Recognition of regulatory sites by genomic comparison

Research in Microbiology

Volumn 150, Issue 9-10, 1999, Pages 755-771

  Gelfand, Mikhail S ^a  

^a Stt Res Ctr for Biotech G   (Russian Federation)

Author keywords

Activator; Complete genome; Computer analysis; Operator; Regulation; Repressor; Transcription

Indexed keywords

DNA;

ARCHAEBACTERIUM; DNA FINGERPRINTING; EUBACTERIUM; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REGULATOR GENE; REVIEW; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 0033374594     PISSN: 09232508     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0923-2508(99)00117-5     Document Type: Article

References (167)

1. Ansari-Lari M.A., Oeltjen J.C., Schwartz S., Zhang Z., Muzny D.M., Lu J., Gorrell J.H., Chinault A.C., Belmont J.W., Miller W., Gibbs R.A. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Res. 8:1998;29-40.
2. Aparicio S., Morrison A., Gould A., Gilthorpe J., Chaudhuri C., Rigby P., Krumlauf R., Brenner S. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl. Acad. Sci. USA. 92:1995;1684-1688.
3. Auerbach S., Gao J., Gussin G.N. Nucleotide sequences of the trpI, trpB, and trpA genes of Pseudomonas syringae: positive control unique to fluorescent pseudomonads. Gene. 123:1993;25-32.
4. Babitzke P. Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel. Mol. Microbiol. 26:1997;1-9.
5. Bart A., Dankert J., vander Ende A. Operator sequences for the regulatory proteins of restriction-modification systems. Mol. Microbiol. 31:1999;1277-1278.
6. Bell A.I., Gaston K.L., Cole J., Busby S.J.W. Cloning of binding sequences for the Escherichia coli transcription activators FNR and CRP, location of bases involved in discrimination between FNR and CRP. Nucleic Acids Res. 17:1989;3865-3874.
7. Berg O.G., VonHippel P.H. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193:1987;723-750.
8. Berg O.G. Selection of DNA binding sites by regulatory proteins. Functional specificity and pseudosite competition. J. Biomol. Struct. Dyn. 6:1988;275-297.
9. Berg O.G. Selection of DNA binding sites by regulatory proteins: the LexA and the arginine repressor use different strategies for functional specificity. Nucleic Acids Res. 16:1988;5089-5105.
10. Billoud B., Kontic M., Viari A. Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database. Nucleic Acids Res. 24:1996;1395-1403.
11. Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M., Yuan Y. Predicting function: From genes to genomes and back. J. Mol. Biol. 283:1998;707-725.
12. Bourn W.R., Babb B. Computer assisted identification and classification of streptomycete promoters. Nucleic Acids Res. 23:1995;3696-3703.
13. Bsat N., Herbig A., Casillas-Martinez L., Setlow P., Helmann J.D. Bacillus subtilis contains multiple Fur homologues: identification of the iron uptake (Fur) and peroxide regulon (PerR) repressors. Mol. Microbiol. 29:1998;189-198.
14. Bucca G., Ferina G., Puglia A.M., Smith C.P. The dnaK operon of Streptomyces coelicolor encodes a novel heat-shock protein which binds to the promoter region of the operon. Mol. Microbiol. 17:1995;663-674.
15. Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated sequences. J. Mol. Biol. 212:1990;563-578.
16. Cardon L.R., Stormo G.D. Expectation maximization algorithm for identifying protein-binding sites with variable length from unaligned DNA fragments. J. Mol. Biol. 223:1992;159-170.
17. Chen Q.K., Hertz G.Z., Stormo G.D. MATRIX SEARCH 1. 0: A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci. 11:1995;563-566.
18. Chen Q.K., Hertz G.Z., Stormo G.D. PromFD 1. 0: A computer program that predicts eukaryotic polII promoters using strings and IMD matrices. Comput. Appl. Biosci. 13:1997;29-35.
19. Claverie J.M., Audic S. The statistical significance of nucleotide position-weight matrix matches. Comput. Appl. Biosci. 12:1996;431-439.
20. Cohen M.B., Koener J.F., Feyereisen R. Structure and chromosomal localization of CYP6A1, a cytochrome P450-encoding gene from the house fly. Gene. 146:1994;267-272.
21. Dandekar T., Snel B., Huynen M.A., Bork P. Conservation of gene order: a fingerprint of physically interacting proteins. Trends Biochem. Sci. 23:1998;324-328.
22. Dandekar T., Beyer K., Bork P., Kenealy M.R., Pantopoulos K., Hentze M., Sonntag-Buck V., Flouriot G., Cannon F., Keller W., Schreiber S. Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches. Bioinformatics. 14:1999;271-278.
23. Darwin A.J., Stewart V. The narmo dulon systems: nitrate and nitrite regulation of anaerobic gene c expression. Line C.C, Lynch A.S. Regulation of Gene Expression inEscherichia coli. 1996;343-359 R.G. Landes Company, Austin TX.
24. Darwin A.J., Tyson K.L., Busby S.J.W., Stewart V. Differential regulation by the homologous NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement. Mol. Microbiol. 25:1997;583-595.
25. Day W.H.E., McMorris F.R. Critical comparison of consensus methods for molecular sequences. Nucleic Acids Res. 20:1992;1093-1099.
26. Delihas N. Regulation of gene expression by trans-encoded antisense RNAs. Mol. Microbiol. 15:1995;411-414.
27. De Lorenzo V., Perez-Martin J. Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals. Mol. Microbiol. 19:1996;1177-1184.
28. Demeler B., Zhou G. Neural network optimization for E. coli promoter prediction. Nucleic Acids Res. 19:1991;1593-1599.
29. Derre I., Rapoport G., Msadek T. CtsR, a novel regulator of stress and heat shock response, controls clp and molecular chaperone gene expression in Gram-positive bacteria. Mol. Microbiol. 31:1999;117-131.
30. Dhawale S.S., Lane A.C. Compilation of sequence-specific DNA-binding proteins implicated in transcriptional control in fungi. Nucleic Acids Res. 21:1993;5537-5546.
31. Duret L., Dorkeld F., Gautier C. Strong conservation of non-coding sequences during vertebrates evolution - potential involvement in post-translational regulation of gene expression. Nucleic Acids Res. 21:1993;2315-2322.
32. Duret L., Bucher P. Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol. 7:1997;399-406.
33. Ebright R.H. Transcription activation at class II CAP-dependent promoters. Mol. Microbiol. 8:1993;797-802.
34. Eddy S.R. Hidden Markov models. Curr. Opin. Struct. Biol. 6:1996;361-365.
35. Espinosa-Urgel M., Chamizo C., Tormo A. A consensus structure for (S-dependent promoters. Mol. Microbiol. 21:1996;657-659.
36. Ferreyra R., Soncini F., Viale A.M. Cloning, characterization, and functional expression in Escherichia coli of chaperonin (groESL) genes from the sulfur phototrophic bacterium Chromatium vinosum. J. Bacteriol. 175:1993;1514-1523.
37. Fickett J.W., Hatzigeorgiou A.G. Eukaryotic promoter recognition. Genome Res. 7:1997;861-878.
38. Fickett J.W. Coordinate positioning of MEF-2 and myogenin binding sites. Gene. 172:1996;GC19-GC32.
39. Fournier T., Mejdoubi N., Lapoumeroulie C., Hamelin J., Durand G., Porquet D. Transcriptional regulation of rat alpha 1-acid glycoprotein gene by phenobarbital. J. Biol. Chem. 269:1994;27175-27178.
40. Frech K., Quandt K., Werner T. Software for the analysis of DNA sequence elements of transcription. Comput. Appl. Biosci. 13:1997;89-97.
41. Frech K., Quandt K., Werner T. Muscle actin genes: A first step towards computational classification of tissue specific promoters. Silico Biol. 1998;. http://www.bioinfo.de/isb/1998/01/0005.
42. Galas D.J., Eggert M., Waterman M.S. Rigorous pattern-recognition methods for DNA sequences: analysis of promoter sequences from Escherichia coli. J. Mol. Biol. 186:1985;117-128.
43. Gelfand M.S. Prediction of function in DNA sequence analysis. J. Comput. Biol. 2:1995;87-115.
44. Gelfand M.S., Mironov A.A. Computer analysis of regulatory patterns in complete bacterial genomes. LexA and DinR binding sites, (In Russian, Engl. transl.). Mol. Biol. 33:1999;439-442.
45. Gelfand M.S., Miornov A.A., Jomantas J., Kozlov Y.U.I., Perumov D.A. A conserved RNA structure element involved in regulation of bacterial ribioflavin genes. Trends Genet. 15:1999;. in press.
46. Ghosh D. OOTFD (Object-Oriented Transcription Factors Database): an object-oriented successor to TFD. Nucleic Acids Res. 26:1998;360-361.
47. Goldstein L., Waterman M.S. Approximations to profile score distributions. J. Comput. Biol. 1:1994;93-104.
48. Gonzales-Gil G., Bringmann P., Kahmann R. FIS is a regulator of metabolism in Escherichia coli. Mol. Microbiol. 22:1996;21-29.
49. Goodrich J.A., Schwartz M.L., McClure W.R. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 18:1990;4993-5000.
50. Gross C.A. Function and regulation of the heat shock proteins. Neidhardt F.C. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;1382-1399 AMS Press, Washington DC.
51. Gumucio D.L., Shelton D.A., Zhu W., Millinoff D., Gray T., Bock J.H., Slightom J.L., Goodman M. Evolutionary strategies for the elucidation of cis and trans factors that require the developmental switching programs of the β-like globin genes. Mol. Phylogenet. Evol. 5:1996;18-32.
52. Hancock J.M., Shaw P.J., Bonneton F., Dover G.A. High sequence turnover in the regulatory regions of the developmental gene hunchback in insects. Mol. Biol. Evol. 16:1999;253-265.
53. Hardison R.C., Oeltjen J., Miller W. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res. 7:1997;759-766.
54. He B., Zalkin H. Repression of Escherichia coli purB is by a transcriptional roadblock mechanism. J. Bacteriol. 174:1992;7121-7127.
55. He B., Choi K.Y., Zalkin H. Regulation of Escherichia coli glnB, prsA, and speA by the purine repressor. J. Bacteriol. 175:1993;3598-3606.
56. He J.S., Fulco A.J. A barbiturate-regulated protein binding to a common sequence in the cytochrome P450 genes of rodents and bacteria. J. Biol. Chem. 266:1991;7864-7869.
57. He J.S., Liang Q., Fulco A.J. The molecular cloning and characterization of BM1P1 and BM1P2 proteins, putative positive transcription factors involved in barbiturate-mediated induction of the genes encoding cytochrome P450BM-1 of Bacillus megaterium. J. Biol. Chem. 270:1995;18615-18625.
58. Hecker M., Schumann W., Volker U. Heat-shock and general stress response in Bacillus subtilis. Mol. Microbiol. 19:1996;417-428.
59. Heinemeyer T., Wingender E., Ruter I., Hermjacob H., Hel A.E., Kel O.V., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Kolpakov F.A., Podkolodny N.L., Kolchanov N.A. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 26:1998;362-367.
60. Helmann J.D. Compilation and analysis of Bacillus subtilis (A promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res. 23:1995;2351-2360.
61. Hertz G.Z., Hartzell III G.W., Stormo G.D. Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci. 6:1990;81-92.
62. Hirst J.D., Sternberg M.J. Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks. Biochemistry. 31:1992;7211-7218.
63. Honkakoski P., Moore R., Gynther J., Negishi M. Characterization of phenobarbital-inducible mouse CYP2B10 gene transcription in primary hepatocytes. J. Biol. Chem. 271:1996;9746-9753.
64. Horton P.B., Kanehisa M. An assessment of neural network and statsitical approaches for prediction of E. coli promoter sites. Nucleic Acids Res. 20:1992;4331-4338.
65. X factor using a consensus-directed search. J. Mol. Biol. 279:1998;165-173.
66. W. Mol. Microbiol. 31:1999;361-371.
67. Hung C.F., Holzmacher R., Connolly E., Berenbaum M.R., Schuler M.A. Conserved promoter elements in the CYP6B gene family suggest common ancestry for cytochrome P450 monooxygenases mediating furanocoumarin detoxification. Proc. Natl. Acad. Sci. USA. 93:1996;12200-12205.
68. Jack R.W., Tagg J.R., Ray B. Bacteriocins of Gram-positive bacteria. Microbiol. Rev. 59:1995;171-200.
69. Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Nakamura Y., Robb T.F., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5:1998;55-76.
70. Keener J., Nomura M. Regulation of ribosome synthesis. Neidhardt F.C. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;1417-1431 AMS Press, Washington DC.
71. Kemper B. Regulation of cytochrome P450 gene transcription by phenobarbital. Prog. Nucleic Acid Res. Mol. Biol. 61:1998;23-64.
72. Kennedy B.P., Aamodt E.J., Allen F.L., Chung M.A., Heschl M.F.P., McGhee J.D. The gut esterase gene (ges-1) from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J. Mol. Biol. 229:1993;890-908.
73. Kleerebezem M., Quadri L.E.N., Kuippers O.P., DeVos W.M. Quorum sensing by peptide pheromones and two-component signal-transduction systems in Gram-positive bacteria. Mol. Microbiol. 24:1997;895-904.
74. Klement J.F., Moorefeld M.B., Jorgensen E., Brown J.E., Risman S., McAllister W.T. Discrimination between bacteriophage T3 and T7 promoters by the T3 and T7 RNA polymerases depends primarily upon three base-pair region located 10 to 12 base-pairs upstream from the start site. J. Mol. Biol. 215:1990;21-29.
75. Koop B.F., Hood L. Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nature Genet. 7:1994;48-53.
76. Koop B.F. Human and rodent sequence comparisons: A mosaic model of genomic evolution. Trends Genet. 11:1995;367-371.
77. Krause M., Harrison S.W., Xu S.Q., Chen L., Fire A. Elements regulating cell- and stage-specific expression of the C. elegans MyoD family homolog hlh-1. Dev. Biol. 166:1994;133-148.
78. Kuwabara P.E. Interspecies comparison reveals evolution of control regions in the nematode sex-determining gene tra-2. Genetics. 144:1996;597-607.
79. Landick R., Turnboughjr C.L., Yanofsky C. Transcription attenuation. Neidhardt F.C. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;1263-1286 AMS Press, Washington DC.
80. Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., Neuwald A.F., Wootton J.C. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 262:1993;208-214.
81. Lawrence C.E., Reilly A.A. An expectation maximisation (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Struct. Func. Genet. 7:1990;41-51.
82. Liang Q., He J.S., Fulco A.J. The role of Barbie box sequences as cis-acting elements involved in the barbiturate-mediated induction of cytochromes P450BM-1 and P450BM-3 in Bacillus megaterium. J. Biol. Chem. 270:1995;4438-4450.
83. Liang Q., Chen L., Fulco A.J. In vivo roles of BM3R1 repressor in he barbiturate-mediated induction of the cytochrome P450 genes (P450BM-3 and P450BM-1) of Bacillus megaterium. Biochim. Biophys. Acta. 1380:1998;183-197.
84. Liao D., Dennis P.P. The organization and expression of essential transcription translation component genes in the extremely thermophilic eubacterium Thermotoga maritima. J. Biol. Chem. 267:1992;22787-22797.
85. Lipman D. Making (anti) sense of non-coding sequence conservation. Nucleic Acids Res. 25:1997;3580-3583.
86. Lisser S., Margalit H. Compilation of E. coli mRNA promoter sequences. Nucleic Acids Res. 21:1993;1507-1516.
87. Liu W., Hulett F.M. Comparison of PhoP binding to tuaA promoter with PhoP binding to other Pho-regulon promoters establishes a Bacillus subtilis Pho core binding site. Microbiology. 144:1998;1443-1450.
88. Liu X.D., Liu P.C., Santoro N., Thiele D.J. Conservation of a stress response: human heat shock transcription factors substitute for yeast HSF. EMBO J. 16:1997;6466-6477.
89. Malewski T. Computer analysis of distribution of putative cis- and trans-regulatory elements in milk protein gene promoters. BioSystems. 45:1998;29-44.
90. Margarit E., Guillen A., Rebordosa C., Vidal-Taboada J., Sanchez M., Ballesta F., Oliva R. Identification of conserved potentially regulatory sequences of the SRY gene from 10 different species of mammals. Biochem. Biophys. Res. Commun. 245:1998;370-377.
91. Mengeritsky G., Smith T.F. Recognition of characteristic patterns in sets of functionally equivalent DNA sequences. Comput. Appl. Biosci. 3:1987;223-227.
92. Miller C., McDonald J., Francis D. Evolution of promoter sequences: elements of a canonical promoter for prespore genes of Dictyostelium. J. Mol. Evol. 43:1996;185-193.
93. Minty A., Kedes L. Upstream regions of the human cardiac actin gene that modulate its transcription in muscle cells: presence of an evolutionarily conserved repeated motif. Mol. Cell. Biol. 6:1986;2125-2136.
94. Mironov A.A., Gelfand M.S. Computer analysis of regulatory patterns in complete bacterial genomes. PurR binding sites. Mol. Biol. 33:1999;109-114.
95. Mironov A.A., Koonin E.V., Roytberg M.A., Gelfand M.S. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 27:1999;2981-2989.
96. Morozov S.Y.A., Merits A., Chernov B.K. Computer search of transcription control sequences in small plant virus DNA reveals a sequence highly homologous to the enhancer element of histone promoters. DNA Seq. 4:1994;395-397.
97. Muday G.K., Herrmann K.M. Regulation of the Salmonella typhimurium aroF gene in Escherichia coli. J. Bacteriol. 172:1990;2259-2266.
98. Mulligan M.E., Hawley D.K., Entriken R., McClure W.R. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 12:1984;789-800.
99. Narberhaus F. Negative regulation of bacterial heat shock genes. Mol. Microbiol. 31:1999;1-8.
100. Narberhaus F., Kaser R., Nocker A., Hennecke H. A novel DNA element that controls bacterial heat shock gene expression. Mol. Microbiol. 28:1998;315-323.
101. Negre D., Bonod-Bidaud C., Geourjon G., Deleage G., Cozzone A.J., Cortay J.C. Definition of a consensus DNA-binding site for the Escherichia coli pleiotropic regulatory protein, FruR. Mol. Microbiol. 21:1996;257-266.
102. O'Neill M.C. Consensus methods for finding and ranking DNA binding sites: application to E. coli promoters. J. Mol. Biol. 207:1989;301-310.
103. O'Neill M.C. Training back-propagation neural networks to define and detect DNA binding sites. Nucleic Acids Res. 19:1991;313-318.
104. Overbeek R., Fonstein M., D'Souza M., Pusch G.D., Maltsev N. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA. 96:1999;2896-2901.
105. Park Y., Li H., Kemper B. Phenobarbital induction mediated by a distal CYP2B2 sequence in rat liver transiently transfected in situ. J. Biol. Chem. 271:1996;23725-23728.
106. Paton E.B., Zhyvoloup A.N. Binding site of the ribosomal protein L10 in the untranslated leader of rplJ gene in Thermotoga maritima suggests that this gene is under autogenous control, (in Russian, Engl. transl.). Genetika. 32:1996;140-145.
107. Pedersen A.G., Engelbrecht J. Investigations of Escherichia coli promoter sequences with artificial neural networks: new signals discovered upstream of the transcriptional startpoint. Intelligent Systems Mol. Biol. 3:1995;292-299.
108. Perez-Rueda E., Gralla J.D., Collado-Vides J. Genomic position analyses and the transcription machinery. J. Mol. Biol. 275:1998;165-170.
109. Pittard A.J. Biosynthesis of aromatic amino acids. Neidhardt F.C. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;458-484 AMS Press, Washington DC.
110. Polaczek P. Is the dnaA promoter region in Escherichia coli an evolutionary junkyard of physiologically insignificant regulatory elements? Mol. Microbiol. 27:1998;1089-1090.
111. Popperl H., Bienz M., Studer M., Chan S.K., Aparicio S., Brenner S., Mann R.S., Krumlauf R. Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx. Cell. 81:1995;1031-1042.
112. Prestridge D.S. SIGNAL SCAN 4.0 - additional databases and sequence formats. Comput. Appl. Sci. 12:1996;157-160.
113. Prestridge D.S., Burks C. The density of transcriptional elements in promoter and non-promoter sequences. Hum. Mol. Genet. 2:1993;1449-1453.
114. Qi Y., Kobayashi Y., Hulett F.M. The pst operon of Bacillus subtilis has a phosphate-regulated promoter and is involved in phosphate transport but not in regulation of the pho regulon. J. Bacteriol. 179:1997;2534-2539.
115. Renucci A., Zappavigna V., Zakany J., Izpisua-Belmonte J.C., Burki K., Duboule D. Comparison of mouse and human HOX-4 complexes defines conserved sequences involved in the regulation of Hox-4. EMBO J. 11:1992;1459-1468.
116. Retallack D.M., Johnson L.L., Ziegler S.F., Strauch M.A., Friedman D.I. A single-base-pair mutation changes the specificities of both a transcription regulation protein and its binding site. Proc. Natl. Acad. Sci. USA. 90:1993;9562-9565.
117. Rincon-Limas D.E., Lu C.H., Canal I., Calleja M., Rodriguez-Esteban C., Izpisua-Belmonte J.C., Botas J. Conservation of the expression and function of apterous orthologs in Drosophila and mammals. Proc. Natl. Acad. Sci. USA. 96:1999;2165-2170.
118. Roberts R.C., Toochinda C., Avedissian M., Baldini R.L., Gomes S.L., Shapiro L. Identification of a Caulobacter crescentus operon encoding hrcA, involved in negatively regulating heat-inducible transcription, and the chaperone gene grpE. J. Bacteriol. 178:1996;1829-1841.
119. Robison K., McGuire A.M., Church G.M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genomes. J. Mol. Biol. 284:1998;241-254.
120. Rosenblueth D.A., Thieffry D., Huerta A.M., Salgado H., Collado-Vides J. Syntactic recognition of regulatory regions in Escherichia coli. Comput. Appl. Biosci. 12:1996;415-422.
121. Roth F.P., Hughes J.D., Estep P.W., Church G.M. Revealing regulons by whole-genome expression monitoring and upstream sequence alignment. Nature Biotechnol. 16:1998;239-245.
122. Roulet E., Fisch I., Junier T., Bucher P., Mermod N. Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA. In Silico Biol. 1998;. http://www.bioinfo.de/isb/1998/01/0004.
123. Savchenko A., Charlier D., Dion M., Weigel P., Hallet J.N., Holtham C., Baumberg S., Glansdorff N., Sakayan V. The arginine operon of Bacillus stearothermophilus: characterization of the control region and its interaction with the heterologous B. subtilis arginine repressor. Mol. Gen. Genet. 252:1996;69-78.
124. Sawers G., Kaiser M., Sirko A., Freundlich M. Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition. Mol. Microbiol. 23:1997;835-845.
125. Schneider T.D., Stormo G.D., Gold L., Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188:1986;415-431.
126. Schneider T.D. Information content of individual genetic sequences. J. Theor. Biol. 189:1997;427-442.
127. Schultzaberger R.K., Schneider T.D. Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX. Nucleic Acids Res. 27:1999;882-887.
128. Schulz A., Schumann W. hrcA, the first gene of Bacillus subtilis dnaK operon encodes a negative regulator of class I heat shock genes. J. Bacteriol. 178:1996;1088-1093.
129. Segal G., Ron E.Z. Regulation and organization of the groE and dnaK operons in Eubacteria. FEMS Microbiol. Lett. 138:1996;1-10.
130. Shain D.H., Zuber M.X., Norris J., Yoo J., Neuman T. Selective conservation of an E-protein gene promoter during vertebrate evolution. FEBS Lett. 440:1998;332-336.
131. Shaw G.C., Sung C.C., Liu C.H., Lin C.H. Evidence against the Bm1P1 protein as a positive transcription factor for barbiturate-mediated induction of cytochrome P450BM-1 in Bacillus megaterium. J. Biol. Chem. 273:1998;7996-8002.
132. Shimmin L.C., Dennis P. Characterization of the L11, L1, L10 and L12 equivalent ribosomal protein gene cluster of the halophilic archaebacterium Halobacterium cutirubrum. EMBO J. 8:1989;1225-1235.
133. Shumilov V.Y. Mutual positioning of promoters and operators in DNA of Escherichia coli (in Russian). Mol. Biol. 32:1998;384.
134. Smith M.C., Czaplewski L., North A.K., Baumberg S., Stockley P.G. Sequences required for regulation of arginine biosynthesis promoters are conserved between Bacillus subtilis and Escherichia coli. Mol. Microbiol. 3:1989;23-28.
135. Spek C.A., Bertina R.M., Reitsma P.H. Identification of evolutionarily invariant sequences in the protein C gene promoter. J. Mol. Evol. 47:1998;663-669.
136. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell. 9:1998;3273-3297.
137. Staden R. Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res. 12:1984;515-519.
138. Stephens R.S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R.L., Zhao Q., Koonin E.V., Davis R.W. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 282:1998;754-759.
139. Stormo G.D., Hartzell III G.W. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. USA. 86:1989;1183-1187.
140. Stormo G.D. Information content and free energy in DNA-protein interactions. J. Theor. Biol. 195:1998;135-137.
141. Svetlov V.V., Cooper T.G. Compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. Yeast. 11:1995;1439-1484.
142. Tagle D.A., Koop B.F., Goodman M., Slightom J.L., Hess D.L., Jones R.T. Embryionic (and (globin genes of a prosimian primate (Galago crassicaudatus) nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203:1988;439-455.
143. Taylor H.S. A regulatory element of the empty spiracles homeobox gene is composed of three distinct conserved regions that bind regulatory proteins. Mol. Reprod. Dev. 49:1998;246-253.
144. Thacker C., Marra M.A., Jones A., Baillie D.L., Rose A.M. Functional genomics in Caenorhabditis elegans: An approach involving comparisons from related nematodes. Genome Res. 9:1999;348-359.
145. Thieffry D., Salgado H., Huerta A.M., Collado-Vides J. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics. 14:1998;391-400.
146. Tronche F., Ringeisen F., Blumenfeld M., Yaniv M., Pontoglio M. Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol. 266:1997;231-245.
147. Ulyanov A.V., Stormo G.D. Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions. Nucleic Acids Res. 23:1995;1434-1440.
148. Umbarger H.E. Biosynthesis of branched-chain amino acids. Neidhardt F.C. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;442-457 AMS Press, Washington DC.
149. Valentin-Hansen P., Sogaard-Andersen L., Pedersen H. A flexible partnership: the CytR anti-activator and the cAMP-CRP activator protein, comrades in transcription control. Mol. Microbiol. 20:1996;461-466.
150. Van Helden J., Andre B., Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281:1998;827-842.
151. Vaughan A., Hawkes N., Hemingway J. Co-amplification explains linkage disequilibrium of two mosquito diesterase genes in insecticide-resistant Culex quinquefasciatus. Biochem. J. 325:1997;359-365.
152. Vitreschak A., Bansal A.K., Titov I.I., Gelfand M.S. Computer analysis of regulatory patterns in complete bacterial genomes. Translation initiation of the ribosomal protein operons, (In Russian, Engl. transl.). Biophysics. 44:1999;. in press.
153. Wagner A. A computational 'genome walk' technique to identify regulatory interactions in gene networks. Pac. Symp. Biocomput. 1998;264-278.
154. Wagner A. A computational genomics approach to the identification of gene networks. Nucleic Acids Res. 25:1997;3594-3604.
155. Walker G.C. The SOS response of Escherichia coli. Neidhardt F.C. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;1400-1416 AMS Press, Washington DC.
156. Wanner B.L. Phosphorus assimilation and control of the phosphate regulon. Neidhardt F.C. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;1357-1381 AMS Press, Washington DC.
157. Wang D., Marsh J.L., Ayala F.J. Evolutionary changes in the expression pattern of a developmentally essential gene in three Drosophila species. Proc. Natl. Acad. Sci. USA. 93:1996;7103-7107.
158. Washio T., Sasayama J., Tomita M. Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination. Nucleic Acids Res. 26:1998;5456-5463.
159. Wasserman W.W., Fickett J.W. Identification of regulatory regions which confer muscle-specific gene expession. J. Mol. Biol. 278:1998;167-181.
160. Waterman M.S., Arratia R., Galas D.J. Pattern recognition in several sequences: consensus and alignment. Bull. Math. Biol. 45:1984;515-527.
161. Winterling K.W., Chafin D., Hayes J.J., Sun J., Levine A.S., Yasbin R.E., Woodgate R. The Bacillus subtilis DinR binding site: redefinition of the consensus sequence. J. Bacteriol. 180:1998;2201-2211.
162. Wolfertstetter F., Frech K., Herrmann G., Werner T. Identification of functional elements in unaligned nucleic sequences by a novel tuple search algorithm. Comput. Appl. Biosci. 12:1996;71-80.
163. Yada T., Totoki Y., Ishii T., Nakai K. Functional prediction of B. subtilis genes from their regulatory sequences. Intelligent Systems Mol. Biol. 5:1997;354-357.
164. Yuh C.H., Bolouri H., Davidson E.H. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science. 279:1998;1896-1902.
165. Zhu Q., Zhao S., Somerville R.L. Expression, purification, and functional analysis of the TyrR protein of Haemophilus inlfuenzae. Protein Expr. Purif. 10:1997;237-246.
166. Zuber U., Schumann W. CIRCE, a novel heat shock element involved in regulation of heat shock operon dnaK of Bacillus subtilis. J. Bacteriol. 176:1994;1359-1363.
167. Zucker-Aprison E., Blumenthal T. Potential regulatory elements of nematode vitellogenin genes revealed by interspecies sequence comparison. J. Mol. Evol. 28:1989;487-496.