Transcription of histone gene cluster by differential core-promoter factors

Genes and Development

Volumn 21, Issue 22, 2007, Pages 2936-2949

  Isogai, Yoh ^a   Keles, Sündüz ^b   Prestel, Matthias ^c   Hochheimer, Andreas ^c   Tjian, Robert ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITY OF MUNICH   (Germany)

Author keywords

Chip on chip; Chromatin organization; Core promoter recognition; Histone gene cluster; TATA box binding protein (TBP); TBP related factor 2 (TRF2)

Indexed keywords

HISTONE; HISTONE H1; RNA; TATA BINDING PROTEIN; TELOMERIC REPEAT BINDING FACTOR 2;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BIOCHEMISTRY; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; EMBRYO; FEMALE; FLUORESCENCE ANALYSIS; GENE; GENE CLUSTER; GENETIC TRANSCRIPTION; GENETICS; GENOME; MALE; METAZOON; MICROCHIP ANALYSIS; NONHUMAN; POLYTENE CHROMOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN SYNTHESIS; REGULATORY MECHANISM; RNA INTERFERENCE; STRUCTURAL CHROMOSOME ABERRATION;

ANIMALS; BASE SEQUENCE; CELLS, CULTURED; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOMES; CLUSTER ANALYSIS; DROSOPHILA; GENES, INSECT; GENES, REPORTER; HISTONES; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION, FLUORESCENCE; LUCIFERASES, FIREFLY; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PROMOTER REGIONS (GENETICS); RNA INTERFERENCE; SEQUENCE HOMOLOGY, NUCLEIC ACID; TATA BOX BINDING PROTEIN-LIKE PROTEINS; TATA-BOX BINDING PROTEIN; TRANSCRIPTION, GENETIC;

METAZOA;

EID: 36249011467     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.1608807     Document Type: Article

References (57)

1. Andrew, D.J., Henderson, K.D., and Seshaiah, P. 2000. Salivary gland development in Drosophila melanogaster. Mech. Dev. 92: 5-17.
2. Bailey, T.L. and Elkan, C. 1995. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Mach. Learn. 21: 51-80.
3. Bembom, O., Keles, S., and van der Laan, M.J. 2007. Supervised detection of conserved motifs in DNA sequences with cosmo. In Statistical applications in genetics and molecular biology: vol. 6, issue 1, article 8. http://www.bepress.com/sagmd/vol6/iss1/art8.
4. Berk, A.J. 2000. TBP-like factors come into focus. Cell 103: 5-8.
5. Crowley, T.E., Hoey, T., Liu, J.K., Jan, Y.N., Jan, L.Y., and Tjian, R. 1993. A new factor related to TATA-binding protein has highly restricted expression patterns in Drosophila. Nature 361: 557-561.
6. Dantonel, J.C., Wurtz, J.M., Poch, O., Moras, D., and Tora, L. 1999. The TBP-like factor: An alternative transcription factor in metazoa? Trends Biochem. Sci. 24: 335-339.
7. Dantonel, J.C., Quintin, S., Lakatos, L., Labouesse, M., and Tora, L. 2000. TBP-like factor is required for embryonic RNA polymerase II transcription in C. elegans. Mol. Cell 6: 715-722.
8. Darzynkiewicz, Z. and Juan, G. 1997. DNA content measurement for DNA ploidy and cell cycle analysis. In Current protocols in cytometry (eds. J.P. Robinson et al.), pp. 7.5.1-7.5.24. Wiley, New York.
9. Fan, Y., Nikitina, T., Zhao, J., Fleury, T.J., Bhattacharyya, R., Bouhassira, E.E., Stein, A., Woodcock, C.L., and Skoultchi, A.I. 2005. Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell 123: 1199-1212.
10. Gershenzon, N.I. and Ioshikhes, I.P. 2005. Synergy of human Pol II core promoter elements revealed by statistical sequence analysis. Bioinformatics 21: 1295-1300.
11. Hansen, S.K., Takada, S., Jacobson, R.H., Lis, J.T., and Tjian, R. 1997. Transcription properties of a cell type-specific TATA-binding protein, TRF. Cell 91: 71-83.
12. Henikoff, S. 1984. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene 28: 351-359.
13. Herold, A., Teixeira, L., and Izaurralde, E. 2003. Genome-wide analysis of nuclear mRNA export pathways in Drosophila. EMBO J. 22: 2472-2483.
14. Hertz, G.Z. and Stormo, G.D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563-577.
15. Hirose, F., Yamaguchi, M., Handa, H., Inomata, Y., and Matsukage, A. 1993. Novel 8-base pair sequence (Drosophila DNA replication-related element) and specific binding factor involved in the expression of Drosophila genes for DNA polymerase α and proliferating cell nuclear antigen. J. Biol. Chem. 268: 2092-2099.
16. Hirose, F., Yamaguchi, M., Kuroda, K., Omori, A., Hachiya, T., Ikeda, M., Nishimoto, Y., and Matsukage, A. 1996. Isolation and characterization of cDNA for DREF, a promoter-activating factor for Drosophila DNA replication-related genes. J. Biol. Chem. 271: 3930-3937.
17. Hochheimer, A. and Tjian, R. 2003. Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. Genes & Dev. 17: 1309-1320.
18. Hochheimer, A., Zhou, S., Zheng, S., Holmes, M.C., and Tjian, R. 2002. TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 420: 439-445.
19. Holmes, M.C. and Tjian, R. 2000. Promoter-selective properties of the TBP-related factor TRF1. Science 288: 867-870.
20. Holmgren, P., Johansson, T., Lambertsson, A., and Rasmuson, B. 1985. Content of histone H1 and histone phosphorylation in relation to the higher order structures of chromatin in Drosophila. Chromosoma 93: 123-131.
21. Hyun, J., Jasper, H., and Bohmann, D. 2005. DREF is required for efficient growth and cell cycle progression in Drosophila imaginal discs. Mol. Cell. Biol. 25: 5590-5598.
22. Isogai, Y., Takada, S., Tjian, R., and Keles, S. 2007. Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription. EMBO J. 26: 79-89.
23. Jin, V.X., Singer, G.A., Agosto-Perez, F.J., Liyanarachchi, S., and Davuluri, R.V. 2006. Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics 7: 114. doi: 10.1186/1471-2105-7-114.
24. Kaltenbach, L., Horner, M.A., Rothman, J.H., and Mango, S.E. 2000. The TBP-like factor CeTLF is required to activate RNA polymerase II transcription during C. elegans embryogenesis. Mol. Cell 6: 705-713.
25. Keles, S. 2007. Mixture modeling for genome-wide localization of transcription factors. Biometrics 63: 10-21.
26. Kopytova, D.V., Krasnov, A.N., Kopantceva, M.R., Nabirochkina, E.N., Nikolenko, J.V., Maksimenko, O., Kurshakova, M.M., Lebedeva, L.A., Yerokhin, M.M., Simonova, O.B., et al. 2006. Two isoforms of Drosophila TRF2 are involved in embryonic development, premeiotic chromatin condensation, and proper differentiation of germ cells of both sexes. Mol. Cell. Biol. 26: 7492-7505.
27. Lambertsson, A. 1998. The minute genes in Drosophila and their molecular functions. Adv. Genet. 38: 69-134.
28. Larsson, J., Svensson, M.J., Stenberg, P., and Makitalo, M. 2004. Painting of fourth in genus Drosophila suggests autosome-specific gene regulation. Proc. Natl. Acad. Sci. 101: 9728-9733.
29. Lavrov, S., Dejardin, J., and Cavalli, G. 2004. Combined immunostaining and FISH analysis of polytene chromosomes. Methods Mol. Biol. 247: 289-303.
30. Lee, Y.S. and Carthew, R.W. 2003. Making a better RNAi vector for Drosophila: Use of intron spacers. Methods 30: 322-329.
31. Lifton, R.P., Goldberg, M.L., Karp, R.W., and Hogness, D.S. 1978. The organization of the histone genes in Drosophila melanogaster: Functional and evolutionary implications. Cold Spring Harb. Symp. Quant. Biol. 42: 1047-1051.
32. Liu, J.L., Murphy, C., Buszczak, M., Clatterbuck, S., Goodman, R., and Gall, J.G. 2006. The Drosophila melanogaster Cajal body. J. Cell Biol. 172: 875-884.
33. MacAlpine, D.M., Rodriguez, H.K., and Bell, S.P. 2004. Coordination of replication and transcription along a Drosophila chromosome. Genes & Dev. 18: 3094-3105.
34. Maldonado, E. 1999. Transcriptional functions of a new mammalian TATA-binding protein-related factor. J. Biol. Chem. 274: 12963-12966.
35. Maresca, T.J., Freedman, B.S., and Heald, R. 2005. Histone H1 is essential for mitotic chromosome architecture and segregation in Xenopus laevis egg extracts. J. Cell Biol. 169: 859-869.
36. Marr II, M.T., Isogai, Y., Wright, K.J., and Tjian, R. 2006. Coactivator cross-talk specifies transcriptional output. Genes & Dev. 20: 1458-1469.
37. Martianov, I., Fimia, G.M., Dierich, A., Parvinen, M., Sassone-Corsi, P., and Davidson, I. 2001. Late arrest of spermiogenesis and germ cell apoptosis in mice lacking the TBP-like TLF/TRF2 gene. Mol. Cell 7: 509-515.
38. Martianov, I., Brancorsini, S., Gansmuller, A., Parvinen, M., Davidson, I., and Sassone-Corsi, P. 2002. Distinct functions of TBP and TLF/TRF2 during spermatogenesis: Requirement of TLF for heterochromatic chromocenter formation in haploid round spermatids. Development 129: 945-955.
39. Matsuo, Y. and Yamazaki, T. 1989. tRNA derived insertion element in histone gene repeating unit of Drosophila melanogaster. Nucleic Acids Res. 17: 225-238.
40. Muller, F., Lakatos, L., Dantonel, J., Strahle, U., and Tora, L. 2001. TBP is not universally required for zygotic RNA polymerase II transcription in zebrafish. Curr. Biol. 11: 282-287.
41. Ner, S.S. and Travers, A.A. 1994. HMG-D, the Drosophila melanogaster homologue of HMG 1 protein, is associated with early embryonic chromatin in the absence of histone H1. EMBO J. 13: 1817-1822.
42. Ohbayashi, T., Makino, Y., and Tamura, T.A. 1999. Identification of a mouse TBP-like protein (TLP) distantly related to the Drosophila TBP-related factor. Nucleic Acids Res. 27: 750-755.
43. Ohler, U., Liao, G.C., Niemann, H., and G.M. Rubin. 2002. Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3: RESEARCH0087. doi: 10.1186/gb-2002-3-12-research0087.
44. Ohshima, N., Takahashi, M., and Hirose, F. 2003. Identification of a human homologue of the DREF transcription factor with a potential role in regulation of the histone H1 gene. J. Biol. Chem. 278: 22928-22938.
45. Rabenstein, M.D., Zhou, S., Lis, J.T., and Tjian, R. 1999. TATA box-binding protein (TBP)-related factor 2 (TRF2), a third member of the TBP family. Proc. Natl. Acad. Sci. 96: 4791-4796.
46. Ruddell, A. and Jacobs-Lorena, M. 1985. Biphasic pattern of histone gene expression during Drosophila oogenesis. Proc. Natl. Acad. Sci. 82: 3316-3319.
47. Skantar, A.M. and Greenleaf, A.L. 1995. Identifying a transcription factor interaction site on RNA polymerase II. Gene Expr. 5: 49-69.
48. Smale, S.T. and Kadonaga, J.T. 2003. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72: 449-479.
49. Spradling, A.C. and Rubin, G.M. 1982. Transposition of cloned P elements into Drosophila germ line chromosomes. Science 218: 341-347.
50. Storey, J.D. 2002. A direct approach to false discovery rates. J. R. Stat. Soc. Ser. B Methodol. 64: 479-498.
51. Sun, F.L., Cuaycong, M.H., Craig, C.A., Wallrath, L.L., Locke, J., and Elgin, S.C. 2000. The fourth chromosome of Drosophila melanogaster: Interspersed euchromatic and heterochromatic domains. Proc. Natl. Acad. Sci. 97: 5340-5345.
52. Takada, S., Lis, J.T., Zhou, S., and Tjian, R. 2000. A TRF1:BRF complex directs Drosophila RNA polymerase III transcription. Cell 101: 459-469.
53. Thoma, F., Koller, T., and Klug, A. 1979. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J. Cell Biol. 83: 403-427.
54. Tupler, R., Perini, G., and Green, M.R. 2001. Expressing the human genome. Nature 409: 832-833.
55. Veenstra, G.J., Weeks, D.L., and Wolffe, A.P. 2000. Distinct roles for TBP and TBP-like factor in early embryonic gene transcription in Xenopus. Science 290: 2312-2315.
56. Weinzierl, R.O., Dynlacht, B.D., and Tjian, R. 1993. Largest subunit of Drosophila transcription factor IID directs assembly of a complex containing TBP and a coactivator. Nature 362: 511-517.
57. Zhang, D., Penttila, T.L., Morris, P.L., Teichmann, M., and Roeder, R.G. 2001. Spermiogenesis deficiency in mice lacking the Trf2 gene. Science 292: 1153-1155.