Компьютерный анализ конформационных и физико-химических особенностей сайтов связывания транскрипционных факторов эукариот
Диссертация
В главе 3 диссертации подробно рассмотрены результаты исследования с использованием системы ACTIVITY сайтов связывания факторов USF, MEF-2, c-Myb, YY1, ТВР и Inr-элемента. Исследованы различные последовательности ДНК сайтов: природные, мутантные, а также полученные методами селекции через связывание с определенным фактором и последующей амплификации рандомизированных последовательностей… Читать ещё >
Содержание
- Глава 1. ОБЗОР ЛИТЕРАТУРЫ
- 1. 1. Регуляция транскрипции в геномах эукариот: роль сайтов связывания ТФ
- 1. 1. 1. Основные типы регуляторных геномных последовательностей, контролирующих транскрипцию генов эукариот
- 1. 1. 2. Формирование транскрипционных комплексов в геномах эукариот
- 1. 1. 3. Взаимодействие ТВР белка с ТАТА-боксом
- 1. 1. 4. Транскрипционные факторы и их взаимодействие с ДНК
- 1. 1. 5. Активность сайтов связывания ТФ
- 1. 1. 6. Роль хроматина в регуляции транскрипции
- 1. 2. ДНК: конформация, физико-химические свойства
- 1. 2. 1. Структура ДНК
- 1. 2. 2. Конформационные параметры и физико-химические свойства ДНК
- 1. 2. 3. Зависимость конформации ДНК от последовательности
- 1. 2. 4. Конформация ДНК в комплексах с транскрипционными факторами
- 1. 3. Компьютерные методы анализа сайтов связывания ТФ эукариот
- 1. 3. 1. Базы данных по регуляции транскрипции
- 1. 3. 2. Методы распознавания сайтов связывания ТФ
- 1. 3. 3. Методы предсказания активности сайтов
- 1. 1. Регуляция транскрипции в геномах эукариот: роль сайтов связывания ТФ
Список литературы
- Вингендер, Э. (1997) Классификация транскрипционных факторов эукариот. Молекулярная биология. 31, 584−600.
- Дикерсон, Р.Э. (1984) Спираль ДНК. В Мире Науки. 2, 34−48.
- Зенгер, В. (1987) Принципы структурной организации нуклеиновых кислот. Москва, Мир, стр. 413−463.
- Квандт, К, Фреш, К, Вернер, Т (1997) Анализ регуляторных районов транскрипции основанный на изучение мутантных позиций сайтов связывания транскрипционных факторов. Мол, Биол., 31, 749−758.
- Кель, А.Э. (1991) Теоретический анализ структуры, функции и эволюции коротких повторов в геномах. Автореферат диссертации на соискание ученой степени кандидата биологических наук. Новосибирск, 1991.
- Кель, О.В. (2000) Регуляция транскрипции генов эукариот: композиционные элементы, базы данных и компьютерный анализ. Автореферат диссертации на соискание ученой степени кандидата биологических наук. Новосибирск, 2000.
- Кель, О.В., Кель, А.Э., Ромащенко, А.Г., Вингендер, Э., Колчанов, Н.А. (1997) Композиционные регуляторные элементы: классификация и описание в базе данных COMPEL. Молекулярная биология. 31, 601−615
- Кузин, Ф.Э. (2001) Топологическое состояние ДНК в интерфазных ядрах и метафазных хромосомах. Автореферат диссертации на соискание ученой степени кандидата биологических наук. Новосибирск, 2001.
- Леман, Э. (1979) Проверка статистических гипотез. М.:Наука.
- Подколодная, О.А., Степаненко, И.Л. (1997) Механизмы транскрипционной регуляции эритроид-специфичных генов, Молекулярная биология, 31, 671−683.
- Пономаренко, М.П., Пономаренко, Ю.В., Под колодная, О. А., Фролов, А.С., Воробьев, Д.В., Колчанов, Н.А., Овертон, Г. К. (1999) Усреднее результатов распознавания сайтов может увеличить точность аннотации генома человека. Биофизика, Т. 44, С. 649−654.
- Пономаренко, М.П., Пономаренко, Ю.В., Кель, А.Э., Колчанов, Н.А., Карас, Х., Вингендер, Э., Скленар, Х. (1997а) Компьютерный анализ конформационных особенностей ДНК ТАТА-боксов промоторов эукариот. Молекулярная биология. 31, 733−740.
- Пономаренко, М.П., Савинкова, Л.К., Кель, А.Э., Колчанов, Н.А. (1997в) Компьютерноемоделирование последовательностей ТАТА-боксов промоторов эукариот. Доклады Академии наук, 355, 557−561.
- Пономаренко, М.П., Савинкова, J1.К., Пономаренко, Ю.В., Кель, А.Э., Титов, И.И., Колчанов, Н.А. (19 976) Моделирование последовательностей TATA боксов генов эукариот. Молекулярная биология. 31, 726−732
- Трифонов, Э.Н. (1997) Генетическое содержание последовательностей ДНК определяется суперпозицией многих кодов. Молекулярная биология. 31, 759−767.
- Фишберн, П. (1978) Теория полезности для принятия решений. М.: Наука.
- International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860−921.
- Adams, C.C., Workman, J.L. (1995) Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol. Cell Biol. 15, 1405−1421.
- Almouzni, G, Khochbin, S, Dimitrov, S, Wolffe, AP (1994) Histone acetylation influences both gene expression and development of Xenopus laevis. Dev. Biol. 165, 654−669.
- Apone, L.M., Green, M.R. (1998) Transcription sans TBP. Nature, 393, 114−116.
- Apone, LM, Virbasius, CM, Reese, JC, Green, MR (1996) Yeast TAF (II)90 is required for cell-cycle progression through G2/M but not for general transcription activation. Genes Dev. 10, 2368−2380.
- Babcock, M.S., Pednault, E.P.D., Olson, W.K. (1993) Nucleic acid structure analysis: a users guide to a collection of new analysis programs. J. Biomol. Struct. Dynamics 11, 597−628-
- Babcock, M.S., Pednault, E.P.D., Olson, W.K. (1994) Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237, 125−156
- Babenko, V. N., P. S. Kosarev, О. V. Vishnevsky, V. G. Levitsky, V. V. Basin, A. S. Frolov (1999) Investigating extended regulatory regions of genomic DNA sequences. Bioinformatics, 15, 7/8, 644−653.|
- Baker W, van den Broek A, Camon E, Hingamp P, Sterk P, Stoesser G, Tuli MA (2000) The EMBL nucleotide sequence database. Nucleic Acids Res, 28(1), 19−23.
- Barrick, D., Villanueba, K., Childs, J., Kalil, R., Schneider, T.D., Lawrence, C.E., Gold, L., Stormo, G.D. (1994) Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res., 22, 1287−1295.
- Beato, M, Eisfeld, К (1997) Transcription factor access to chromatin. Nucleic Acids Res, 25, 3559−3563.
- Becker, P.B. (1997) DNA-transcription factor interactions in the context of chromatin. In
- Transcription factors in eukaryotes, Ed. Papavassiliou, A.G.
- Bell, В., Tora, L. (1999) Regulation of gene expression by multiple forms of TFIID, other novel TAFII-containing complexes. Exp Cell Res., 246(1):11−19.
- Bellorini, M, Dantonel, JC, Yoon, JB, Roeder, RG, Tora, L, Mantovani, R (1996) The major histocompatibility complex class II Ea promoter requires TFIID binding to an initiatorsequence. Mol Cell Biol, 16, 503 512.
- Bendall, A.J., Molloy, P.L., (1994) Base preferences for DNA binding by the bHLH-Zip protein USF: effects of MgC12 on specificity, comparison with binding of Мус family members. Nucleic Acids Res., 22, 2801−2810.
- Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000) GenBank. Nucleic Acids Res, 28(1):15−18.
- Berg, O.G., von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins.
- Statistical-mechanical theory, application to operators, promoters. J. Mol. Biol. 193. 723 750.
- Berg, O.G." von Hippel, P.H. (1988) Selection of DNA binding sites by regulatory proteins.1. The binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol., 200, 709−723.
- Berk, AJ (1999) Activation of RNA polymerase II transcription. Curr. Opin. Cell Biol., 11, 330−335.
- Bewley, CA, Gronenborn, AM, Clore, GM (1998) Minor groove-binding architectural proteins: structure, function, DNA recognition. Annu Rev Biophys Biomol Struct., 27, 105 131.
- Biedenkapp, H, Borgmeyer, U, Sippel, AE, Klempnauer, KH (1988) Viral myb oncogene encodes a sequence-specific DNA-binding activity. Nature, 335, 835−837.
- Blomquist, P, Li Q, Wrange О (1996) The affinity of nuclear factor 1 for its DNA site is drastically reduced by nucleosome organization irrespective of its rotational or translational position. J Biol Chem, 271, 153−159.
- Bolshoy, A., McNamara, P., Harrington, R.E., Trifonov, E.N. (1991) Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Nath. Acad. Sci. U.S.A., 88, 2312−2316.
- Boulikas, T. (1996) Common structural features of replication origins in all life forms. J. Cell Biochem. 60, 297−316.
- Boyd, D.C., Turner, P.C., Watkins, N.J., Gerster, T., Murphy, S. (1995) Functional redundancy of promoter elements ensures efficient transcription of the human 7SK gene in vivo. J. Mol. Biol., 253, 677−690.
- Bruckner, I., Sanchez, R., Suck, D., Pongor, S. (1995) Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J., 14, 1812−1818.
- 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.
- Buratowski, S. (1994) The basics of basal transcription by RNA polymerase II. Cell, 77, 1−3.
- Buratowski, S. (1997) Multiple TATA-binding factors come back into style. Cell, 91,13−15.
- Buratowski, S., Hahn, S., Guarente, L., Sharp, P. (1989) Five intermediate complexes in transcription initiation by RNA polymerase II. Cell, 56, 549−561.
- Burke, Т.W., Kadonaga, J.T. (1996) Drosofila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev. 10, 711−724.
- Burley, S.K. (1996) The TATA box binding protein. Curr. Opin. Struct. Biol., 6, 69−75.
- Burley, S.K., Roeder, R.G. (1996) Biochemistry, structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem., 65, 769−799.
- Calladine, C.R. (1982) Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol., 161, 343−352.
- Calladine, C.R., Drew, H.R. (1984) A base-centered explanation of the B-to-A transition in DNA. J. Mol. Biol., 178, 773−785.
- Calladine, C.R., Drew, H.R. (1986) Principles of sequence-dependent flexure of DNA. J Mol Biol., 192, 907−918.
- Calladine, C.R., Drew, H.R., McCall, M.J. (1988) The intrinsic structure of DNA in solution. J. Mol. Biol. 201, 127−137.
- Chalkley, GE, Verrijzer, CP (1999) DNA binding site selection by RNA polymerase II TAFs: a TAF (II)250-TAF (II)150 complex recognizes the initiator. EMBO J, 18, 48 354 845.
- Chen, H, Li, B, Workman, JL (1994) A histone-binding protein, nucleoplasmin, stimulates transcription factor binding to nucleosomes, factor-induced nucleosome disassembly. EMBO ЛЪ, 380−390
- Chen, L. (1999) Combinatorial gene regulation by eukaryotic transcription factors. Curr. Opin. Struct. Biol., 9, 48−55.
- Chen, Q., Hertz, G., Stormo, G. (1995) Matrix search 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Applic. Biosci., 11, 563−566.
- Chen, Q.K., Hertz, G.Z., Stormo, G.D. (1997) PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings, IMD matrices. Comput. Appl. Biosci., 13, 29−35.
- Chen, X, Vinkemeier, U, Zhao, Y et al. (1998) Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA. Cell, 93, 827−839.
- Cho, Y, Gorina, S, Jeffrey, PD, Pavletich, NP. (1994) Crystal structure of a p53 tu-mor suppressor-DNA complex: under-standing tumorigenic mutations. Science, 265, 346−455.
- Choo, Y, Klug, A (1997) Physical basis of a protein-DNA recognition code. Current Opinion in Structural Biology, 1, 117−125.
- Clark, KL, Hal ay, ED, Lai, E, Burley, SK. (1993) Co-crystal structure of the HNF-3/fork head DNA-recognition motif re-sembles histone H5. Nature, 364, 412−420.
- Claverie, J.-M. (1997) Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet. 6, 1735−1744.
- Coleman, R., Taggart, A., Benjamin, L., Pugh, B. (1995) Dimerization of the TATA binding protein./. Biol. Chem. 270, 13 842−13 849.
- Coleman, R.A., Pugh, B.F. (1995) Evidence for functional binding, stable sliding of the TATA binding protein on nonspecific DNA. J. Biol. Chem., 270, 13 850−13 859.
- Coleman, R.A., Pugh, B.F. (1997) Slow dimer dissociation of the NFNF binding protein dictates the kinetics of DNA binding. PNAS USA, 94, 7221−7226.
- Colgan, J., ManleyJ.L. (1995) Cooperation between core promoter elements influences transcriptional activity in vivo. Proc. Natl. Acad. Sci. USA, 92, 1955−1959.
- Conaway, R.C., Conaway, J.W. (1993) General initiation factors for RNA polymerase II. Annu. Rev. Biochem. 62, 161−190.
- Cox, JM, Hayward, MM, Sanchez, JF, Gegnas, LD, van der Zee, S, Dennis, JH, Sigler, PB, Schepartz, A (1997) Bidirectional binding of the TATA box binding protein to the TATA box. PNAS USA, 94, 13 475−13 480.
- Cox, JM, Kays, AR, Sanchez, JF, Schepartz, A (1998) Preinitation complex assembly: potentially a bumpy path. Curr Opin Chem Biol. 2, 11−17.
- Crowley, E.M., Roeder, K, Bina, M (1997) A statistical model for locating regulatory regions in genomic DNA, J. Mol. Biol., 268, 8−14.
- Davis, NA, Majee, SS, KahnJD (1999) TATA box DNA deformation with and without the TATA box-binding protein. J. Mol. Biol., 291, 249−265.
- Davis, NA, Majee, SS, KahnJD (1999) TATA box DNA deformation with and without the TATA box-binding protein. J Mol Biol, 291(2), 249−265.
- Deng QL, Ishii S, Sarai A. (1996) Binding site analysis of c-Myb: screening of potentialbinding sites by using the mutation matrix derived from systematic binding affinity measurements. Nucleic Acids Res., 24, 766−774.
- Diagana, T.T., North, D.L., Jabet, C., Fiszman, M.Y., Takeda, S., Whalen, R.G. (1997) The transcriptional activity of a muscle-specific promoter depends critically on the structure of the TATA element, its binding protein. J. Mol. Biol., 265, 480−493.
- Dickerson, R.E. (1983,) Base sequence, helix structure variation in B, A DNA. J. Mol. Biol., 166,419−425.
- Dickerson, R.E. et al. (1989a) Definitions, nomenclature of nucleic acid strucutre parameters. «EMBO Workshop». EMBOJ. 8. 1−5.
- Dickerson, R.E., Bansal, M., Calladine, C.R., Diekmann, S., Hunter, W.N., Kennard, 0.(1989b) Definitions, nomenclature of nucleic acid strucutre parameters. «EMBO Workshop». J. Mol. Biol. 205, 787−791.
- Dickerson, T.D., Drew, H.R. (1981) Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J. Mol. Biol. 149, 761−786.
- Drew, HR, Travers, AA (1985) DNA bending and its relation to nucleosome positioning. J Mol Biol., 186(4), 773−790.
- Drew, HR, Wing, RM, Takano, T, Broka, C, Tanaka, S, Itakura, K, Dickerson, RE (1981) Structure of a B-DNA dodecamer: conformation and dynamics. Proc Natl Acad Sci USA, 78(4), 2179−2183.
- Durbin, R, Dear, S (1998) Base qualities help sequencing software. Genome Res, 8(3), 161 162.
- Duret, L, Bucher, P (1997) Searching for regulatory elements in human noncoding sequences. Curr Opin Struct Biol, 7(3), 399−406.
- Eddy, SR (1996) Hidden Markov models. Curr Opin Struct Biol. 6(3), 361−365.
- Efron, B., Tibshirani, R.J. (1991) Statistical data analysis in the Computer Age. Science, 253, 390
- El Hassan, H.A., Calladine, C.R. (1995) The assessment of the geometry of dinucleotidesteps in double-helical DNA- a new local calculation scheme. J. Mol. Biol., 251, 648−664.
- El Hassan, H. A., Calladine, C.R. (1996) Propeller-twisting of base-pairs, the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol., 259, 95−103.
- El Hassan, M.A., Calladine, C.R. (1997) Conformational characterics of DNA: empirical classification, a hypothesis for the conformational behaviour of dinucleotide steps. Phil. Trans. Roy. Soc. ser. A, 355, 43−100.
- Ellenberger, T, Fass, D, Arnaud, M, Harrison, SC. (1994b) Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. Genes Dev., 8, 970 980.
- Ellenberger, T. (1994a) Getting a grip on DNArecognition: structures of the basic region leucine zipper, the basic region helix-loop-helix DNA-binding domains. Curr. Opin. Struct. Biol., A, 12−21.
- Ellenberger, TE, Brandl, CJ, Struhl, K, Harrison, SC. (1992) The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted -helices: crys-tal structure of the protein-DNA com-plex. Cell, 71, 1223−1237.
- Emami, K.H., Navarre, W.W., Smale, S.T. (1995) Core promoter specificities of the Spl, VP16 transcroptional activation domains. Mol. Cell Biol., 15, 5906−5916.
- Emili, A, Ingles, CJ (1995) Promoter-dependent photocross-linking of the acidic transcriptional activator E2F-1 to the TATA-binding protein. J. Biol. Chem., 270, 1 367 413 680.
- Etzold, T., Argos, P. (1993) SRS an indexing, retrieval tool for flat file data libraries. Comput. Applic. Biosci., 9, 49−57.
- Fairall, L, Schwabe, JW, Chapman, L, Finch, JT, Rhodes, D. (1993) The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNArecognition. Nature, 366, 483−487.
- Falvo, JV, Thanos, D, Maniatis, T. (1995) Reversal of intrinsic DNA bend in the IFN beta gene enhancer by transcription factors, architectural protein HMG I (Y). Cell, 83, 11 011 111.
- Felsenfeld, G. (1992) Chromatin as essential part of the transcription mechanism. Nature, 355, 219−224.
- Ferre-D'Amare, AR, Burley, SK. (1995) DNA recognition by helix-loop-helix proteins. Nucleic Acids Mol. Biol. 9:285−98
- Ferre-D'Amare, AR, Pognonec, P, Roeder, RG, Burley, SK. (1994) Structure, function of the b/HLH/Z domain of USF. EMBOJ. 13, 180−189.
- Ferre-D'Amare, AR, Prendergast, GC, Ziff, EB, Burley, SK. (1993) Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature, 363, 38−45.
- Fickett, JW, Wasserman, WW (2000) Discovery, modeling of transcriptional regulatory regions. Curr. Opin. Biothechnology, 11, 19−24.
- Fickett, J.W., Hatzigeorgiou, A.G. (1997) Eukaryotic promoter recognition. Genome Res., 1, 861−878.
- Fickett, JW (1996) Finding genes by computer: the state of the art. Trends Genet, 12(8), 316−320.
- Flatters, D., Lavery, R. (1998) Sequence-dependent dynamics of TATA-Box binding sites.1. Biophys. J., 75, 372−381.
- Forster, E., Ronr, B. (1979) Methoden der korrelations- und regressions analyse. Verlag Die Wirtschafit, Berlin.
- Freeh, K., Dietze, P., Werner, T. (1997b). Conslnspector 3.0: new library, enhanced functionality. Сотр. Applic. Biosci., 13, 109−110.
- Freeh, K., Herrmann, G., Werner, T. (1993). Computer-assisted prediction, classification, delimitation of protein binding sites in nucleic acids. Nucleic Acids Res., 21, 1655−1664.
- Freeh, K., Quandt, K., Werner, T. (1997a). Software for the analysis of DNA sequence elements of transcription. Сотр. Applic. Biosci., 13, 89−97.
- French, K., Quandt, K., Werner, T. (1998) Muscle actin genes: a first step towards computational classification of tissue specific promoters. In Sylico Biology, 1, 29−38.
- Gall, JG, Bellini, M, Wu, Z, Murphy, C. (1999) Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes. Mol Biol Cell, 10(12): 4385−4402.
- Gartenberg, M.R., Crothers, D.M., (1988) DNA sequence determinants of CAP-induced bending, protein binding affinity. Nature, 333, 824−829.
- Gelfand, M. (1995) Prediction of function in DNA sequence analysis. J. Comput. Biol., 2, 87−115.
- Gewirth, DT, Sigler, PB (1995) The basis for half-site specificity explored through a non-cognate steroid receptor-DNA complex. Nat Struct Biol., 2(5), 386−394.
- Ghosh, D. (2000) Object-oriented transcription factors database (ooTFD). Nucleic Acids Res., 28(1), 308−310.
- Ghosh, G, Duyne, GV, Ghosh, S, Sigler, PB. (1995) Structure of the NF-kappaB p50 homodimer bound to a kB site. Nature, 373, 303−310.
- Ghosh, G, Van Duyne, GD (1996) Pieces of the puzzle: assembling the preinitiation complex of Pol II. Structure. 4, 891−895.
- Glover, J.N., Harrison, S.C. (1995) Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature, 373, 257−261.
- Goodrich, JA, Schwartz, ML, McClure, WR (1990) Searching for predicting the activity of sites for DNA binding proteind: compilation, analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 18, 4993−5000.
- Goodsell, D.S., Dickerson, R.E. (1994) Bending, curvature calculations in B-DNA. Nucleic Acids Res. 22, 5497−5503.
- Gorin, A.A., Zhurkin, V.B., Olson, W.K., (1995) B-DNA twisting correlates with base-pair morphology. J. Mol. Biol., 247, 34−48.
- Gotoh, 0., Tagashira, Y. (1981) Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers, 20, 1033−1042.
- Grotewold, E, Drummond, BJ, Bowen, B, Peterson, T (1994) The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset. Cell, 76, 543−553.
- Grove, A, Galeone, A, Yu, E, Mayol, L, Geiduschek, EP (1998) Affinity, stability and polarity of binding of the TATA binding protein governed by flexure at the TATA Box. J. Mol. Biol., 282, 731−739
- Grzeskowiak, K. (1996) Sequence-dependent structural variation in B-DNA. Chem. Biol., 3, 785−790.
- Guigo, R. (1997) Computational gene identification: an open problem. Comput. Chem. 21, 215−222.
- Hagerman, P.J. (1984) Evidence for the existence of stable curvature of DNA in solution. Proc. Natl. Acad. Sci. USA 81, 4632−4636.
- Hahn, S. (1998) The role of TAFs in RNA polymerase II transcription. Cell, 95, 579−582.
- Hajek, P., Havranek, T. (1978) Mechanizing hypothesis formation Mathematical foundations for a general theory. Springer Verlag, Heidelberg.
- Hampsey, M. (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev. 1998 Jun-62(2):465−503. Review.
- Hampsey, M., Reinberg, D. (1999) RNA polymerase II as a control panel for multiple coactivator complexes. Curr. Opin. Gen. Dev., 9, 132−139.
- Hardenbol, P., Wang, J.C., van Dyke, M.W. (1997) Identification of preferred hTBP DNA binding sites by the combinatorial method REPSA. Nucleic Acids Res., 25, 3339−3344.
- Hawley, DK, McClure, WR (1983) Compilation, analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11, 2237−2255.
- Hegde, RS, Grossman, SR, Laimins, LA, Sigler, PB. (1992) Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature, 359, 505−512.
- Helmann, JD, Chamberlin, MJ (1988) Structure and function of bacterial sigma factors. Annu Rev Biochem, 51, 839−872
- Herrera, RE, Nordheim, A, Stewart, AF (1997) Chromatin structure analysis of the human c-fos promoter reveals a centrally positioned nucleosome. Chromosoma, 106(5), 284−292.
- Higo, K., Ugawa, Y., Iwamoto, M., Korenaga, T. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res., 27, 297−300.
- Hirsch, JA, Aggarwal, AK. (1995) Structure of the even-skipped homeodomain complexed with AT-rich DNA: new perspectives on homeodomain specificity. EMBO J., 14, 6280 -6291.
- Hirst, J.D., Sternberg, MJ (1992) Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks. Biochemistry, 31, 7211−7218.
- Hoffman, A, Sinn, E, Yamamoto, T, Wang, J, Roy, A, Horikoshi, M, Roeder, RG (1990) Highly conserved core domain and unique N terminus with presumptive regulatory motifs in a human TATA factor (TFIID). Nature, 346, 387−390.
- Hoffmann, A., Oelgeschlager, T., Roeder, R. (1997) Considerations of transcriptional control mechanisms: do TFIID-core promoter complexes recapitulate nucleosome-like functions? PNAS USA, 94, 8928−8935.
- Hogan, M.E., Austin, R.H. (1987) Importance of DNA stiffness in protein-DNA binding specificity. Nature, 329, 263−266.
- Hoopes, B.C., LeBlanc, J.F., Hawley, D.K. (1998) Contributions of the TATA box sequence to rate-limiting steps in transcription initiation by RNA polymerase II. J. Mol. Biol., 277, 1015−1031
- Houbaviy, H.B., Usheva, A., Shenk, T., Burley, S.K. (1996) Cocrystal structure of YY1 bound to the adeno-associated Virus P5 Initiator. Proc. Nat. Acad. Sci. USA, 93, 1 357 713 582.
- Howe, KM, Watson, RJ (1991) Nucleotide preferences in sequence-specific recognition of DNA by c-myb protein. Nucleic Acids Res, 19, 3913−3919.
- Hunter, C.A., Lu, X-J. (1997) DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 265, 603−619.
- Huth, JR, Bewley, CA, Nissen, MS, Evans, JN, Reeves, R, Gronenborn, AM, Clore, GM (1997) The solution structure of an HMG-I (Y)-DNA complex defines a new architectural minor groove binding motif. Nat Struct Biol, 4(8), 657−665.
- Hyde-DeRuyscher, R.P., Jennings, E., Shenk, T. (1995) DNA binding sites for the transcriptional activator/repressor YY1. Nucleic Acids Res., 23, 4457−4465.
- Ince, T., Scotto, K.W. (1995) A conserved downstream element defines a new class of RNA polymerase II promoters. J. Biol. Chem. 270, 30 249−30 252.
- Jackson, DA. (1997) Chromatin domains, nuclear compartments: establishing sites of gene expression in eukaryotic nuclei. Mol Biol Rep., 24, 209−220.
- Jacobson, EM, Peng, L, Leon-del-Rio, A, Rosenfeld, MG, Aggarwal, AK (1997) Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement, flexibility. Gen. Dev. 11, 198−212.
- Javahery, R, Khachi, A, Lo, K, Zenzie-Gregory, B, Smale, ST (1994) DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol. Cell Biol. 14, 116−127.
- Johnson, PF, McNight, SL (1989) Eukaryotic transcriptional regulatory proteins. Annu. Rev. Biochem., 58, 799−839.
- Jonsson, J., Norberg, T., Carlsson, L., Gustafsson, C., Wold, S. (1993) Quantitative sequence-activity models (QSAM) tools for sequence design. Nucleic Acids Res., 21, 733−739.
- Juo, Z.S., Chiu, T.K., Leiberman, P.M., Baikalov, I., Berk, A.J., Dickerson, R.E. (1996) How proteins recognize the TATA box. J. Mol. Biol., 261, 239−254.
- Kabsch, W., Sander, S., Trifonov, E.N. (1982) The ten helical twist angles of B-DNA. Nucleic Acids Res. 10, 1097−1104.
- Kadonaga, J.T. (1998) Eukaryotic transcription: an interlaced network of transcription factors, chromatin-modifying machines. Cell, 92, 307−317.
- Kahn, JD (2000) Topological effects of the TATA box binding protein on minicircle DNA and a possible thermodynamic linkage to chromatin remodeling. Biochemistry, 39(13), 3520−3524.
- Kaiser, К, Meisterernst, M (1996) The human general co-factors. Trends Biochem Sci. 21, 342−345.
- Karas, H., Knuppel, R., Schulz, W., Sklenar, H., Wingender, E., (1996) Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements. Comput. Applic. Biosci., 12, 441−446.
- Karlin, S., Brendel, V. (1992) Chance, statistical significance in protein, DNA sequence analysis. Science, 257, 39−49.
- Kaufmann, J, Smale, ST (1994) Direct recognition of initiator elements by a component of the transcription factor IID complex. Genes Dev, 8, 821−829.
- Kel, A, Kel-Margoulis, 0, Babenko, V, Wingender, E. (1999) Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells. J. Mol. Biol., 288, 353.
- Kel, AE, Kel-Margoulis, OV, Farnham, PJ, Bartley, SM, Wingender, E, Zhang, MQ (2001) Computer-assisted identification of cell cycle-related genes: new targets for E2 °F transcription factors. J Mol Biol, 309(1):99−120.
- Keller, W., Konig, P., Richmond, T.J. (1995) Crystal Structure of a bZIP/DNA Complex at 2.2 Angstroms: Determinants of DNA Specific Recognition. J. Mol. Biol., 254, 657−667.
- Kel-Margoulis OV, Romashchenko AG, Kolchanov NA, Wingender E, Kel AE (2000) COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res, 28(1), 311−315.
- Kim, J., de Haan, G., Shapiro, D.J. (1996) DNA bending between upstream activator sequences increases transcriptional synergy. Biochemical, Biophisical Res. Communications, 226, 638−644.
- Kim, J.L., Nikolov, D.B., Burley, S.K. (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520−527.
- Kim, Y., Geiger, J.H., Hahn, S., Sigler, P.B. (1993) Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512−520.
- Kirchhamer, C.V., Yuh, C.-H., Davidson, E.H. (1996) Modular cis-regulatory organization of developmentally exspressed genes transcribed territorially in the sea urchin embryo, additinal examples. Proc. Natl. Acad. Sci. USA, 93, 9322−9328.
- Kissinger, C.R., Liu, В., Martin-Blanco, E" Kornberg, T.B., Pabo, C.O. (1990) Crystal Structure of an Engrailed Homeodomain-DNA Complex at 2.8 Angstroms Resolution: A Framework for Understanding Homeodomain-DNA Interactions. Cell, 63, 579−590.
- Klages, N., Strubin, M. (1995) Stimulation of RNA polymerase II transcription initiation by recruitment of TBP in vivo. Nature, 374, 822−823.
- Klemm, JD, Rould, MA, Aurora, R, Herr, W, Pabo, CO. (1994) Crystal structure of the Oct-1 POU domain bound to an ос-tamer site: DNA recognition with teth-ered DNA-binding domains. Cell 77, 21−32.
- Klug, A. (1993) Transcription. Opening the gateway. Nature, 365, 486−487.
- Klug, A., Jack, A, Wiswamitra, M.A., Kennard, 0, Shakked, Z., Steitz, T.A. (1979) A hypothesis on a specific sequence-dependent conformation of DNA, its relation to the binding of the /ас-repressor protein. J. Mol. Biol. 131, 669−680.
- Klug, J, Knapp, S, Castro, I, Beato, M (1994) Two distinct factors bind to the rabbit uteroglobin TATA-box region and are required for efficient transcription. Mol Cell Biol, 14(9), 6208−6218.
- Knight, JC, Udalova, I, Hill, AV, Greenwood, BM, Peshu, N, Marsh, K, Kwiatkowski, D (1999) A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria. Nature Genetics, 22, 145−150.
- Kodandapani, R, Pio, F, Ni, C-Z, Piccailli, G, Klemsz, M, et al. (1996) A new pattern for helix-turn-helix recognition revealed by the PU. l Ets-domain-DNA complex. Nature 380, 456−459.
- Koleske, A., Young, R. (1995) The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem. Sci., 20, 113−116.
- Kondrakhin, Y.V., Kel, A.E., Kolchanov, N.A., Romashchenko, A.G., Milanesi, L. (1995) Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci., 11,477−488.
- Konig, P, Richmond, TJ. (1993) The X-ray structure of the GCN4-bZip bound to ATF/CREB site DNA shows the com-plex depends on DNA flexibility. J. Mol. Biol. 233, 139−154.
- Kono, H, Sarai, A (1999) Structure-based prediction of DNA taget sites by regulatory proteins. Proteins: Struct., Function, Genetics, 35, 114−131.
- Kornberg, R.D., Lorch, Y. (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell, 98, 285−294.
- Koudelka, G.B., Harrison, S.C., Ptashne, M. (1987) Effect of non-contacted bases on the affinity of 434 operator for 434 repressor, Cro. Nature, 326, 886−888.
- Kraus, R.J., Murray, E.E., Wiley, S.R., Zink, N.M., Loritz, K., Gelembiuk, G.W., Mertz, J.E. (1996) Experimentally determined weight matrix definitions of the initiator, TBP binding site elements of promoters. Nucleic Acids Res., 24, 1531−1539.
- Krogh, A. (1998) Guide to Human Genome Computing (2nd edn) (Bishop, M.J., ed.) Academic Press, 261−274.
- Lagrange, T, Kapanidis, AN, Tang, H, Reinberg, D, Ebright, RH (1998) New core promoter element in RNA polymerase Il-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev, 12(1), 34−44.
- Latchman, D.S. (1995) Eukaryotic transcription factors. Academic Press, London.
- Lavery, R., Zakrzewska, K., Sklenar, H. (1995) Сотр. Phys. Commun. 91, 135−158.
- Lawrence, CE, Gold, L, Stormo, GD (1994) Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res 22, 1287−1295.
- Lee, TI, Young, RA (1998) Regulation of gene expression by TBP-associated proteins. Genes Dev. 12(10):1398−408.
- Levitsky, V.G., Ponomarenko, M.P., Ponomarenko, J.V., Frolov, A.S., Kolchanov, N.A. (1999) Nucleosomal DNA property database. Bioinformatics, 15, 7/8, 582−592.
- Li, G, Chandler, SP, Wolffe, AP, Hall, TC (1998) Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon beta-phaseolin gene activation. Proc Natl Acad Sci USA, 95(8), 4772−4777.
- Li, Q, Wrange, 0 (1995) Accessibility of a glucocorticoid response element in a nucleosome depends on its rotational positioning. Mol Cell Biol., 15, 4375−4384.
- Li, Q, Wrange, 0, Eriksson, P (1997) The role of chromatin in transcriptional regulation. Int J Biochem Cell Biol., 29(5), 731−742.
- Li, T, Stark, MR, Johnson, AD, Wolberger, C. (1995) Crystal structure of the Matal/Mata2 homeodomain het-erodimer bound to DNA. Science, 270, 262−269.
- Liao, W.-C., Geng, Y., Johnson, L.F. (1994) In vitro transcription of the TATAA-less mouse thymidylate synthase promoter: multiple transcription start points, evidence for bidirectionality. Gene, 146, 183−189.
- Liston, DR, Johnson, PJ (1993) Analysis of a ubiquitous promoter element in a primitive eukaryote: early evolution of the initiator element. Moll Cell Biol, 19, 2380−2388.
- Love, JJ, Li, X, Case, DA, Giese, K, Grosschedl, R, et al. (1995) Structural basis by DNA bending by the architectural tran-scription factor LEF-1. Nature 376, 791−795.
- Lu, X-J., El Hassan, M.A., Hunter, C.A. (1997) Structure, conformation of helical nucleic acids: rebuilding program (SCHNArP). J. Mol. Biol. 273, 681−691.
- Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature, 389, 251−260.
- Luisi, BF, Xu WX, Otwinowski Z, Feedman LP, Yamamoto KR, et al. (1991) Crystallographic analysis of the interac-tion of the glucocorticoid receptor with DNA. Nature, 352, 497−505.
- Ma, PCM, Rould, MA, Weintraub, H, Pabo, CO. (1994) Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition, implications for transcriptional activation. Cell 77, 451−459.
- Marmorstein, R, Carey, M, Ptashne, M, Harrison, SC. (1992) DNA recognition by Gal4: structure of a protein-DNA complex. Nature, 356, 408−414.
- Marmorstein, R, Harrison, SC. (1994) Crystal structure of a PPR1-DNA com-plex: DNA recognition by proteins containing a Zn 2 Cys 6 binuclear cluster. Genes Dev. 8, 25 042 512.
- Marth, G., Yeh, R., Minton, M., Donaldson, R., Li, Q., Duan, S., Davenport, R., Miller, R.D., and Kwok, P.-Y. (2001) Single-nucleotide polymorphisms in the public domain: how useful are they? Nat. Genet., 27, 371−372.
- Matthews, BW. (1988) Protein-DNA interaction. No code for recognition. Nature 335, 294 295.
- McCormick, A, Brady, H, Fukushima, J, Karin, M. (1991) The pituitary-specific regulatory gene GHF1 contains a minimal cell type-specific promoter centered around its TATA box. Genes Dev, 5, 1490 1503.
- McKnight, S.L., Yamamoto, K.R. (1992) Transcriptional regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
- Meierhans, D., Allemann, R. K (1998) The N-terminal methionine is a major determinant of the DNA binding specificity of MEF-2C. J. Biol. Chem., 273, 26 052−26 060
- Meierhans, D., Sieber, M., Allemann, R.K. (1997) High affinity binding of MEF-2C correlates with DNA bending. Nucleic Acids Res., 25, 4537−4544.
- Milanesi, L., Muselli, M., Arrigo, P. (1996) Hamming clustering method for signals prediction in 5', 3' regions of eukaryotic genes. Comput. Appl. Biosci. 12, 399−404.
- Montecino, M, Lian, J, Stein, G, Stein, J (1996) Changes in chromatin structure support constitutive and developmentally regulated transcription of the bone-specific osteocalcin gene in osteoblastic cells. Biochemistry, 35(15), 5093−5102.
- Muller, CW, Rey, FA, Sodeoka, M, Verdine, GL, Harrison, SC. (1995) Structure of the NF-kB p50 homodimer bound to DNA. Nature 373, 311−317.
- Mulligan, M.E., Hawley, D.K., Entriken, R., McClure, W.R. (1984) Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res., 12, 789−800.
- Myer, V.E., Young, R.A. (1998) RNA polymerase II holoenzymes, subcomplexes. J. Biol. Chem., 273, 27 757−27 760.
- Nandi, A, Das, G, Salzman, NP (1985) Characterization of a surrogate TATA box promoter that regulates in vitro transcription of the simian virus 40 major late gene. Mol Cell Biol., 5(3), 591−594.
- Neidle, S. (1994) DNA structure, recognition. New York: IRL Press.
- Ng, KW, Ridgway, P, Cohen, DR, Tremethick, DJ (1997) The binding of Fos/Jun heterodimer can completely disrupt the structure of nucleosome. EMBO, 16, 2072−2085.
- Nikolov, DB, Burley, SK (1997) RNA polymerase II transcription initiation: A structural view. Proc. Natl. Acad. Sci., 94, 15−22.
- Nikolov, DB, Chen, H, Halay, ED, Hoffmann, A, Roeder, RG, et al. (1996) Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl. Acad. Sci. USA 93,4956−4961.
- Novina, CD, Roy, AL (1996) Core promoters, transcriptional control. Trends Genet., 12(9), 351−355.
- Nussinov, R. (1985) Large helical conformational deviations from ideal B-DNA, procaryotic regulatory sites. J. Theor. Biol. 115, 179−189.
- O’Neill, M.C. (1990) Training back-propagation neural networks о define, detect DNA-binding sites. Nucleic Acids Res. 19, 313−318.
- Ogata, K, Morikawa, S, Nakamura, H, Serikawa, A, Inoue, T, et al. (1994) Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell 79, 639−648.
- Ohler, U., Niemann, H, Liao, Gc, Rubin, GM (2001) Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics, 17 Suppl l: S199−206.
- Orphanides, G, Lagrange, T, Reinberg, D (1996) The general transcription factors of RNA polymerase II. Genes Dev 10, 2657−2683.
- Owen-Hughes, Т., Workman, J.L. (1994) Experimental analysis of chromatin function in transcriptional control. Crit. Rev. Euk. Gene Expr. 8, 1−39.
- Pabo, CO, Sauer, RT. (1992) Transcription factors: structural families, principles of DNA recognition. Annu. Rev. Biochem. 61, 1053−1095.
- Papavassilious, A.G. (1997) Transcription factors in eukaryotes. Springer-Verlag GmbH & Co. KG, Heidelberg, Germany.
- Parvin, J, McCormick, R, Sharp, P, Fisher, D. (1995) Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor. Nature 273, 724—727.
- Patikoglou, G., Burley, S.K. (1997) Eukaryotic transcription factor-DNA complexes. Annu Rev Biophys Biomol Struct. 26, 289−325.
- Pauly, M, Treger, M, Westhof, E, Chambon, P (1992) The initiation accuracy of the SV40 early transcription is determined by the functional domains of two TATA elements. Nucleic Acids Res, 20, 975 982.
- Pavletich, NP, Pabo, CO (1991) Zinc finger-DNA recognition: crystal struc-ture of a Zif268-DNA complex at 2.1 ° A. Science 252, 809−817.
- Pavletich, NP, Pabo, CO (1993) Crystal structure of a five-finger GLI-DNAcom-plex: new perspectives on zinc fingers. Science 261, 1701−1707.
- Pazin, MJ, Sheridan, PL et al. (1996) NF-kappa B-mediated chromatin reconfiguration, transcriptional activation of the HIV-1 enhancer in vitro. Genes Dev., 10, 37−49.
- Pedersen, AG, Baldi, P, Brunak, S, Chauvin, Y (1996) Characterization of prokaryotic and eukaryotic promoters using hidden Markov models. Proc Int Conf Intell Syst Mol Biol 4, 182−191.
- Pedersen, AG, Baldi, P, Brunak, S, Chauvin, Y (1998) DNA structure in human RNA polymerase II promoters. J Mol Biol, 281(4), 663−673.
- Pellegrini, L, Tan, S, Richmond, TJ (1995) Structure of serum response fac-tor core bound to DNA. Nature 376, 490−498.
- PerierRC, Praz, V, Junier, T, Bonnard, C, Bucher, P (2000) The eukaryotic promoter database (EPD). Nucleic Acids Res 28(1), 302−303.
- Pickert, L., Reuter, I, Klawonn, F, Wingender, E (1998) Transcription regulatory region analysis using signal detection, fuzzy clustering, Bioinformatics, 14, 244−251.
- Pio, F, Kodandapani R, Ni CZ, Shepard W, Klemsz M, McKercher SR, Maki RA, Ely KR (1996) New insights on DNA recognition by ets proteins from the crystal structure of the PU. l ETS domain-DNA complex. J Biol Chem, 271(38), 23 329−23 337.
- Ponomarenko, J.V., Ponomarenko, M.P., Frolov, A.S., Vorobyev, D.G., Overton, G.C., Kolchanov, N.A. (1999) Conformational, physicochemical DNA features specific for transcription factor binding sites. Bioinformatics, 15, 7/8, 654−668.
- Ponomarenko, M.P., Kolchanova, A.N., Kolchanov, N.A. (1997) Generating programs for predicting the activity of functional sites. J. Comput. Biol., 4, 83−90.
- Ponomarenko, M.P., Ponomarenko, J.V., Kel, A.E., Kolchanov, N.A. (1997) Search for DNA conformational features for functional sites. Investigation of the TATA box. Proceedings of the 1997 Pacific Symposium. Altman, R. (ed), Singapore, World Sci., 340−351.
- Ponomarenko, M.P., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.G., Kolchanov N.A., Overton G.C. (1999) Oligonucleotide frequency matrices addressed to recognising functional DNA sites. Bioinformatics, 15, 7/8, 631−643.
- Prestridge, D.S. (1996) SIGNAL SCAN 4.0: additional databases and sequence formats. Comput Appl Biosci. 12(2), 157−160.
- Prestridge, D.S. (1999) Computer software for eukaryotic promoter analysis. Methods Mol Biol. 130, 265−295.
- Pugh, BF (1996) Mechanisms of transcription complex assembly. Curr Opin Cell Biol. 8(3), 303−311.
- Quandt, K., Freeh, K" Karas, H., Wingender, E., Werner, T. (1995b). Matlnd, Matlnspector: new fast, versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878−4884.
- Ranish, JA, Hahn, S, (1996) Transcription: basal factors, activation. Curr. Opin. Genetics Dev., в, 151−158.
- Rao, A, Luo, C., Hogan, PG (1997) Transcription factors of NFAT family: regulation, function. Ann. Rev. Immunol., 15, 707−747.
- Rastinejad, F, Perlmann, T, Evans, RM, Sigler, PB. (1995) Structural determinants of nuclear receptor assembly on DNAdi-rectrepeats. Nature 375, 203−211.
- Rippe, K., Vonhippel, P.H., Langowski, J. (1995) Action at a distance: DNA-looping, initiation of transcription. Trends Biochem. Sci. 20, 500−506.
- Roberts, R.W., Ja, W.W. (1999) In vitro selection of nucleic acids and proteins: what are we learning? Curr. Opin. Struct. Biol., 9, 521−529.
- Robison, K., McGuire, A.M., Church, G.M. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol., 284, 241−254.
- Roeder, RG (1991) The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly. Trends Biochem Sci. 16(11), 402−408.
- Roeder, RG (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci. 21(9), 327−335.
- Rombauts, S, DMiais, P., Van Montagu, M., Rouzfi, P. (1999) PlantCARE, a plant czs-acting regulatory element database. Nucleic Acids Res., 27, 295−296.
- Roses, A.D. (2000) Pharmacogenetics and the practice of medicine. Nature, 405, 857−865
- Rost, B. (1990) Some basic principles of neural networks. Heidelberg, EMBL, preprint 28.
- Roulet, E, Bucher, P, Schneider, R, Wingender, E, Dusserre, Y, Werner, T, Mermod, N (1999) Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J. Mol. Biol., 297(4), 833−848.
- Roulet, E., Fisch, I., Bucher, P., Mermod, N. (1998) Evaluation of computer tools for prediction of transcription factor binding sites on genomic DNA. In Silico Biology, 1,2128.
- Sadovsky, Y, Webb, P, Lopez G, Baxter JD, Fitzpatrick PM, Gizang-Ginsberg E, Cavailles V, Parker MG, Kushner PJ (1995) Transcriptional activators differ in their responses to overexpression of TATA-binding protein. Mol. Cell Biol., 15, 1554−1563.
- Salgado, H., Santos, A., Garza-Ramos, U., van Helden, J., Diaz, E., Collado-Vides, J. (1999) RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res., 27, 59−60
- Sarai, A, Takeda, Y (1989) Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc Natl Acad Sci USA, 86, 65 136 517.
- Sarai, A., Mazur, J., Nussinov, R., Jernigan, R.L. (1988) Origin of DNA helical structure, its sequence dependence. Biochemistry, 27, 8498−8502.
- Sarai, A., Mazur, J., Nussinov, R., Jernigan, R.L. (1989) Sequence dependence of DNA conformational flexibility. Biochemistry, 28, 7842−7849.
- Satchwell, S.C., Drew, R., Travers, A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol., 191, 659−675
- Schmiedeskamp, M., Klevit, R.E. (1994) Zinc finger diversity. Curr. Opin. Struct. Biol. 4, 28−35.
- Schneider, T.D., Stormo, G.D., Gold, L., Ehrenfeucht, A. (1986) Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415−431
- Schneider, TD, Stephens, RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res, 18(20), 6097−6100.
- Schug, J., Overton, G. C. (1997). TESS: Transcription Element Search Software on the WWW. Technical Report CBIL-TR-1997−1001-vO.O of the Computational Biology, Informatics Laboratory, School of Medicine, University of Pennsylvania, 1997
- Schwabe, JWR, Chapman, L, Finch, JT, Rhodes, D. (1993) The crystal structure of the oestrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response el-ements. Cell 75, 567−578.
- Seledtsov, IA, Solovyev, VV, Merkulova, TI (1991) New elements of glucocorticoid-receptor binding sites of hormone-regulated genes. Biochim Biophys Acta, 1089(3), 367−376.
- Shakked, Z, Rabinovich, D (1986) The effect of the base sequence on the fine structure of the DNA double helix. Prog. Biophys. Molec. Biol., 47, 159−195.
- Shapiro, B. A, Nussinov R, Lipkin LE, Maizel JV Jr (1986) A sequence analysis system encompassing rules for DNA helical distortion. Nucleic Acids Res. 14, 75−86.
- Shim, Y.H., Bonner, J. J., Blumenthal, T. (1995) Activity of a C. elegans GATA transcription factor, ELT-1, expressed in RT yeast. J. Mol. Biol., 253, 665−676.
- Shimizu, T, Toumoto A, Ihara K, Shimizu M, Kyogoku Y, Ogawa N, Oshima Y, Hakoshima T (1997) Crystal structure of PH04 bHLH domain-DNA complex: flanking base recognition. EMBO J, 16(15), 4689−4697.
- Shpigelman, E.S., Trifonov, E.N., Bolshoy, A. (1993) CURVATURE: software for the analysis of curved DNA. Comput. Appl. Biosci., 9, 435−140.
- Sjottem, E., Nersen, C., Johansen, T. (1997) Structural, functional analyses of DNA bending induced by Spl family transcription factors. J. Mol. Biol., 267, 490−504.
- Sklenar, H. (1996) Proceedings of the International Workshop on Computational analysis of eukaryotic transcriptional regulatory elements / H: GBF. 1996. P. 44−47.
- Smale, S. T (1997) Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim Biophys Acta. 1351(1−2), 73−88.
- Smale, S.T., Baltimore, D. (1989) The «initiator» as a trnscription control element. Cell, 57, 103−113.
- Sokolenko, AA, Sandomirskii, II, Savinkova, LK (1996) Interaction of yeast TATA-binding protein with short promotor segments. Mol Biol (Mosk) 30(2), 279−85.
- Solano, R, Nieto, C, Avila, J, Canas, L, Diaz, I, Paz-Ares, J (1995) Dual DNA binding specificity of a petal epidermis-specific MYB transcription factor (MYB.Ph3) from Petunia hybrida. EMBO J, 14, 1773−1784.
- Solovyev, V.V., Salamov, A.A., Lawrence, C.B. (1994a) Predicting internal exons by oligonucleotide composition, discriminant analysis of spliceable open reading frames. Nucleic Acids Res., 22, 5156−5163.
- Spek, CA, Lannoy, VJ, Lemaigre, FP, Rousseau, GG, Bertina, RM, Reitsma, PH (1998) Type I protein С deficiency caused by disruption of a hepatocyte nuclear factor (HNF)-6/HNF-l binding site in the human protein С gene promoter. J Biol Chem, 273, 10 168−10 173.
- Sponer, J., Kyrp, J. (1993) Theoretical analysis of the base stacking in DNA choice of the force-field, a comparison with the oligonucleotide crystal-structures. J. Biomol. Struct.1. Dynam. 11,277−292.
- Staden, R (1989) Methods for calculating the probabilities of finding patterns in sequences. Comput Appl Biosci. 5(2), 89−96.
- Staden, R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucl. Acids Res. 12, 505−519.
- Stamatoyannopoulos"J.A., Clegg, C.H., Li, Q. (1997) Sheltering of gamma-globin expression from position effects requires both an upstream locus control region, a regulatory element 3' to the (A)gamma-globin gene. Mol. Cell Biol. 17, 240−247.
- Starich, MR, Wikstrom, M, Arst, HN Jr, Clore, GM, Gronenborn, AM (1998) The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factor. J. Mol. Biol., 277, 605−620.
- Starr, D.B., Hoopes, B.C., Hawley, D.K. (1995) DNA bending is an important component of site-specific recognition by the TATA binding protein. J. Mol. Biol., 250, 434−446.
- Steitz, TA (1990) Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q. Rev. Biophys. 23, 105−180.
- Stepchenko, AG (1994) Noncanonical Oct-sequences are targets for mouse Oct-2B transcription factor. FEBSLett, 337, 175 178.
- Stoeckert, JrC.J., Salas, F., Brunk, B., Overton, G.C. (1999) EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis. Nucleic Acids Res., 27, 200−203
- Stormo, G.D., Schneider, T.D., Gold, L. (1986) Quantitative analysis of the relationship between nucleotide sequence, functional activity. Nucleic Acids Res., 14, 6661−6679.
- Stormo, GD (1990) Consensus patterns in DNA. Methods Enzymol. 183, 211−221.
- Stormo, GD, Schneider, TD, Gold, L, Ehrenfeucht, A (1982) Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res, 10(9), 2997−3011.
- Sugimoto, N, Nakano, S., Yoneyama, M., Honda, K. (1996) Improved thermodynamic parameters, helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res., 24, 4501−4505.
- Suzuki, M. (1994) A framework for the DNA-protein recognition code. Structure, 2, 317 326.
- Suzuki, M., Amano, N., Kakinuma, J., Tateno, M. (1997) Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA. J. Mol. Biol., 274, 421 435.
- Suzuki, M., Yagi, N. (1995) Stereochemical basis of DNA bending by transcription factors. Nucleic Acids Res., 23, 2083−2091.
- Suzuki, M., Yagi, N., Finch, J.T. (1996) Role of base-backbone, base-base interactions in alternating DNA conformations. FEBSL., 379, 148−152.
- Sykes, K., Kaufman, R. (1990) A naturally occurring gamma globin gene mutation enhances SP1 binding activity. Mol. Cell Biol., 10, 95−102.
- Swaminathan, K., Flynn, P., Reece, RJ, Marmostein, R. (1997) Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster. Nature Struct. Biology, 4, 751−759.
- Tachibana, H, Ishihama, A (1985) Correlation between the rate of productive transcription initiation and the strand-melting property of Escherichia coli promoters. Nucleic Acids Res, 13(24), 9031−9042.
- Taggart, A.K., Pugh, B.F. (1996) Dimerizasion of TFIID when not bound to DNA. Science, 272,1331−1333.
- Takeda, Y, Sarai, A, Rivera, VM (1989) Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments. Proc Natl Acad Sci USA, 86, 439−443.
- Tan, S, Richmond, TJ (1998) Eukaryotic transcription factors. Curr Opin Struct Biol. 8(1), 41−48.
- Tanikawa J, Yasukawa T, Enari M, Ogata K, Nishimura Y, Ishii S, Sarai A (1993) Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain. Proc Natl Acad Sci USA, 90, 9320−9324.
- Taylor, 1С, Workman, JL, Schuetz, TJ, Kingston, RE (1991) Facilitated binding of GAL4, heat shock factor to nucleosomal templates: differential function of DNA-binding domains. Genes Dev 5, 1285−1298.
- Tjian, R (1996) The biochemistry of transcription in eukaryotes: a paradigm for multisubunit regulatory complexes. Philos Trans R Soc bond В Biol Sci. 351(1339), 491 499.
- Travers, A (1996) Transcription: building an initiation machine. Curr Biol. 6(4), 401−403.
- Trifonov, E.N. (1982) Sequence-dependent variations of B-DNA structure, protein-DNA recognition. Cold Spring Harbor Symp. Quant. Biol. 47, 271−278.
- Tranche, F, Ringeisen F, Blumenfeld M, Yaniv M, Pontoglio M (1997) Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J Mol Biol, 266(2), 231−245.
- Usheva, A., Shenk, T. (1994) TATA-binding protein-independent initiation: YY1, TFIIB, RNA polymerase II direct basal transcription on supercoiled template DNA. Cell, 76, 11 151 121.
- Van Dyke, M., Roeder R.G., Sawadogo M. (1988) Physical analysis of transcription preinitiation complex assembly on a class II gene promoter. Science 241, 1335−1338.
- Verrijzer, CP, Tjian, R. (1996) TAFs mediate transcriptional activation, promoter selectivity. Trends Bio chem Sci. 21(9), 338−342.
- Wang, A.H.-J., Fujii, S., van Boom, J.H., Rich, A. (1982) Molecular structure of the octamer d (GGCCGGCC): modified A-DNA. Proc. Natl. Acad. Sci. USA. 79, 3968−3972.
- Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G., Rich, A. (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature, 282, 680−686.
- Wang, JC, Van Dyke, MW (1993) Initiator sequences direct downstream promoter binding by human transcription factor IID. Biochim Biophys Acta, 1216(1), 73−80
- Wasserman, WW, Fickett, JW (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol., 278, 167−181.
- Watson, J.D., Crick, F.H.C. (1953) Nature, 171, 737
- Weis, L, Reinberg, D (1997) Accurate positioning of RNA polymerase II on a natural TATA-less promoter is independent of TATA-binding-protein-associated factors, initiator-binding proteins. Mol Cell Biol., 17, 2973−2984.
- Werner, M, Huth J, Gronenborn A, Clore M. (1995) Molecular basis of human 46X, Y sex reversal revealed from the three-dimensional structure of the hu-man SRY-DNA complex. Cell 81, 705−714.
- Werner, MH, Clore GM, Fisher CL, Fisher RJ, Trihn L, et al. (1996) The solution structure of the human Etsl-DNA complex reveals a novel mode of DNA binding, true side chain intercalation. Cell 83, 761−771.
- Werner, T (1999) Models for prediction and recognition of eukaryotic promoters. Mamm Genome. 10(2), 168−175.
- Weston, K. (1992) Extension of the DNA binding consensus of the chicken c-Myb and v-Myb proteins. Nucleic Acids Res., 20, 3043−3049.
- Wieczorek, E., Brand, M., Jacq, X., Tora, L. (1998) Function of TAF-containing complex without TBP in transcription by RNA polymerase II. Nature, 393, 187−191.
- Wiley, S.R., Kraus, R.J., Mertz, J.E. (1992) Functional binding of the «TATA» box binding component of transcription factor TFIID to the -30 region of TATA-less promoters. Proc Natl Acad Sci U.S.A., 89, 5814−5818.
- Wilson, DS, Guenther, B, Desplan, C, Kuriyan, J. (1995) Crystal structure of a paired (PAX) class cooperative home-odomain dimer on DNA. Cell 82:709−19
- Wing, R.M., Drew, H.R., et al. (1980) Crystal structure analysis of a complete turn of B-DNA. Nature, 287, 755−758.
- Wingender, E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res, 28(1), 316−319.
- Wingender, E. (1993) Gene Regulation in Eukariotes. VCH, Germany.
- Wolberger, C, Vershon, AK, Liu, B, Johnson, AD, Pabo, C (1991) Crystal structure of a MAT2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell 67, 517−528.
- Wolfertstetter, F., Freeh, K., Herrmann, G., Werner, T. (1996). Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Сотр. Appl. Biosci., 12, 71−80.
- Wolffe, A.P., Hayes, J.J. (1999) Chromatin disruption, modification. Nucl. Acids Res., 27, 711−720.
- Wolffe, AP (1994) Transcriptional activation. Switched-on chromatin. Curr Biol. 4(6), 525 528.
- Wolffe, AP, Kurumizaka, H (1998) The nucleosome: a powerful regulator of transcription. Prog Nucleic Acid Res Mol Biol. 61, 379−422.
- Workman, JL, Kingston, RE (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem 67, 545−579.
- Wuttke, DS, Foster, MP, Case, DA, Gottesfeld, JM, Wright, PE (1997) Ssolution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity, sequence specificity. J. Mol. Biol. 273, 183−206.-225
- Xu, W, Rould, MA, Jun, S, Desplan, C, Pabo, CO (1995) Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations. Cell 80, 639−650.
- Yanagi, K., Prive, G.D., Dickerson, R.E. (1991) An analysis of local helix geometry in three decamers, eight dodecamers. J. Mol. Biol., 217, 201−214.
- Yean, D., Gralla, J. (1997) Transcription reinitiation rate: a special role for the TATA box. Mol. Cell Biol., 17, 3809−3816.
- Zadeh, L.A. (1965) Fuzzi sets. Information, Control. 8, 338−353.
- Zawel, L., Reinberg, D. (1995) Common themes in assembly, function of eukaryotic transcription complexes. Annu. Rev. Biochem. 64, 533−561.
- Zhao, YY, Zhou, J, Narayanan, CS, Cui, Y, Kumar, A (1999) Role of C/A polymorphism at -20 on the expression of human angiotensinogen gene. Hyperstension, 33, 108−115.
- Zhu, J, Zhang, MQ (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15(7−8), 607−611.
- Zhurkin, V.B. (1983) Local mobility in the DNA double helix: comparison of conformational calculations with experiment. J. Mol. Biol. 17, 495−509.