter or player, namely, mRNA, and then a major functional player, namely, protein. Transcription is the first step in gene expression. Since the temporal and spatial regulation of gene expression define cellular identity, transcription is the most critical and fundamental step in the cellular functions of a gene. We have classified transcriptional regulation into three functional stages on the basis of the complexity of the DNA structures involved. The first level concerns the activation/inactivation of promoters on naked DNA, the second level entails activation/inactivation of nucleosomes, while the third level involves the activation/inactivation of chromosomal regions (Fig. 1). We denote the components that determine which genes are activated or repressed at each of these levels as “gene selectors.” We have categorized the gene selectors into three main groups, namely, DNA-binding proteins, histones (non-specific DNA-binding proteins), and histone-binding proteins. These three types of gene selectors work in cooperation to select the genes that are to be expressed (Fig. 2).


Chromatin Remodel Complex Curr Opin Cell Biol Histone Chaperone Nucleosome Assembly Nucleosome Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Adkins MW, Howar SR, Tyler JK (2004) Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol Cell 14:657–666PubMedGoogle Scholar
  2. Akey CW, Luger K (2003) Histone chaperones and nucleosome assembly. Curr Opin Struct Biol 13:6–14PubMedGoogle Scholar
  3. Battaglioli E, Andres ME, Rose DW, Chenoweth JG, Rosenfeld MG, Anderson ME, Mandel G (2002) REST repression of neuronal genes requires components of the hSWI.SNF complex. J Biol Chem 277:41038–41045PubMedGoogle Scholar
  4. Becker PB, Horz W (2002) ATP-dependent nucleosome remodeling. Annu Rev Biochem 71:247–273PubMedGoogle Scholar
  5. Belandia B, Orford RL, Hurst HC, Parker MG (2002) Targeting of SWI/SNF chromatin remodeling complexes to estrogen-responsive genes. EMBO J 21:4094–4103PubMedGoogle Scholar
  6. Bi X, Broach JR (1999) UASrpg can function as a heterochromatin boundary element in yeast. Genes Dev 13: 1089–1101PubMedGoogle Scholar
  7. Blackwood EM, Eisenman RN (1991) Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. Science 251:1211–1217PubMedGoogle Scholar
  8. Bonner WM, Stedman JD (1979) Histone 1 is proximal to histone 2A and to A24. Proc Natl Acad Sci 76:2190–2194PubMedGoogle Scholar
  9. Brehm A, Tufteland KR, Aasland R, Becker PB (2004) The many colours of chromodomains. Bioessays 26:133–40PubMedGoogle 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 418:498PubMedGoogle Scholar
  11. Brownell JE, Zhou J, Ranalli T, Kobayashi R, Edmondson DG, Roth SY, Allis CD (1996) Tetrahymena histone acetyltransferase A: a homolog to yeaset Gcn5p linking histone acetylation to gene activation. Cell 84:843–851PubMedGoogle Scholar
  12. Buratowski S (2000) Snapshots of RNA polymerase II transcription initiation. Curr Opin Cell Biol 12:320–325PubMedGoogle Scholar
  13. Buratowski S, Hahn S, Guarente L, Sharp PA (1989) Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56:549–561PubMedGoogle Scholar
  14. 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 298:1039–1043PubMedGoogle Scholar
  15. Chadwick BP, Willard HF (2003) Barring gene expression after XIST: maintaining facultative heterochromatin on the inactive X. Semin Cell Dev Biol 14:359–367PubMedGoogle Scholar
  16. Chambon P (2004) How I became one of the fathers of a superfamily. Nat Med 10:1027–1031PubMedGoogle Scholar
  17. Cheung WL, Briggs SD, Allis CD (2000a) Acetylation and chromosomal functions. Curr Opin Cell Biol 12:326–333PubMedGoogle Scholar
  18. Cheung P, Tanner KG, Cheung WL, Sassone-Corsi P, Denu JM, Allis CD (2000b) Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Mol Cell 5:905–915PubMedGoogle Scholar
  19. Chimura T, Kuzuhara T, Horikoshi M (2002) Identification and characterization of CIA/ASF 1 as an interactor of bromodomains associated with TFIID. Proc Natl Acad Sci USA 99:9334–9339PubMedGoogle Scholar
  20. Cockell M, Gasser SM (1999) Nuclear compartments and gene regulation. Curr Opin Genet Dev 9:199–205PubMedGoogle Scholar
  21. Cote J, Peterson CL, Workman JL (1998) Perturbation of nucleosome core structure by the SWI/SNF complex persists after its detachment, enhancing subsequent transcription factor binding. Proc Natl Acad Sci USA 95:4947–4952PubMedGoogle Scholar
  22. Craig JM (2005) Heterochromatin—many flavours, common themes. Bioessays 27:17–28PubMedGoogle Scholar
  23. Delaval K, Feil R (2004) Epigenetic regulation of mammalian genomic imprinting. Curr Opin Genet Dev 14:188–195PubMedGoogle Scholar
  24. Dhillon N, Kamakaka RT (2002) Breaking through to the other side: silencers and barriers. Curr Opin Genet Dev 12:188–192PubMedGoogle Scholar
  25. Dilworth SM, Black SJ, Laskey RA (1987) Two complexes that contain histones are required for nucleosome assembly in vitro: role of nucleoplasmin and N1 in Xenopus egg extracts. Cell 51:1009–1018PubMedGoogle Scholar
  26. Dimitri P, Corradini N, Rossi F, Verni F (2005) The paradox of functional heterochromatin. Bioessays 27:29–41PubMedGoogle Scholar
  27. Donze D, Kamakaka RT (2001) RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J 20:520–531PubMedGoogle Scholar
  28. Dutta S, Akey IV, Dingwall C, Hartman KL, Laue T, Nolte RT, Head JF, Akey CW (2001) The crystal structure of nucleoplasmin-core: implications for histone binding and nucleosome assembly. Mol Cell 8:841–853PubMedGoogle Scholar
  29. Evans T, Felsenfeld G, Reitman M (1990) Control of globin gene transcription. Annu Rev Cell Biol 6:95–124PubMedGoogle Scholar
  30. Feaver WJ, Gileadi O, Li Y, Kornberg RD (1991) CTD kinase associated with yeast RNA polymerase II initiation factor b. Cell 67:1223–1230PubMedGoogle Scholar
  31. Finley D, Chau V (1991) Ubiquitination. Annu Rev Cell Biol 7:25–69PubMedGoogle Scholar
  32. Fourel G, Magdinier F, Gilson E (2004) Insulator dynamics and the setting of chromatin domains. Bioessays 26:523–532PubMedGoogle Scholar
  33. Flaus A, Owen-Hughes T (2004) Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr Opin Genet Dev 14:165–173PubMedGoogle Scholar
  34. Gaillard PH, Martini EM, Kaufman PD, Stillman B, Moustacchi E, Almouzni G (1996) Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I. Cell 86:887–896PubMedGoogle Scholar
  35. Gehring WJ (1992) The homeobox in perspective. Trends Biochem Sci 17:277–280PubMedGoogle Scholar
  36. Geng F, Cao Y, Laurent BC (2001) Essential roles of Snf5p in Snf-Swi chromatin remodeling in vivo. Mol Cell Biol 21:4311–4320PubMedGoogle Scholar
  37. Gill G (2004) SUMO and ubiquitin in the nucleus: different functions, similar mechanisms? Genes Dev 18:2046–2059PubMedGoogle Scholar
  38. Goto H, Tomono Y, Ajiro K, Kosako H, Fujita M, Sakurai M, Okawa K, Iwamatsu A, Okigaki T, Takahashi T, Inagaki M (1999) Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation. J Biol Chem 274:25543–25549PubMedGoogle Scholar
  39. Green MR (2000) TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes. Trends Biochem Sci 25:59–63PubMedGoogle Scholar
  40. Grewal SI, Elgin SC (2002) Heterochromatin: new possibilities for the inheritance of structure. Curr Opin Genet Dev 12:178–187PubMedGoogle Scholar
  41. Grunstein M (1998) Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell 93:325–328PubMedGoogle Scholar
  42. Guarente L (1999) Diverse and dynamic functions of the Sir silencing complex. Nat Genet 23:281–285PubMedGoogle Scholar
  43. Hai TW, Horikoshi M, Roeder RG, Green MR (1988) Analysis of the role of the transcription factor ATF in the assembly of a functional preinitiation complex. Cell 54:1043–1051PubMedGoogle Scholar
  44. Harp JM, Hanson BL, Timm DE, Bunick GJ (2000) Asymmetries in the nucleosome core particle at 2.5A resolution. Acta Crystallogr D Biol Crystallogr. 56:1513–1534PubMedGoogle Scholar
  45. Hassan AH, Prochasson P, Neely KE, Galasinski SC, Chandy M, Carrozza MJ, Workman JL (2002) Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111:369–379PubMedGoogle Scholar
  46. Henikoff S (1990) Position-effect variegation after 60 years. Trends Genet 6:422–426PubMedGoogle Scholar
  47. 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 17:2648–2663PubMedGoogle Scholar
  48. Hecht A, Laroche T, Strahl-Bolsinger S, Gasser SM, Grunstein M (1995) Histone H3 and H4 N-terminal interact with SIR3 and SIR4 protein: a molecular model for the formation of heterochromatin in yeast. Cell 80:583–592PubMedGoogle Scholar
  49. Holstege FC, van der Vliet PC, Timmers HT (1996) Opening of an RNA polymerase II promoter occurs in two distinct steps and requires the basal transcription factors IIE and IIH. EMBO J 15:1666–1677PubMedGoogle Scholar
  50. Horikoshi M, Carey MF, Kakidani H, Roeder RG (1988a) Mechanism of action of a yeast activator: direct effect of GAL4 derivatives on mammalian TFIID-promoter interactions. Cell 54:665–669PubMedGoogle Scholar
  51. Horikoshi M, Hai T, Lin YS, Green MR, Roeder RG (1988b) Transcription factor ATF interacts with the TATA factor to facilitate establishment of a preinitiation complex. Cell 54:1033–1042PubMedGoogle Scholar
  52. Horikoshi M, Wang CK, Fujii H, Cromlish JA, Weil PA, Roeder RG (1989a) Purification of a yeast TATA box-binding protein that exhibits human transcription factor IID activity. Proc Natl Acad Sci USA 86:4843–4847PubMedGoogle Scholar
  53. Horikoshi M, Wang CK, Fujii H, Cromlish JA, Weil PA, Roeder RG (1989b) Cloning and structure of a yeast gene encoding a general transcription initiation factor TFIID that binds to the TATA box. Nature 341:299–303PubMedGoogle Scholar
  54. Horikoshi M, Bertuccioli C, Takada R, Wang J, Yamamoto T, Roeder RG (1992) Transcription factor TFIID induces DNA bending upon binding to the TATA element. Proc Natl Acad Sci USA 89:1060–1064.PubMedGoogle Scholar
  55. Huang H, Kahana A, Gottschling DE, Prakash L, Liebman SW (1997) The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae. Mol Cell Biol 17:6693–6699PubMedGoogle Scholar
  56. Imai S, Armstrong CM, Kaeberlein M, Guarente L (2000) Transcripational silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:795–800PubMedGoogle Scholar
  57. Ishimi Y, Hirosumi J, Sato W, Sugasawa K, Yokota S, Hanaoka F, Yamada M (1984) Purification and initial characterization of a protein which facilitates assembly of nucleosome-like structure from mammalian cells. Eur J Biochem 142:431–439PubMedGoogle Scholar
  58. Ito T, Bulger M, Kobayashi R, Kadonaga JT (1996) Drosophila NAP-1 is a core histone chaperone that functions in ATP-facilitated assembly of regularly spaced nucleosomal arrays. Mol Cell Biol 16:3112–3124PubMedGoogle Scholar
  59. Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356PubMedGoogle Scholar
  60. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080PubMedGoogle Scholar
  61. Kadam S, Emerson BM (2002) Mechanisms of chromatin assembly and transcription. Curr Opin Cell Biol 14:262–268PubMedGoogle Scholar
  62. Kadonaga JT (2002) The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med 34:259–264PubMedGoogle Scholar
  63. Kal AJ, Mahmoudi T, Zak NB, Verrijzer CP (2000) The Drosophila brahma complex is an essential coactivator for the trithorax group protein zesta. Genes Dev 14:1058–1071PubMedGoogle Scholar
  64. Kellogg DR, Murray AW (1995) NAP1 acts with Clbl to perform mitotic functions and suppress polar bud growth in budding yeast. J Cell Biol 130:675–685PubMedGoogle Scholar
  65. Khorasanizadeh S (2004) The nucleosome: from genomic organization to genomic regulation. Cell 116:259–272PubMedGoogle Scholar
  66. Kim JL, Nikolov DB, Burley SK (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:520–527PubMedGoogle Scholar
  67. Kimura A, Horikoshi M (2004) Partition of distinct chromosomal regions: negotiable border and fixed border. Genes Cell 9:499–508Google Scholar
  68. Kimura A, Umehara T, Horikoshi M (2002) Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nat Genet 32:370–377PubMedGoogle Scholar
  69. Kleinschmidt JA, Fortkamp E, Krohne G, Zentgraf H, Franke WW (1985) Coexistence of two different types of soluble histone complexes in nuclei of Xenopus laevis oocytes. J Biol Chem 260:1166–1176PubMedGoogle Scholar
  70. Kornberg RD (1974) Chromatin structure: a repeating unit of histones and DNA. Science 184:868–871PubMedGoogle Scholar
  71. Kornberg RD, Lorch Y (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294PubMedGoogle Scholar
  72. Kuzuhara T, Horikoshi M (2004) A nuclear FK506-binding protein is a histone chaperone regulating rDNA silencing. Nat Struct Mol Biol 11:275–283PubMedGoogle Scholar
  73. Labrador M, Corces VG (2002) Setting the boundaries of chromatin domains and nuclear organization. Cell 111:151–154PubMedGoogle Scholar
  74. Lachner M, Jenuwein T (2002) The many faces of histone lysine methylation. Curr Opin Cell Biol 14:286–298PubMedGoogle Scholar
  75. Laskey RA, Honda BM, Mills AD, Finch JT (1978) Nucleosomes are assembled by an acidic protein which binds histones and transfers them to DNA. Nature 275:416–420PubMedGoogle Scholar
  76. Latham KE (2005) X chromosome imprinting and inactivation in preimplantation mammalian embryos. Trends Genet 21:120–127PubMedGoogle Scholar
  77. Laurent BC, Treich I, Carlson M (1993) The yeast SNF2/SWI2 protein has DNA-stimulated ATPase activity required for transcriptional activation. Genes Dev 7:583–591PubMedGoogle Scholar
  78. Le S, Davis C, Konopka JB, Sternglanz R (1997) Two new S-phase-specific genes from Saccharomyces cerevisiae. Yeast 13:1029–1042PubMedGoogle Scholar
  79. Litt MD, Simpson M, Recillas-Targa F, Prioleau MN, Felsenfeld G (2001) Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci. EMBO J 20:2224–2235PubMedGoogle Scholar
  80. Lo WS, Trievel RC, Rojas JR, Duggan L, Hsu JY, Allis CD, Marmorstein R, Berger SL (2000) Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. Mol Cell 5:917–926PubMedGoogle Scholar
  81. Lu H, Zawel L, Fisher L, Egly JM, Reinberg D (1992) Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II. Nature 358:641–645PubMedGoogle Scholar
  82. Luger K (2003) Structure and dynamic behavior of nucleosomes. Curr Opin Genet Dev 13:127–135PubMedGoogle Scholar
  83. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8A resolution. Nature 389:251–260PubMedGoogle Scholar
  84. Ma J (2005) Crossing the line between activation and repression. Trends Genet 21:54–59PubMedGoogle Scholar
  85. Marmorstein R (2003) Structure of SET domain proteins: a new twist on histone methylation. Trends Biochem Sci. 28:59–62PubMedGoogle Scholar
  86. Martens JA, Winston F (2002) Evidence that Swi/Snf directly represses transcription in S. cerevisiae. Genes Dev 16:2231–2236PubMedGoogle Scholar
  87. Martens JA, Winston F (2003) Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr Opin Genet Dev 13:136–142PubMedGoogle Scholar
  88. Matsui T, Segall J, Weil PA, Roeder RG (1980) Multiple factors required for accurate initiation of transcription by RNA polymerase II. J Biol Chem 255:11992–11996PubMedGoogle Scholar
  89. Matsumoto K, Nagata K, Ui M, Hanaoka F (1993) Template activating factor I, a novel host factor required to stimulate the adenovirus core DNA replication. J Biol Chem 268:10582–10587PubMedGoogle Scholar
  90. Matsumoto K, Okuwaki M, Kawase H, Handa H, Hanaoka F, Nagata K (1995) Stimulation of DNA transcription by the replication factor from the adenovirus genome in a chromatin-like structure. J Biol Chem 270:9645–9650PubMedGoogle Scholar
  91. McKnight S, Tjian R (1986) Transcriptional selectivity of viral genes in mammalian cells. Cell 46:795–805PubMedGoogle Scholar
  92. Mello JA, Almouzni G (2001) The ins and outs of nucleosome assembly. Curr Opin Genet Dev 11:136–141PubMedGoogle Scholar
  93. Mello, JA, Sillje HH, Roche DM, Kirschner DB, Nigg EA, Almouzni G (2002) Human Asf1 and CAF-1 interact and synergize in a repair-coupled nucleosome assembly pathway. EMBO Rep 3:329–334PubMedGoogle Scholar
  94. Miyaji-Yamaguchi M, Kato K, Nakano R, Akashi T, Kikuchi A, Nagata K (2003) Involvement of nucleocytoplasmic shuttling of yeast Nap1 in mitotic progression. Mol Cell Biol 23:6672–6684PubMedGoogle Scholar
  95. Miyamoto S, Suzuki T, Muto S, Aizawa K, Kimura A, Mizuno Y, Nagino T, Imai Y, Adachi N, Horikoshi M, Nagai R (2003) Positive and negative regulation of the cardiovascular transcription factor KLF5 by p300 and the oncogenic regulator SET through interaction and acetylation on the DNA-binding domain. Mol Cell Biol 23:8528–8541PubMedGoogle Scholar
  96. Mousson F, Lautrette A, Thuret JY, Agez M, Courbeyrette R, Amigues B, Becker E, Neumann JM, Guerois R, Mann C, Ochsenbein F (2005) Structural basis for the interaction of Asf1 with histone H3 and its functional implications. Proc Natl Acad Sci USA 102:5975–5980PubMedGoogle Scholar
  97. Munakata T, Adachi N, Yokoyama N, Kuzuhara T, Horikoshi M (2000) A human homologue of yeast anti-silencing factor has histone chaperone activity. Genes Cells 5:221–233PubMedGoogle Scholar
  98. Murre C, McCaw PS, Vaessin H, Caudy M, Jan LY, Jan YN, Cabrera CV, Buskin JN, Hauschka SD, Lassar AB Weintraub H. Baltimore D (1989) Interactions between heterologous helix-loop-helix proteins generate complexes that bind specifically to a common DNA sequence. Cell 58:537–544PubMedGoogle Scholar
  99. Mutskov VJ, Farrell CM, Wade PA, Wolffe AP, Felsenfeld G (2002) The barrier function of an insulator couples high histone acetylation levels with specific protection of promoter DNA from methylation. Genes Dev 16:1540–1554PubMedGoogle Scholar
  100. 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 292:110–113PubMedGoogle Scholar
  101. Naresh A, Saini S, Singh J (2003) Identification of Uhpl, a ubiquitinated histone-like protein, as a target/mediator of Rhp6 in mating-type silencing in fission yeast. J Biol Chem 278:9185–9194PubMedGoogle Scholar
  102. Narlikar GJ, Fan HY, Kingston RE (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475–487PubMedGoogle Scholar
  103. Nielsen AL, Sanchez C, Ichinose H, Cervino M, Lerouge T, Chambon P, Losson R (2002) Selective interaction between the chromatin-remodeling factor BRG1 and the heterochromatin-associated protein HP1 alpha. EMBO J 21:5797–5806PubMedGoogle Scholar
  104. Okuwaki M, Nagata K (1998) Template activating factor-I remodels the chromatin structure and stimulates transcription from the chromatin template. J Biol Chem 273:34511–34518PubMedGoogle Scholar
  105. Peterson CL, Tamkun JW (1995) The SWI-SNF complex: a chromatin remodeling machine?. Trends Biochem Sci. 22:143–146Google Scholar
  106. Peterson CL (2002) Chromatin remodeling: nucleosomes bulging at the seams. Curr Biol 2:R245–247Google Scholar
  107. Peterson CL, Laniel MA (2004) Histones and histone modifications. Curr Biol 14:R546–551PubMedGoogle Scholar
  108. Ptashne M (1988) How eukaryotic transcriptional activators work. Nature 335:683–689PubMedGoogle Scholar
  109. Ptashne M (2004) A genetic switch: phage lambda revisited, 3rd edn. Blackwell Science, Maiden, MA and Cell Press, Cambridge, MAGoogle Scholar
  110. Ptashne M, Gann A (2001) Genes and signals. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NYGoogle Scholar
  111. Rangwala SH, Richards EJ (2004) The value-added genome: building and maintaining genomic cytosine methylation landscapes. Curr Opin Genet Dev 14:686–691PubMedGoogle Scholar
  112. Rice JC, Allis CD (2001) Histone methylation versus histone acetylation: new insights into epigenetic regulation. Curr Opin Cell Biol 13:263–273PubMedGoogle Scholar
  113. Rippe K, von Hippel PH, Langowski J (1995) Action at a distance: DNA-looping and initiation of transcription. Trends Biochem Sci 20:500–506PubMedGoogle Scholar
  114. Roeder RG (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci. 21:327–335PubMedGoogle Scholar
  115. Roeder RG (2003) Lasker Basic Medical Research Award. The eukaryotic transcriptional machinery: complexities and mechanisms unforeseen. Nat Med 9:1239–1244PubMedGoogle Scholar
  116. Roeder RG, Rutter WJ (1969) Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms. Nature 224:234–237PubMedGoogle Scholar
  117. Roth SY, Denu JM, Allis CD (2001) Histone acetyltransferases. Annu Rev Biochem 70:81–120PubMedGoogle Scholar
  118. Saha A, Wittmeyer J, Cairns BR (2002) Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev 16:2120–2134PubMedGoogle Scholar
  119. 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 14:67–75PubMedGoogle Scholar
  120. Seo SB, McNamara P, Heo S, Turner A, Lane WS, Chakravarti D (2001) Regulation of histone acetylation and transcription by INHAT, a human cellular complex containing the set oncoprotein. Cell 104:119–130PubMedGoogle Scholar
  121. Serizawa H, Conaway RC, Conaway JW (1992) A carboxyl-terminal-domain kinase associated with RNA polymerase II transcription factor delta from rat liver. Proc Natl Acad Sci USA 89:7476–7480PubMedGoogle Scholar
  122. Shibahara K, Stillman B (1999) Replication-dependent marking of DNA by PCNA facilitates CAF-I coupled inheritance of chromatin. Cell 96:575–585PubMedGoogle Scholar
  123. Smith S, Stillman B (1989) Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro. Cell 58:15–25PubMedGoogle Scholar
  124. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45PubMedGoogle Scholar
  125. Sun ZW, Allis CD (2002) Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418:104–108PubMedGoogle Scholar
  126. Suzuki T, Muto S, Miyamoto S, Aizawa K, Horikoshi M, Nagai (2003) Functional interaction of the DNA-binding transcription factor Spl through its DNA-binding domain with the histone chaperone TAF-I. J Biol Chem 278:28758–28764PubMedGoogle Scholar
  127. Taunton J, Hassig CA, Schreiber SL (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272:408–411PubMedGoogle Scholar
  128. Tsukiyama T, Wu C (1997) Chromatin remodeling and transcription. Curr Op in Genet Dev 7:182–191Google Scholar
  129. Tsukiyama T, Becker PB, Wu C (1994) ATP-dependent nucleosome disruption a heat-shock promoter mediated by binding of GAGA transcription factor. Nature 367:525–532PubMedGoogle Scholar
  130. Turner BM (2001) Chromatin and gene regulation: mechanism in epigenetics. Blackwell ScienceGoogle Scholar
  131. Tyler JK (2002) Chromatin assembly. Cooperation between histone chaperones and ATP-dependent nucleosome remodeling machines. Eur J Biochem 269:2268–2274PubMedGoogle Scholar
  132. Tyler JK, Adams CR, Chen SR, Kobayashi R, Kamakaka RT, Kadonaga JT (1999) The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402:555–560PubMedGoogle Scholar
  133. Tyler JK, Collins KA, Prasad-Sinha J, Amiott E, Bulger M, Harte PJ, Kobayashi R, Kadonaga JT (2001) Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. Mol Cell Biol 21:6574–6584PubMedGoogle Scholar
  134. Umehara T, Horikoshi M (2003) Transcription initiation factor IID-interactive histone chaperone CIA-II implicated in mammalian spermatogenesis. J Biol Chem 278:35660–35667PubMedGoogle Scholar
  135. van Leeuwen F, Gottschling DE (2002) Genome-wide histone modifications: gaining specificity by preventing promiscuity. Curr Opin Cell Biol 14:756–762PubMedGoogle Scholar
  136. Verreault A, Kaufman PD, Kobayashi R, Stillman B (1996) Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell 87:95–104PubMedGoogle Scholar
  137. Wagner S, Green MR (1994) DNA-binding domains: targets for viral and cellular regulators. Curr Opin Cell Biol 6:410–414PubMedGoogle Scholar
  138. Wang H, Huang ZQ, Xia L, Feng Q, Erdjumnet-Bromage H, Strahl BD, Briggs SD, Allis CD, Wong J, Tempst P, Zhang Y (2001) Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science 293:853–857PubMedGoogle Scholar
  139. Wei Y, Mizzen CA, Cook RG, Gorovsky MA, Allis CD (1998) Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena. Proc Natl Acad Sci USA 95:7480–7484PubMedGoogle Scholar
  140. Weintraub H, Davis R, Tapscott S, Thayer M, Krause M, Benezra R, Blackwell TK, Turner D, Rupp R, Hollenberg S, Zhuang Y, Lassar A (1991) The MyoD gene family: nodal point during specification of the muscle cell lineage. Science 251:761–766PubMedGoogle Scholar
  141. West AG, Gaszner M, Felsenfeld G (2002) Insulators: many functions, many mechanisms. Genes Dev 16:271–288PubMedGoogle Scholar
  142. White CL, Suto RK, Luger K (2001) Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J 20:5207–5218PubMedGoogle Scholar
  143. Wolffe AP (1997) Histone HI. Int J Biochem Cell Biol 29:1463–1466PubMedGoogle Scholar
  144. Wolffe AP (1998) Chromatin: structure and function, 3rd edn. Academic Press, San DiegoGoogle Scholar
  145. Workman JL, Kingston RE (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem 67:545–579PubMedGoogle Scholar
  146. Workman JL, Roeder RG (1987) Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell 51:613–622PubMedGoogle Scholar
  147. Yang XJ (2004) Lysine acetylation and the bromodomain: a new partnership for signaling. Bioessays 26:1076–1087PubMedGoogle Scholar
  148. Zhang Y (2003) Transcriptional regulation by histone ubiquitination and deubiq-uitination. Genes Dev 17:2733–2740PubMedGoogle Scholar
  149. Zhang ZK, Davies KP, Allen J, Zhu L, Pestell RG, Zagzag D, Kalpana GV (2002) Cell cycle arrest and repression of cyclin Dl transcription by INIl/hSNF5. Mol Cell Biol 22:5975–5988PubMedGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Shinsuke Muto
    • 1
    • 2
  • Masami Horikoshi 
    • 1
    • 2
  1. 1.Laboratory of Developmental Biology, Institute of Molecular and Cellular BiosciencesUniversity of TokyoTokyoJapan
  2. 2.Horikoshi Gene Selector Project, Exploratory Research for Advanced Technology (ERATO)Japan Science and Technology Corporation (JST)Tsukuba, IbarakiJapan

Personalised recommendations