TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation

BMC Biochemistry

Volumn 10, Issue 1, 2009, Pages

  Pitulescu, Mara E ^a   Teichmann, Martin ^b   Luo, Lingfei ^a   Kessel, Michael ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b INSTITUT EUROPÉEN DE CHIMIE ET BIOLOGIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; GEMININ; TATA BINDING PROTEIN; TATA BINDING PROTEIN LIKE FACTOR INTERACTING PROTEIN 2; TATA BINDING PROTEIN RELATED FACTOR; UNCLASSIFIED DRUG; CELL CYCLE PROTEIN; GMNN PROTEIN, MOUSE; NONHISTONE PROTEIN; NUCLEAR PROTEIN; TIPT PROTEIN, MOUSE; TRANSCRIPTION FACTOR;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BINDING SITE; CHROMATIN; CONTROLLED STUDY; CYTOPLASM; EMBRYO; GENE ACTIVATION; HUMAN; HUMAN CELL; MALE; MOUSE; NONHUMAN; NUCLEOLUS; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; AMINO ACID SEQUENCE; ANIMAL; CELL LINE; CELL NUCLEUS; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HELA CELL; METABOLISM; MOLECULAR GENETICS; PROTEIN TRANSPORT;

AMINO ACID SEQUENCE; ANIMALS; CELL CYCLE PROTEINS; CELL LINE; CELL NUCLEUS; CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; PROTEIN TRANSPORT; TATA-BOX BINDING PROTEIN; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION;

EID: 68149107677     PISSN: None     EISSN: 14712091     Source Type: Journal    
DOI: 10.1186/1471-2091-10-16     Document Type: Article

References (74)

1. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. A Sandelin P Carninci B Lenhard J Ponjavic Y Hayashizaki DA Hume, Nat Rev Genet 2007 8 424 436 (Pubitemid 46789243)
2. The general transcription machinery and general cofactors. MC Thomas CM Chiang, Crit Rev Biochem Mol Biol 2006 41 105 178 10.1080/10409230600648736 16858867
3. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. SJ Cooper ND Trinklein ED Anton L Nguyen RM Myers, Genome Res 2006 16 1 10 16344566 10.1101/gr.4222606
4. Synergy of human Pol II core promoter elements revealed by statistical sequence analysis. NI Gershenzon IP Ioshikhes, Bioinformatics 2005 21 1295 1300 (Pubitemid 40542675)
5. Computational analysis of core promoters in the Drosophila genome. U Ohler GC Liao H Niemann GM Rubin, Genome Biol 2002 3 RESEARCH0087 12537576 10.1186/gb-2002-3-12-research0087
6. Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. U Ohler, Nucleic Acids Res 2006 34 5943 5950 17068082 10.1093/nar/gkl608
7. Genome wide analysis of Arabidopsis core promoters. C Molina E Grotewold, BMC Genomics 2005 6 25 15733318 10.1186/1471-2164-6-25
8. Organization and expression of eucaryotic split genes coding for proteins. R Breathnach P Chambon, Annu Rev Biochem 1981 50 349 383
9. Genome-wide analysis of mammalian promoter architecture and evolution. P Carninci A Sandelin B Lenhard S Katayama K Shimokawa J Ponjavic CA Semple MS Taylor PG Engstrom MC Frith, Nat Genet 2006 38 626 635 (Pubitemid 43927303)
10. Promoter features related to tissue specificity as measured by Shannon entropy. J Schug WP Schuller C Kappen JM Salbaum M Bucan CJ Stoeckert Jr, Genome Biol 2005 6 R33
11. A Drosophila RNA polymerase II transcription factor contains a promoter-region-specific DNA-binding activity. CS Parker J Topol, Cell 1984 36 357 369 (Pubitemid 14126227)
12. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. M Sawadogo RG Roeder, Cell 1985 43 165 175 (Pubitemid 16199703)
13. The RNA polymerase II core promoter. ST Smale JT Kadonaga, Annu Rev Biochem 2003 72 449 479 (Pubitemid 36930452)
14. Transcriptional Regulatory Elements in the Human Genome. GA Maston SK Evans MR Green, Annu Rev Genomics Hum Genet 2006 7 29 59 (Pubitemid 44627921)
15. Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles. J Kim VR Iyer, Mol Cell Biol 2004 24 8104 8112 (Pubitemid 39167460)
16. Identification and distinct regulation of yeast TATA box-containing genes. AD Basehoar SJ Zanton BF Pugh, Cell 2004 116 699 709 (Pubitemid 38326728)
17. New problems in RNA polymerase II transcription initiation: matching the diversity of core promoters with a variety of promoter recognition factors. F Muller MA Demeny L Tora, J Biol Chem 2007 282 14685 14689 (Pubitemid 47093322)
18. New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. T Lagrange AN Kapanidis H Tang D Reinberg RH Ebright, Genes Dev 1998 12 34 44 (Pubitemid 28083656)
19. Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength. SA Qureshi SP Jackson, Mol Cell 1998 1 389 400 (Pubitemid 128378887)
20. Structural basis of preinitiation complex assembly on human pol II promoters. FT Tsai PB Sigler, Embo J 2000 19 25 36 10619841 (Pubitemid 30009222)
21. A core promoter element downstream of the TATA box that is recognized by TFIIB. W Deng SG Roberts, Genes Dev 2005 19 2418 2423 (Pubitemid 41483689)
22. The TBP-like factor: an alternative transcription factor in metazoa? JC Dantonel JM Wurtz O Poch D Moras L Tora, Trends Biochem Sci 1999 24 335 339 (Pubitemid 29421806)
23. TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. A Hochheimer S Zhou S Zheng MC Holmes R Tjian, Nature 2002 420 439 445 (Pubitemid 35415657)
24. Vertebrate TBP-like protein (TLP/TRF2/TLF) stimulates TATA-less terminal deoxynucleotidyl transferase promoters in a transient reporter assay, and TFIIA-binding capacity of TLP is required for this function. T Ohbayashi M Shimada T Nakadai T Wada H Handa T Tamura, Nucleic Acids Res 2003 31 2127 2133 (Pubitemid 37442080)
25. TATA-binding protein-like protein (TLP/TRF2/TLF) negatively regulates cell cycle progression and is required for the stress-mediated G(2) checkpoint. M Shimada T Nakadai TA Tamura, Mol Cell Biol 2003 23 4107 4120 (Pubitemid 36666416)
26. TATA-binding protein (TBP)-like factor (TLF) is a functional regulator of transcription: reciprocal regulation of the neurofibromatosis type 1 and c-fos genes by TLF/TRF2 and TBP. JA Chong MM Moran M Teichmann JS Kaczmarek R Roeder DE Clapham, Mol Cell Biol 2005 25 2632 2643 15767669 (Pubitemid 40381627)
27. TATA-binding protein-related factor 2 is localized in the cytoplasm of mammalian cells and much of it migrates to the nucleus in response to genotoxic agents. KA Park Y Tanaka Y Suenaga TA Tamura, Mol Cells 2006 22 203 209 (Pubitemid 46357824)
28. Transcriptional repression of the mouse wee1 gene by TBP-related factor 2. Y Tanaka YA Nanba KA Park T Mabuchi Y Suenaga S Shiraishi M Shimada T Nakadai TA Tamura, Biochem Biophys Res Commun 2007 352 21 28 (Pubitemid 44821088)
29. Variations in intracellular levels of TATA binding protein can affect specific genes by different mechanisms. SD Bush P Richard JL Manley, Mol Cell Biol 2008 28 83 92
30. Transcription of histone gene cluster by differential core-promoter factors. Y Isogai S Keles M Prestel A Hochheimer R Tjian, Genes Dev 2007 15 2936 49
31. Geminin, an inhibitor of DNA replication, is degraded during mitosis. TJ McGarry MW Kirschner, Cell 1998 93 1043 1053 (Pubitemid 28280797)
32. Inhibition of eukaryotic DNA replication by geminin binding to Cdt1. JA Wohlschlegel BT Dwyer SK Dhar C Cvetic JC Walter A Dutta, Science 2000 290 2309 2312 (Pubitemid 32041574)
33. Repression of origin assembly in metaphase depends on inhibition of RLF-B/Cdt1 by geminin. S Tada A Li D Maiorano M Mechali JJ Blow, Nat Cell Biol 2001 3 107 113 (Pubitemid 32118362)
34. The cell-cycle regulator geminin inhibits Hox function through direct and polycomb-mediated interactions. L Luo X Yang Y Takihara H Knoetgen M Kessel, Nature 2004 427 749 753 (Pubitemid 38294595)
35. Geminin coordinates cell cycle and developmental control. L Luo M Kessel, Cell Cycle 2004 3 711 714 (Pubitemid 40187895)
36. Direct interaction of geminin and Six3 in eye development. F Del Bene K Tessmar-Raible J Wittbrodt, Nature 2004 427 745 749 (Pubitemid 38294594)
37. Geminin regulates neuronal differentiation by antagonizing Brg1 activity. S Seo A Herr JW Lim GA Richardson H Richardson KL Kroll, Genes Dev 2005 19 1723 1734 (Pubitemid 41058368)
38. A repressor complex, AP4 transcription factor and geminin, negatively regulates expression of target genes in nonneuronal cells. MY Kim BC Jeong JH Lee HJ Kee H Kook NS Kim YH Kim JK Kim KY Ahn KK Kim, Proc Natl Acad Sci USA 2006 103 13074 13079 (Pubitemid 44338918)
39. TIPT, a male germ cell-specific partner of TRF2, is chromatin-associated and interacts with HP1. S Brancorsini I Davidson P Sassone-Corsi, Cell Cycle 2008 7 1415 1422 (Pubitemid 351872580)
40. Cell-specific nucleolar localization of TBP-related factor 2. P Kieffer-Kwon I Martianov I Davidson, Mol Biol Cell 2004 15 4356 4368 (Pubitemid 39299087)
41. Immunofluorescence studies on proteins B23 and C23 in nucleoli of human lymphocytes. K Smetana R Ochs MA Lischwe F Gyorkey E Freireich V Chudomel H Busch, Exp Cell Res 1984 152 195 203 (Pubitemid 14143621)
42. Functional interaction of a novel 15.5 kD [U4/U6.U5] tri-snRNP protein with the 5' stem-loop of U4 snRNA. S Nottrott K Hartmuth P Fabrizio H Urlaub I Vidovic R Ficner R Luhrmann, Embo J 1999 18 6119 6133 (Pubitemid 29515687)
43. A human TATA binding protein-related protein with altered DNA binding specificity inhibits transcription from multiple promoters and activators. PA Moore J Ozer M Salunek G Jan D Zerby S Campbell PM Lieberman, Mol Cell Biol 1999 19 7610 7620 (Pubitemid 29493424)
44. Human TATA-binding protein-related factor-2 (hTRF2) stably associates with hTFIIA in HeLa cells. M Teichmann Z Wang E Martinez A Tjernberg D Zhang F Vollmer BT Chait RG Roeder, Proc Natl Acad Sci USA 1999 96 13720 13725
45. Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation. DE Nowak B Tian AR Brasier, Biotechniques 2005 39 715 725
46. In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation. PY Zeng CR Vakoc ZC Chen GA Blobel SL Berger, Biotechniques 2006 41 694 696, 698
47. PcG complexes and chromatin silencing. V Pirrotta, Curr Opin Genet Dev 1997 7 249 258 (Pubitemid 27206764)
48. Stabilization of chromatin structure by PRC1, a Polycomb complex. Z Shao F Raible R Mollaaghababa JR Guyon CT Wu W Bender RE Kingston, Cell 1999 98 37 46 (Pubitemid 29331194)
49. A Drosophila Polycomb group complex includes Zeste and dTAFII proteins. AJ Saurin Z Shao H Erdjument-Bromage P Tempst RE Kingston, Nature 2001 412 655 660
50. Mechanisms of transcriptional memory. NJ Francis RE Kingston, Nat Rev Mol Cell Biol 2001 2 409 421 (Pubitemid 33680580)
51. The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. SS Levine A Weiss H Erdjument-Bromage Z Shao P Tempst RE Kingston, Mol Cell Biol 2002 22 6070 6078 (Pubitemid 34857827)
52. Polycomb complexes repress developmental regulators in murine embryonic stem cells. LA Boyer K Plath J Zeitlinger T Brambrink LA Medeiros TI Lee SS Levine M Wernig A Tajonar MK Ray, Nature 2006 441 349 353 (Pubitemid 44050199)
53. General transcription factors bind promoters repressed by Polycomb group proteins. A Breiling BM Turner ME Bianchi V Orlando, Nature 2001 412 651 655
54. Polycomb silencing blocks transcription initiation. GI Dellino YB Schwartz G Farkas D McCabe SC Elgin V Pirrotta, Mol Cell 2004 13 887 89315053881 (Pubitemid 38438483)
55. Tissue-specific TAFs counteract Polycomb to turn on terminal differentiation. X Chen M Hiller Y Sancak MT Fuller, Science 2005 310 869 872 (Pubitemid 41567348)
56. Nucleolar proteome dynamics. JS Andersen YW Lam AK Leung SE Ong CE Lyon AI Lamond M Mann, Nature 2005 433 77 83 (Pubitemid 40101146)
57. Nucleolar release of Hand1 acts as a molecular switch to determine cell fate. DM Martindill CA Risebro N Smart M Franco-Viseras Mdel CO Rosario CJ Swallow JW Dennis PR Riley, Nat Cell Biol 2007 9 1131 1141 (Pubitemid 47500489)
58. TATA-flanking sequences influence the rate and stability of TATA-binding protein and TFIIB binding. BS Wolner JD Gralla, J Biol Chem 2001 276 6260 6266
59. Roles for Non-TATA Core Promoter Sequences in Transcription and Factor Binding. BS Wolner JD Gralla, Mol Cell Biol 2000 20 3608 3615 (Pubitemid 30243906)
60. Core promoter elements and TAFs contribute to the diversity of transcriptional activation in vertebrates. Z Chen JL Manley, Mol Cell Biol 2003 23 7350 7362 (Pubitemid 37211014)
61. Gene structure and expression. D Viskochil, Neurofibromatosis type 1: From genotype to phenotype Oxford: BIOS Scientific, Upadhyaya M, Cooper DN, 1998 39 63
62. Analysis of NF1 transcriptional regulatory elements. TK Lee JM Friedman, Am J Med Genet A 2005 137 130 135 (Pubitemid 41262678)
63. Identification of a mouse TBP-like protein (TLP) distantly related to the drosophila TBP-related factor. T Ohbayashi Y Makino TA Tamura, Nucleic Acids Res 1999 27 750 755 (Pubitemid 29209361)
64. Isolation of cDNA, chromosome mapping, and expression of the human TBP-like protein. T Ohbayashi T Kishimoto Y Makino M Shimada T Nakadai T Aoki T Kawata S Niwa T Tamura, Biochem Biophys Res Commun 1999 255 137 142 (Pubitemid 29292078)
65. Human SWI-SNF component BRG1 represses transcription of the c-fos gene. DJ Murphy S Hardy DA Engel, Mol Cell Biol 1999 19 2724 2733 (Pubitemid 29144516)
66. RB and hbrm cooperate to repress the activation functions of E2F1. D Trouche C Le Chalony C Muchardt M Yaniv T Kouzarides, Proc Natl Acad Sci USA 1997 94 11268 11273 (Pubitemid 27450987)
67. Identification, molecular cloning, and characterization of the sixth subunit of human transcription factor TFIIIC. H Dumay-Odelot C Marck S Durrieu-Gaillard O Lefebvre S Jourdain M Prochazkova A Pflieger M Teichmann, J Biol Chem 2007 282 17179 17189 (Pubitemid 47093196)
68. Identification of human TFIID components and direct interaction between a 250-kDa polypeptide and the TATA box-binding protein (TFIID tau). R Takada Y Nakatani A Hoffmann T Kokubo S Hasegawa RG Roeder M Horikoshi, Proc Natl Acad Sci USA 1992 89 11809 11813 (Pubitemid 23004733)
69. Sequence of general transcription factor TFIIB and relationships to other initiation factors. S Malik K Hisatake H Sumimoto M Horikoshi RG Roeder, Proc Natl Acad Sci USA 1991 88 9553 9557 1946368 10.1073/pnas.88.21.9553 (Pubitemid 21915669)
70. Purification of his-tagged proteins in non-denaturing conditions suggests a convenient method for protein interaction studies. A Hoffmann RG Roeder, Nucleic Acids Res 1991 19 6337 6338 (Pubitemid 21913059)
71. Generation and functional analyses for base-substitution mutants of the adenovirus 2 major late promoter. YT Yu JL Manley, Nucleic Acids Res 1984 12 9309 9321
72. DNA sequences in the promoter region of the NF1 gene are highly conserved between human and mouse. A Hajra A Martin-Gallardo SA Tarle M Freedman S Wilson-Gunn A Bernards FS Collins, Genomics 1994 21 649 652 (Pubitemid 24189900)
73. Factors involved in specific transcription by mammalian RNA polymerase II: role of transcription factors IIA, IID, and IIB during formation of a transcription-competent complex. E Maldonado I Ha P Cortes L Weis D Reinberg, Mol Cell Biol 1990 10 6335 6347 (Pubitemid 120004576)
74. TATA-Binding protein-interacting protein 120, TIP120, stimulates three classes of eukaryotic transcription via a unique mechanism. Y Makino S Yogosawa K Kayukawa F Coin JM Egly Z Wang RG Roeder K Yamamoto M Muramatsu T Tamura, Mol Cell Biol 1999 19 7951 7960 (Pubitemid 30413990)