The biology of eukaryotic promoter prediction - A review

Computers and Chemistry

Volumn 23, Issue 3-4, 1999, Pages 191-207

  Pedersen, Anders Gorm ^a   Baldi, Pierre ^b   Chauvin, Yves ^b   Brunak, Søren ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b Net ID Inc   (United States)

Author keywords

Genome analysis; Initiator; Nucleosomes; TATA box; Transcriptional initiation

Indexed keywords

DNA;

CHROMOSOME; CPG ISLAND; DNA METHYLATION; EUKARYOTIC CELL; GENETIC TRANSCRIPTION; GENETICS; HUMAN; PROMOTER REGION; REGULATORY SEQUENCE; REVIEW;

CHROMOSOMES; CPG ISLANDS; DNA; DNA METHYLATION; EUKARYOTIC CELLS; HUMANS; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION, GENETIC;

EID: 0033563512     PISSN: 00978485     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0097-8485(99)00015-7     Document Type: Article

References (186)

1. Adhya, S., 1989. Multipartite genetic control elements: communication by DNA looping. Annu. Rev. Genet 23, 227-250.
2. Aïssani, B., Bernardi, G., 1991a. CpG islands: features and distribution in the genomes of vertebrates. Gene 106, 173-183.
3. Aïssani, B., Bernardi, G., 1991b. CpG islands, genes, and isochores in the genomes of vertebrates. Gene 106, 185-195.
4. Allison, L.A., Moyle, M., Shales, M., Ingles, C.J., 1985. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell 42, 599-610.
5. Antequera, F., Bird, A., 1993. Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. USA 90, 11995-11999.
6. Audic, S., Claverie, J.-M., 1997. Detection of eukaryotic promoters using Markov transition matrices. Computers Chem 21, 223-227.
7. Audic, S., Claverie, J.M., 1998. Visualizing the competitive recognition of TATA-boxes in vertebrate promoters. Trends Genet 14, 10-11.
8. Baldi, P., Brunak, S., 1998. Bioinformatics: The Machine Learning Approach. MIT Press, Cambridge, MA.
9. Baldi, P., Chauvin, Y., Brunak, S., Gorodkin, J., Pedersen, A.G., 1998. Computational applications of DNA structural scales. ISMB 6.
10. Benham, C.J., 1996. Computation of DNA structural variability - a new predictor of DNA regulatory sequences. CABIOS 12, 375-381.
11. Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J., Ouellette, B.F., 1998. Genbank. Nucleic Acids Res 26, 1-7.
12. Bernardi, G., 1993. The isochore organization of the human genome and its evolutionary history - a review. Gene 135, 57-66.
13. Bernardi, G., 1995. The human genome: organization and evolutionary history. Annu. Rev. Genet 29, 445-476.
14. Bird, A., 1980. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8, 1499-1504.
15. Bird, A., 1993. Functions for DNA methylation in vertebrates. Cold Spring Harbor Symp. Quant. Biol 58, 281-285.
16. Bird, A., Tate, P., Nan, X., Campoy, J., Meehan, R., Cross, S., Tweedle, S., Charlton, J., Macleod, D., 1995. Studies of DNA methylation in animals. J. Cell Sci. Suppl 19, 37-39.
17. Bode, J., Schlake, T., Rí;os-Ramírez, M., Mielke, C., Stengert, M., Kay, V., Klehr-Wirth, D., 1995. Scaffold/ matrix-attached regions: structural properties creating transcriptionally active loci. Int. Rev. Cyt 162A, 389-454.
18. Bolshoy, A., 1995. CC dinucleotides contribute to the bending of DNA in chromatin. Nature Struct. Biol 2, 447-448.
19. Bolshoy, A., McNamara, P., Harrington, R.E., Trifonov, E.N., 1991. Curved DNA without A-A: experimental e3timation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA 88, 2312-2316.
20. Bonifer, C., Hecht, A., Sauressig, H., Winter, D.M., Sippel, A.E., 1991. Dynamic chromatin: the regulatory domain organization of eukaryotic gene loci. J. Cell. Biochem 47, 99-108.
21. Borodovsky, M., McIninch, J., 1993. Genemark: Parallel gene recognition for both DNA strands. Comput. Chem 17, 123-133.
22. Boulikas, T., 1995. Chromatin domains and prediction of MAR sequences. Int. Rev. Cytol 162A, 279-388.
23. Boyes, J., Bird, A., 1992. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J 11, 327-333.
24. Brazma, A., Jonassen, I., Eidhammer, I., Gilbert, D., 1998. Approaches to the discovery of patterns in biosequences. J. Comput. Biol. 5 (2), 279-305.
25. Breant, B., Huet, J., Sentenac, A., Fromageot, P., 1983. Analysis of yeast RNA polymerases with subunit-specific antibodies. J. Biol. Chem 258, 11968-11973.
26. Brownell, J.E., Allis, C.D., 1995. An activity gel assay detects a single catalytically active histone acetyltransferase subunit in Tetrahymena macronuclei. Proc. Natl. Acad. Sci. USA 92, 6364-6368.
27. Brownell, J.E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D.G., Roth, S.Y., Allis, C.D., 1996. Tetrahymena histone acetyltransferase A: a homologue to yeast Gcn5p linking histone acetylation to gene activation. Cell 84, 843-851.
28. Brukner, I., Jurukovski, V., Savic, A., 1990. Sequence-dependent structural variations of DNA revealed by DNase I. Nucleic Acids Res 18, 891-894.
29. Brukner, I., Sanchez, R., Suck, D., Pongor, S., 1995a. Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J 14, 1812-1818.
30. Brukner, I., Sanchez, R., Suck, D., Pongor, S., 1995b. Trinucleotide models for DNA bending propensity: comparison of models based on DNase I digestion and nucleosome positioning data. J. Biomol. Struct. Dyn 13, 309-317.
31. Brunak, S., Engelbrecht, J., Knudsen, S., 1991. Prediction of human mRNA donor and acceptor sites from the DNA sequences. J. Mol. Biol 220, 49-65.
32. Bucher, P., 1990. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol 212, 563-578.
33. Bucher, P., Fickett, J.W., Hatzigeorgiou, A., 1996. Computational analysis of transcriptional regulatory elements: a field in flux. CABIOS 12, 361-362.
34. Buratowski, S., 1997. Multiple TATA-binding factors conic back into style. Cell 91, 13-15.
35. Burge, C., Karlin, S., 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol 268, 78-94.
36. II60 of Drosophila. Genes Dev 11, 3020-3031.
37. Burley, S.K., Roeder, R.G., 1996. Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem 65, 769-799.
38. Calladine, C.R., Drew, H.R., McCall, M.J., 1988. The intrinsic structure of DNA in solution. J. Mol. Biol 201, 127-137.
39. Cavalli, G., Paro, R., 1998. Chromo-domain proteins: linking chromatin structure to epigenetic regulation. Curr. Opin. Cell Biol 10, 354-360.
40. Chen, Q.K., Hertz, G.Z., Stormo, G.D., 1997. Promfd 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. CABIOS 13, 29-35.
41. Chen, Q.K., Stormo, G.Z.H.G.D., 1995. Matrix search 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci 11, 563-566.
42. Coulondre, C., Miller, J.H., Farabough, P.J., Gilbert, W., 1978. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274, 775-780.
43. Craig, J.M., Bickmore, W.A., 1994. The distribution of CpG islands in mammalian chromosomes. Nature Genetics 7, 376-382.
44. Cremer, T., Kurz, A., Zirbel, R., Dietzel, S., Rinke, B., Schröck, E., Speichel, M.R., Mathieu, U., Jauch, A., Emmerich, P., Schertan, H., Ried, T., Cremer, C., Lichter, P., 1993. Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harbor Symp. Quant. Biol 58, 777-792.
45. Cross, S., Kovarik, P., Schmidtke, J., Bird, A., 1991. Nonmethylated islands in fish genomes are GC-poor. Nucleic Acids Res 19, 1469-1474.
46. Cross, S.H., Bird, A., 1995. CpG islands and genes. Curr. Opin. Genet. Dev 5, 309-314.
47. Crossley, M., Orkin, S.H., 1993. Regulation of the beta-globin locus. Curr. Opin. Genet. Dev 3, 232-237.
48. Davie, J.R., 1998. Covalent modification of histones: expression from chromatin templates. Curr. Opin. Gen. Dev 8, 173-178.
49. de Souza, O.N., Ornstein, R.L., 1998. Inherent DNA curvature and flexibility correlate with TATA box functionality. Biopolymers 46, 403-415.
50. Diamond, M.I., Miner, J.N., Yoshinaga, S.K., Yamamoto, K.R., 1990. Transcription factor interactions: selectors of positive or negative regulation from a single DNA element. Science 249, 1266-1274.
51. Dickerson, R.E., Drew, H., 1981. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J. Mol. Biol 149, 761-786.
52. Dillon, N., Grosveld, F., 1994. Chromatin domains as potential units of eukaryotic gene function. Curr. Opin. Genet. Dev 4, 260-264.
53. Drew, H.R., Travers, A.A., 1985. DNA bending and its relation to nucleosome positioning. J. Mol. Biol 186, 773-790.
54. Dynan, W.S., 1989. Modularity in promoters and enhancers. Cell 58, 1-4.
55. Eden, S., Cedar, H., 1994. Role of DNA methylation in the regulation of transcription. Curr. Opin. Genet. Dev 4, 255-259.
56. Evans, T., Felsenfeld, G., Reitman, M., 1990. Control of globin gene transcription. Annu. Rev. Cell Biol 6, 95-124.
57. Fassler, J.S., Gussin, G.N., 1996. Promoters and basal transcription machinery in eubacteria and eukaryotes: concepts, definitions, and analogies. Meth. Enz 273, 3-29.
58. Fickett, J.W., 1996a. Coordinate positioning of MEF2 and myogenin binding sites. Gene 172, GC19-GC32.
59. Fickett, J.W., 1996b. Quantitative discrimination of MEF2 sites. Mol. Cell. Biol 16, 437-441.
60. Fickett, J.W., Hatzigeorgiou, A.G., 1997. Eukaryotic promoter recognition. Genome Res 7, 861-878.
61. Fraser, P., Grosveld, F., 1998. Locus control regions, chromatin activation and transcription. Curr. Opin. Cell Biol 10, 361-365.
62. Frech, K., Danescu-Mayer, J., Werner, T., 1997. A novel method to develop highly specific models for regulatory units detects a new LTR in genbank which contains a functional promoter. J. Mol. Biol 270, 674-687.
63. Gardiner, K., 1995. Human genome organization. Curr. Opin. Genet. Dev 5, 315-322.
64. Gardiner-Garden, M., Frommer, M., 1987. CpG islands in vertebrate genomes. J. Mol. Biol 196, 261-282.
65. Gasser, S.M., Paro, R., Stewart, F., Aasland, R., 1998. Epigenetic control of transcription. Introduction: the genetics of epigenetics. Cell. Mol. Life Sci 54, 1-5.
66. Geyer, P.K., 1997. The role of insulator elements in defining domains of gene expression. Curr. Opin Gen. Dev 7, 242-248.
67. Goodrich, J.A., Tjian, R., 1994. TBP-TAF complexes: selectivity factors for eukaryotic trancription. Curr. Opin. Cell Biol 6, 403-409.
68. Goodsell, D.S., Dickerson, R.E., 1994. Bending and curvature calculations in B-DNA. Nucleic Acids Res 22, 5497-5503.
69. Gottesfeld, J.M., Forbes, D.J., 1997. Mitotic repression of the transcriptional machinery. TIBS 22, 197-202.
70. Greenblatt, J., 1997. RNA polymerase II holoenzyme and transcriptional regulation. Curr. Opin. Cell Biol 9, 310-319.
71. Gregory, P.D., Hörz, W., 1998. Life with nucleosomes: chromatin remodelling in gene regulation. Curr. Opin. Cell. Biol 10, 339-345.
72. Grove, A., Galeone, A., Yu, E., Mayol, L., Geiduschek, E.P., 1998. Affinity, stability and polarity of binding of the TATA binding protein governed by flexure of the TATA box. J. Mol. Biol 282, 731-739.
73. Grunstein, M., 1997. Histone acetylation in chromatin structure and transcription. Nature 389, 349-352.
74. Hagerman, P.J., 1984. Evidence for the existence of stable curvature of DNA in solution. Proc. Natl. Acad. Sci. USA 81, 4632-4636.
75. Hahn, S., Buratowski, S., Sharp, P.A., Guarente, L., 1989. Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus sequences. Proc. Natl. Acad. Sci. USA 86, 5718-5722.
76. Hansen, J., Lund, O., Tolstrup, N., Gooley, A., Williams, K., Brunak, S., 1998. NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconjugate Journal 15, 115-130.
77. Hansen, J.E., Lund, O., Engelbrecht, J., Bohr, H., Nielsen, J.O., Hansen, J.-E.S., Brunak, S., 1995. Prediction of O-glycosylation of mammalian proteins: specificity patterns of UDP-GalNAC: polypeptide N-acetylgalactosaminyl-transferase. Biochem J 308, 801-813.
78. Hansen, S.K., Takada, S., Jacobson, R.H., Lis, J.T., Tjian, R., 1997. Transcription properties of a cell type-specific TATA-binding protein, TRF. Cell 91, 71-83.
79. Hassan, M.A.E., Calladine, C.R., 1996. Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol 259, 95-103.
80. Hayes, J.J., Wolffe, A.P., 1992. The interaction of transcription factors with nucleosomal DNA. BioEssays 14, 597-603.
81. Hecht, A., Strahl-Bolsinger, S., Grunstein, M., 1996. Spreading of transcriptional repressor Sir3 from telomeric hetrochromatin. Nature 383, 92-96.
82. Hernandez, N., 1993. TBP, a universal eukaryotic transcription factor? Genes Dev 7, 1291-1308.
83. Higgs, D.R., Wood, W.G., 1993. Understanding erythroid differentiation. Curr. Biol 3, 548-550.
84. Holliday, R., 1993. Epigenetic inheritance based on DNA methylation. EXS 64, 452-468.
85. Huet, J., Sentenac, A., Fromageot, P., 1982. Spot-immunodetection of conserved determinants in eukaryotic RNA polymerases. Study with antibodies to yeast RNA polymerases subunits. J. Biol. Chem 257, 2613-2618.
86. Hunter, C.A., 1993. Sequence-dependent DNA structure: the role of base stacking interactions. J. Mol. Biol 230, 1025-1054.
87. Hunter, C.A., 1996. Sequence-dependent DNA structure. Bioessays 18, 157-162.
88. Hutchinson, G.B., 1996. The prediction of vertebrate promoter regions .using differential hexamer frequency analysis. CABIOS 12, 391-398.
89. Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M., Trifonov, E.N., 1996. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol 262, 129-139.
90. Iyer, V., Struhl, K., 1995. Poly (dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J 14, 2570-2579.
91. Jackle, H., Sauer, F., 1993. Transcriptional cascades Drosophila. Curr. Opin. Cell Biol 5, 505-512.
92. Johnson, P.F., McKnight, S.L., 1989. Eukaryotic transcription regulatory proteins. Ann. Rev. Biochem 58, 799-839.
93. Jones, P.A., Rideout, W.M., Shen, J.-C., Spruck, C.H., Tsai, Y.C., 1992. Methylation, mutation and cancer. BioEssays 14, 33-36.
94. Karas, H., Knüppel, R., Schultz, W., Sklenar, H., WIngender, E., 1996. Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements. CABIOS 12, 441-446.
95. Karpen, G.H., 1994. Position-effect variegation and the new biology of heterochromatin. Curr. Opin. Genet. Dev 4, 281-291.
96. Kellum, R., Elgin, S.C.R., 1998. Chromatin boundaries: punctuating the genome. Curr. Biol 8, R521-R524.
97. Klug, A., Jack, A., Viswamitra, M.A., Kennard, O., Shakked, Z., Steitz, T.A., 1979. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J. Mol. Biol 131, 669-680.
98. Knudsen, S. Promoter 1.0: a novel algorithm for the recognition of pol-II promoter sequences, submitted.
99. Kondrakhin, Y.V., Kel, A.E., Romashchenko, N.A.K.A.G., Milanesi, L., 1995. Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci 11, 477-488.
100. Kornberg, R.D., 1977. Structure of chromatin. Annu. Rev. Biochem 46, 931-954.
101. Kornberg, R.G., Lorch, Y., 1995. Interplay between chromatin structure and transcription. Curr. Opin. Cell. Biol 7, 371-375.
102. Korning, P.G., Hebsgaard, S.M., Rouze, P., Brunak, S., 1996. Cleaning the GenBank Arabidopsis thaliana data set. Nucleic Acids Res 24, 316-320.
103. Krogh, A., Brown, M., Mian, I.S., Sjolander, K., Haussler, D., 1994. Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol 235, 1501-1531.
104. Laemmli, U.K., Käas, E., Poljak, L., Adachi, Y., 1992. Scaffold-associated regioons: cis-acting determinants of chromatin structural loops and functional domains. Curr. Opin. Gen. Dev 2, 275-285.
105. Lamb, P., McKnight, S.L., 1991. Diversity and specificity in transcriptional regulation: the benefits of heterotypic dimerization. Trends Biochem. Sci 16, 417-422.
106. Lee, T.I., Young, R.A., 1998. Regulation of gene expression by TBP associated proteins. Genes Dev 12, 1398-1408.
107. Li, E., Bestor, T.H., Jaenisch, R., 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915-926.
108. Lisser, S., Margalit, H., 1994. Determination of common structural features in Escherichia coli promoters by computer analysis. Eur J Biochem 223, 823-830.
109. Liu, K., Stein, A., 1997. DNA sequence encodes information for nucleosome array formation. J. Mol. Biol 270, 559-573.
110. Lu, B.Y., Eissenberg, J.C., 1998. Time out: developmental regulation of heterochromatic silencing in. Drosophila. Cell. Mol. Life Sci 54, 50-59.
111. Lu, Q., Wallrath, L.L., Elgin, S.C.R., 1994. Nucleosome positioning and gene regulation. J. Cell. Biochem 55, 83-92.
112. Luger, K., Maeder, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J., 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251-260.
113. Lukashin, A., Borodovsky, M., 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26, 1107-1115.
114. Macleod, D., Charlton, J., Mullins, J., Bird, A., 1994. Sp 1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG islands. Genes Dev 8, 2282-2292.
115. Matis, S., Xu, Y., Shah, M., Guan, X., Einstein, J.R., Mural, R., Uberbacher, E.C., 1996. Detection of RNA polymerase II promoters and polyadenylation sites in human dna sequence. Comput. Chem 20, 135-140.
116. Matthews, K.S., 1992. DNA looping. Microbiol. Rev 56, 123-136.
117. McGhee, J.D., Felsenfeld, G., 1980. Nucleosome structure. Annu. Rev. Biochem 49, 1115-1156.
118. McKnight, S.L., Yamamoto, K.R., 1992. Transcriptional Regulation. In: Cold Spring Harbor Laboratory Press, Plainview, New York.
119. Mihaly, J., Hogga, I., Barges, S., Galloni, M., Mishra, R.K., Hagstrom, K., Müller, M., Schedl, P., Sipos, L., Gausz, J., Gyurkovics, H., Karch, F., 1998. Chromatin domain boundaries in the bithorax complex. Cell. Mol. Life Sci 54, 60-70.
120. Milanesi, L., Muselli, M., Arrigo, P., 1996. Hamming clustering method for signals prediction in 5′ and 3′ regions of eukaryotic genes. CABIOS 12, 399-404.
121. Milanesi, L., Rogozin, I.B. in press. Prediction of human gene structure. Bishop, M.J. (ed.) Guide to Human Genome Computing. Academic Press. Cambridge.
122. Minie, M., Clark, D., Trainor, C., Evans, T., Reitman, M., Hannon, R., Gould, H., Felsenfeld, G., 1992. Developmental regulation of globin gene expression. J. Cell Sci. Suppl 16, 15-20.
123. Mitchell, P.J., Tjian, R., 1989. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science 245, 371-378.
124. Mizzen, C.A., Allis, C.D., 1998. Linking histone acetylation to transcriptional regulation. Cell. Mol. Life Sci 54, 6-20.
125. II250 subunit of TFIID has histone acetyltransferase activity. Cell 87, 1261-1270.
126. Nielsen, H., Engelbrecht, J., Brunak, S., von Heine, G., 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10, 1-6.
127. Nielsen, H., Engelbrecht, J., von Heijne, G., Brunak, S., 1996. Defining a similarity threshold for a functional protein sequence pattern: the signal peptide cleavage site. Proteins 26, 165-177.
128. Ogryzko, V., Schiltz, R.L., Russanova, V., Howard, B.H., Nakatani, Y., 1996. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87, 953-959.
129. Orphanides, G., Lagrange, T., Reinberg, D., 1996. The general transcription factors of RNA polymerase II. Genes Dev 10, 2657-2683.
130. Paranjape, S.M., Kamakaka, R.T., Kadonaga, J.T., 1994. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu. Rev. Biochem 63, 265-297.
131. Pazin, M.J., Kadonaga, J.T., 1997. SWI2/SNF2 and related proteins: ATP-driven motors that disrupt protein-DNA interactions? Cell 88, 737-740.
132. Pedersen, A.G., Baldi, P., Chauvin, Y., Brunak, S., 1998. DNA structure in human RNA polymerase II promoters. J. Mol. Biol 281, 663-673.
133. Pedersen, A.G., Nielsen, H., 1997. Neural network based prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis. ISMB 5, 226-233.
134. Pedersen, A.G., Nielsen, H., Brunak, S. Statistical analysis of translational initiation sites in eukaryotes: patterns are specific for systematic groups, (in prepararion).
135. Perier, R.C., Junier, T., Bucher, P., 1998. The eukaryotic promoter database EPD. Nucleic Acids Res 26, 353-357.
136. Prestridge, D.S., 1995. Prediction of POL II promoter sequences using transcription factor binding sites. J. Mol. Biol 249, 923-932.
137. Prestridge, D.S., 1997. Signal scan: A computer program that scans DNA sequences for eukaryotic transcriptional elements. CABIOS 7, 203-206.
138. Prestridge, D.S., Burks, C., 1993. The density of transcriptional elements in promoter and non-promoter sequences. Hum. Mol. Genet 2, 1449-1453.
139. Ptashne, M., Gann, A., 1997. Transcriptional activation by recruitment. Nature 386, 569-577.
140. Pugh, B.F., Tjian, R., 1990. Mechanism of transcriptional activation by Sp1: evidence for coactivators. Cell 61, 1187-1197.
141. Quandt, K., Frech, K., Karas, H., Wingender, E., Werner, T., 1995. Matind and matinspector - new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucl. Acids Res 23, 4878-4884.
142. Ramakrishnan, V., 1997. Histone HI and chromatin higher-order structure. Crit. Rev. Eukaryot. Gene Expr 7, 215-230.
143. Reese, M.G., Harris, N.L., Eeckman, F.H., 1996. Large scale sequencing specific neural networks for promoter and splice site recognition. In: Hunter, L., Hunter, T.E. (Eds.), Biocomputing: Proceedings of the 1996 Pacific Symposium, . World Scientific Publishing Co, Singapore.
144. Richard-Foy, H., Hager, G.L., 1987. Sequence specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J 6, 2321-2328.
145. Richmond, T.J., Finch, J.T., Rushton, B., Rhodes, D., Klug, A., 1984. Structure of the nucleosome core particle at 7 Å resolution. Nature 311, 532-537.
146. Rosenblueth, D.A., Thieflry, D., Huerta, A.M., Salgado, H., Colladio-Vides, J., 1996. Syntactic recognition of regulatory regions in Escherichia coli. CABIOS 12, 415-422.
147. Saitoh, Y., Laemmli, U.K., 1993. From the chromosomal loops and the scaffold to the classic bands of metaphase chromosomes. Cold Spring Harbor Symp. Quant. Biol 58, 755-765.
148. Satchwell, S.C., Drew, H.R., Travers, A.A., 1986. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol 191, 659-675.
149. Schirm, S., Jiricny, J., Schaffner, W., 1987. The SV40 enhancer can be dissected into multiple segments, each with a different cell type specificity. Genes Dev 1, 65-74.
150. Schübeler, D., Mielke, C., Maas, K., Bode, J., 1996. Scaffold/ matrix attached regions act upon transcription in a context-dependent manner. Biochem 35, 11160-11169.
151. Schug, J., Overton, G.C. 1977. Tess: transcription element search software on the www. Technical Report CBIL-TR-1997-1001-v0.0, of the Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania.
152. Simpson, R.T., 1991. Nucleosome positioning: occurrence, mechanisms, and functional consequences. Prog. Nucleic Acids Res. Mol. Biol 40, 143-184.
153. Simpson, R.T., Roth, S.Y., Morse, R.H., Patterson, H.G., Cooper, J.P., Murphy, M., Kladde, M.P., Shimizu, M., 1994. Nucleosome positioning and transcription. Cold Spring Harbor Symp. Quant. Biol 58, 237-245.
154. Singer, V.L., Wobbe, C.R., Struhl, K., 1990. A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev 4, 636-645.
155. Singh, G.B., 1997. Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Res 25, 1419-1425.
156. Sippel, A.E., Schäfer, G., Faust, N., Hecht, A., Bonifer, C., 1993. Chromatin domains constitute regulatory units for the control of eukaryotic genes. Cold Spring Harbor Symp. Quant. Biol 58, 37-44.
157. Smale, ST., 1994a. Core promoter architecture for eukaryotic protein-coding genes. In: Conaway, R.C., Conaway, J.W. (Eds.), Transcription: Mechanisms and regulation. Raven Press, New York, pp. 63-81.
158. Smale, S.T., 1994b. DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol. Cell. Biol 14, 116-127.
159. Smale, ST., 1997. Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Bioch. Biophys. Acta 1351, 73-88.
160. Small, S., Kraut, R., Hoey, T., Warrior, R., Levine, M., 1991. Transcriptional regulation of a pair-rule stripe Drosophila. Genes Dev 5, 827-839.
161. Solovyev, V., Salamov, A., 1997. The gene-finder computer tools for analysis of human and model organisms genome sequences. In: Proceedings, Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB-97), 294-302.
162. Stargell, L.A., Struhl, K., 1996. Mechanisms of transcriptional activation in vivo: two steps forward. Trends Genet 12, 311-315.
163. Stoesser, G., Moseley, M.A., Sleep, J., McGowran, M., Garcia-Pastor, M., Sterk, P., 1998. The EMBL nucleotide sequence database. Nucleic Acids Res 26, 8-15.
164. Tanese, N., Tjian, R., 1993. Coactivators and TAFs: a new class of eukaryotic transcription factors that connect activators to the basal machinery. Cold Spring Harbor Symp. Quant. Biol 58, 179-185.
165. Tansey, W.P., Herr, W., 1997. TAFs: guilt by association. Cell 88, 729-732.
166. Tateno, Y., Fukami-Kobayashi, K., Miyazaki, S., Sugawara, H., Gojobori, T., 1998. DNA data bank of Japan at work on genome sequence data. Nucleic Acids Res 26, 16-20.
167. Tolstrup, N., Rouzé, P., Brunak, S., 1997. A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res 25, 3159-3163.
168. Tsukiyama, T., Wu, C., 1997. Chromatin remodeling and transcription. Curr. Opin. Gen. Dev 7, 182-191.
169. Turner, B.M., 1998. Histone acetylation as an epigenetic determinant of long-term transcriptional competence. Cell. Mol. Life Sci 54, 21-31.
170. Uberbacher, E.C., Xu, Y., Mural, R.J., 1996. Discovering and understanding genes in human DNA sequence using GRAIL. Meth. Enz 266, 259-281.
171. Vazquez, J., Farkas, G., Gaszner, M., Udvardy, A., Muller, M., Hagstrom, K., Gyurkovics, H., Sipos, L., Gausz, J., Galloni, M., Hogga, I., Karch, F., Schedl, P., 1993. Genetic and molecular analysis of chromatin domains. Cold Spring Harbor Symp. Quant. Biol 58, 45-54.
172. Wasserman, W.W., Fickett, J.W., 1998. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol 24, 167-181.
173. Wasylyk, B., 1988. Transcription elements and factors of RNA polymerase B promoters of higher eukaryotes. CRC Crit Rev Biochem 23, 77-120.
174. Widom, J., 1989. Toward a unified model of chromatin folding. Annu. Rev. Biophys. Biophys. Chem 18, 365-395.
175. Widom, J., 1996. Short-range order in two eukaryotic genomes: relation to chromosome structure. J. Mol. Biol 259, 579-588.
176. Wieczorek, E., Brand, M., Jacq, X., Tora, L., 1998. Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II. Nature 393, 187-191.
177. Wingender, T.H.E., Hermjakob, I.R.H., Kel, A.E., Kel, O.V., Ignatieva, E.V., Ananko, E.A., Podkolodnaya, O.A., Kolpakov, F.A., Kolchanov, N.L.P.N.A., 1998. Databases on transcriptional regulation: TRANSFAC, TRRD, and COMPEL. Nucl. Acids Res 26, 364-370.
178. Wobbc, C.R., Struhl, K., 1990. Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. Mol. Cell. Biol 10, 3859-3867.
179. Wolffe, A.P., 1994. Nucleosome positioning and modification: chromatin structures that potentiate transcription. TIBS 19, 240-244.
180. Wolffe, A.P., Drew, H.R., 1995. DNA structure: implications for chromatin structure and function. In: Elgin, S.C.R (Ed.), Chromatin Structure and Gene Expression. IRL Press, Oxford, pp. 27-48.
181. Wolffe, A.P., Khochbin, S., Dimitrov, S., 1997. What do linker histones do in chromatin? BioEssays 19, 249-255.
182. Workman, J.L., Kingston, R.E., 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem 67, 545-579.
183. Zawel, L., Reinberg, D.R., 1993. Initiation of transcription by RNA polymerase II: a multi-step process. Prog. Nucl. Acids Res. Mol. Biol 44, 67-108.
184. Zhang, M.Q., 1998a. A discrimination study of human core-promoters. In: Altman, R., Donker, A.K., Hunter, L., Klein, T.E. (Eds.), Proc. Pacific Symp. Biocomputing. World Scientific, Singapore, pp. 240-251.
185. Zhang, M.Q., 1998b. Identification of human gene core-promoters in silico. Genome Res 8, 319-326.
186. Zhu, Z., Thiele, D.J., 1996. A specialized nucleosome modulates transcription factor access to a C. glabrata metal responsive promoter. Cell 87, 459-470.