Computational approaches to identify promoters and cis-regulatory elements in plant genomes

Plant Physiology

Volumn 132, Issue 3, 2003, Pages 1162-1176

  Rombauts, Stephane ^a   Florquin, Kobe ^a   Lescot, Magali ^b   Marchal, Kathleen ^c   Rouzé, Pierre ^d   Van De Peer, Yves ^a  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b CNRS   (France)

^c UNIVERSITY OF LEUVEN   (Belgium)

^d GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; GENETIC ENGINEERING; PHYSIOLOGY; PROBABILITY;

BIOINFORMATICS;

PLANTS (BOTANY);

ARABIDOPSIS; EMBRYOPHYTA; VERTEBRATA;

EID: 0038376923     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.102.017715     Document Type: Article

References (197)

1. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
2. Altschmied J, Delfgaauw J, Wilde B, Duschl J, Bouneau L, Volff JN, Schartl M (2002) Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish. Genetics 161: 259-267
3. Antequera F, Bird A (1999) CpG islands as genomic footprints of promoters that are associated with replication origins Curr Biol 9: R661-R667
4. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 23: 1301-1310
5. Ashikawa I (2001) Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. Plant J 26: 617-625
6. Bagga R, Michalowski S, Sabnis R, Griffith JD, Emerson BM (2000) HMG I/Y regulates long range enhancer-dependent transcription on DNA and chromatin by changes in DNA topology. Nucleic Acids Res 28: 2541-2550
7. Bajic V, Seah S, Chong A, Zhang G, Koh J, Brusic V (2002) Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics 18: 198-199
8. Bailey TL, Elkan C (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3: 21-29
9. Baldi P, Chauvin Y, Brunak S, Gorodkin J, Pedersen AG (1998) Computational applications of DNA structural scales. Proc Int Conf Intell Syst Mol Biol 6: 35-42
10. Barton MC, Madani N, Emerson BM (1997) Distal enhancer regulation by promoter derepression in topologically constrained DNA in vitro. Proc Natl Acad Sci USA 94: 7257-7262
11. Beato M, Eisfeld K (1997) Transcription factor access to chromatin. Nucleic Acids Res 25: 3559-3563
12. Bender J (2001) A vicious cycle: RNA silencing and DNA methylation in plants. Cell 106: 129-132
13. Bentin T, Nielsen PE (2002) In vitro transcription of a torsionally constrained template. Nucleic Acids Res 30: 803-809
14. Berk AJ (1999) Activation of RNA polymerase II transcription. Curr Opin Cell Biol 11: 330-335
15. Blanchette M, Sinha S (2001) Separating real motifs from their artifacts. Bioinformatics 17: 30-38
16. Blanchette M, Schwikowski B, Tompa M (2002) Algorithms for phylogenetic footprinting. J Comput Biol 9: 211-223
17. Blanchette M, Tompa M (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res 12: 739-748
18. Bolshoy A, McNamara P, Harrington RE, Trifonov EN (1991) Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci USA 88: 2312-2316
19. Brazma A, Jonassen I, Vilo J, Ukkonen E (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res 8: 1202-1215
20. Breslauer KJ, Frank R, Blocker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 83: 3746-3750
21. Breyne P, Dreesen R, Vandepoele K, De Veylder L, Van Breusegem F, Callewaert L, Rombauts S, Raes J, Cannoot B, Engler G et al. (2002) Transcriptome analysis during cell division in plants. Proc Natl Acad Sci USA 99: 14825-14830
22. Brower-Toland BD, Smith CL, Yeh RC, Lis JT, Peterson CL, Wang MD (2002) Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc Natl Acad Sci USA 99: 1960-1965
23. Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21: 33-37
24. 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
25. Brukner I, Sanchez R, Suck D, Pongor S (1995b) Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data. J Biomol Struct Dyn 13: 309-317
26. Buratowski S (1997) Snapshots of RNA polymerase II transcription initiation. Curr Opin Cell Biol 12: 320-325
27. Bussemaker HJ, Li H, Siggia ED (2000a) Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci USA 97: 10096-10100
28. Bussemaker HJ, Li H, Siggia ED (2000b) Regulatory element detection using a probabilistic segmentation model. Proc Int Conf Intell Syst Mol Biol 8: 67-74
29. Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 99: 16491-16498
30. Cao X, Springer NM, Muszynski MG, Phillips RL, Kaeppler S, Jacobsen SE (2000) Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc Natl Acad Sci USA 97: 4979-4984
31. Cardon LR, Stormo GD (1992) Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J Mol Biol 223: 159-170
32. Colinas J, Birnbaum K, Benfey PN (2002) Using cauliflower to find conserved non-coding regions in Arabidopsis. Plant Physiol 129: 451-454
33. Coward E (1999) Shufflet: shuffling sequences while conserving the k-let counts. Bioinformatics 15: 1058-1059
34. Crothers DM (1998) DNA curvature and deformation in protein-DNA complexes: a step in the right direction. Proc Natl Acad Sci USA 95: 15163-15165
35. Davuluri RV, Grosse I, Zhang MQ (2001) Computational identification of promoters and first exons in the human genome. Nat Genet 29: 412-417
36. de Boer GJ, Testerink C, Pielage G, Nijkamp HJ, Stuitje AR (1999) Sequences surrounding the transcription initiation site of the Arabidopsis enoyl-acyl carrier protein reductase gene control seed expression in transgenic tobacco. Plant Mol Biol 39: 1197-1207
37. Dermitzakis ET, Clark AG (2002) Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 19: 1114-1121
38. De Smet F, Mathys J, Marchal K, Thijs G, De Moor B, Moreau Y (2002) Adaptive quality-based clustering of gene expression profiles. Bioinformatics 18: 735-746
39. Dorsett D (1999) Distant liaisons: long-range enhancer-promoter interactions in Drosophila. Curr Opin Genet Dev 9: 505-514
40. Down TA, Hubbard TJ (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 12: 458-461
41. Duret L, Bucher P (1997) Searching for regulatory elements in human noncoding sequences. Curr Opin Struct Biol 7: 399-406
42. Duret L, Galtier N (2000) The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact. Mol Biol Evol 17: 1620-1625
43. Dynan WS (1989) Modularity in promoters and enhancers. Cell 58: 1-4
44. El Hassan MA, Calladine CR (1996) Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J Mol Biol 259: 95-103
45. Engelen K, Coessens B, Marchal K, De Moor B (2003) MARAN: normalizing micro-array data. Bioinformatics 19: 893-894
46. Featherstone M (2002) Coacfivators in transcription initiation: here are your orders. Curr Opin Genet Dev 12: 149-155
47. Fessele S, Maier H, Zischek C, Nelson PJ, Werner T (2002) Regulatory context is a crucial part of gene function. Trends Genet 18: 60-63
48. Fickett JW, Hatzigeorgiou AG (1997) Eukaryotic promoter recognition. Genome Res 7: 861-878
49. Fickett JW, Wasserman WW (2000) Discovery and modeling of transcriptional regulatory regions. Curr Opin Biotechnol 11: 19-24
50. Finnegan EJ, Genger RK, Kovac K, Peacock WJ, Dennis ES (1998a) DNA methylation and the promotion of flowering by vernalization. Proc Natl Acad Sci USA 95: 5824-5829
51. Finnegan EJ, Genger RK, Peacock WJ, Dennis ES (1998b) DNA methylation in plants. Annu Rev Plant Physiol Plant Mol Biol 49: 223-247
52. Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43: 189-201
53. Finnegan EJ, Peacock WJ, Dennis ES (2000) DNA methylation, a key regulator of plant development and other processes. Curr Opin Genet Dev 10: 217-223
54. Force A, Lynch M, Pickett FB, Amores A, Yan Y-1, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545
55. Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196: 261-282
56. Ghosh D (2000) Object-oriented transcription factors database (ooTFD). Nucleic Acids Res 28: 308-310
57. Gidekel M, Jimenez B, Herrera-Estrella L (1996) The first intron of the Arabidopsis thaliana gene coding for elongation factor 1 β contains an enhancer-like element. Gene 170: 201-206
58. Goodsell DS, Dickerson RE (1994) Bending and curvature calculations in B-DNA. Nucleic Acids Res 22: 5497-5503
59. Gorin AA, Zhurkin VB, Olson WK (1995) B-DNA twisting correlates with base-pair morphology. J Mol Biol 247: 34-48
60. Grabe N (2002) AliBaba2: context specific identification of transcription factor binding sites. In Silico Biol 2: S1-1
61. GuhaThakurta D, Stormo GD (2001) Identifying target sites for cooperatively binding factors. Bioinformatics 17: 608-621
62. Hampson S, Kibler D, Baldi P (2002) Distribution patterns of over-represented k-mers in noncoding yeast DNA. Bioinformatics 18: 513-528
63. Hannenhalli S, Levy S (2001) Promoter prediction in the human genome. Bioinformatics 17: S90-S96
64. Hardison RC (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 16: 369-372
65. Hershkovitz M, Gruenbaum Y, Renbaum P, Razin A, Loyter A (1990) Effect of CpG methylation on gene expression in transfected plant protoplasts. Gene 94: 189-193
66. Hertz GZ, Hartzell GW III, Stormo GD (1990) Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci 6: 81-92
67. Hertz GZ, Stormo GD (1996) Escherichia coli promoter sequences: analysis and prediction. Methods Enzymol 273: 30-42
68. Hertz GZ, Stormo GD (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563-577
69. Heyer LJ, Kruglyak S, Yooseph S (1999) Exploring expression data: identification and analysis of coexpressed genes. Genome Res 9: 1106-1115
70. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27: 297-300
71. Ho PS, Ellison MJ, Quigley GJ, Rich A (1986) A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J 5: 2737-2744
72. Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc R Soc Lond B 256: 119-124
73. Hughes JD, Estep PW, Tavazoie S, Church GM (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296: 1205-1214
74. Hutchinson GB (1996) The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput Appl Biosci 12: 391-398
75. Inamdar NM, Ehrlich KC, Ehrlich M (1991) CpG methylation inhibits binding of several sequence-specific DNA-binding proteins from pea, wheat, soybean and cauliflower. Plant Mol Biol 17: 111-123
76. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921
77. Ioshikhes IP, Trifonov EN, Zhang MQ (1999) Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc Natl Acad Sci USA 96: 2891-2895
78. Ioshikhes IP, Zhang MQ (2000) Large-scale human promoter mapping using CpG islands. Nat Genet 26: 61-63
79. Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S (2001) Sigma A recognition sites in the Bacillus subtilis genome. Microbiology 147: 2417-2424
80. Jeddeloh JA, Bender J, Richards EJ (1998) The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev 12: 1714-1725
81. Jegga AG, Sherwood SP, Carman JW, Pinski AT, Phillips JL, Pestian JP, Aronow BJ (2002) Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res 12: 1408-1417
82. Jensen LJ, Knudsen S (2000) Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics 16: 326-333
83. Johnson PF, McKnight SL (1989) Eukaryotic transcriptional regulatory proteins. Annu Rev Biochem 58: 799-839
84. Jones PA (1999) The DNA methylation paradox. Trends Genet 15: 34-37
85. Juo ZS, Chiu TK, Leiberman PM, Baikalov I, Berk AJ, Dickerson RE (1996) How proteins recognize the TATA box. J Mol Biol 261: 239-254
86. Kass SU, Landsberger N, Wolffe AP (1997) DNA methylation directs a time-dependent repression of transcription initiation. Curr Biol 7: 157-165
87. Kleffe J, Borodovsky M (1992) First and second moment of counts of words in random texts generated by Markov chains. Comput Appl Biosci 8: 433-441
88. Klingenhoff A, Frech K, Werner T (2002) Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico. In Silico Biol 2: S17-26
89. Koch MA, Haubold B, Mitchell-Olds T (2002) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17: 1483-1498
90. Koch MA, Weisshaar B, Kroymann J, Haubold B, Mitchell-Olds T (2001) Comparative genomics and regulatory evolution: conservation and function of the Chs and Apetala3 promoters. Mol Biol Evol 18: 1882-1891
91. Kolchanov NA, Podkolodnaya OA, Ananko EA, Ignatieva EV, Stepanenko IL, Kel-Margoulis OV, Kel AE, Merkulova TI, Goryachkovskaya TN, Busygina TV (2000) Transcription regulatory regions database (TRRD): its status in 2000. Nucleic Acids Res 28: 298-301
92. Kondrakhin YV, Kel AE, Kolchanov NA, Romashchenko AG, Milanesi L (1995) Eukaryotic promoter recognition by binding sites for transcription factors. Comput Appl Biosci 11: 477-488
93. Koop BF (1995) Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution. Trends Genet 11: 367-371
94. Kooter JM, Matzke MA, Meyer P (1999) Listening to the silent genes: transgene silencing, gene regulation and pathogen control. Trends Plant Sci 4: 340-347
95. Kornberg RD, Lorch Y (2002) Chromatin and transcription: Where do we go from here? Curr Opin Genet Dev 12: 249-251
96. Krivan W, Wasserman WW (2001) A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 11: 1559-1566
97. Langst G, Becker PB (2001) Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors. J Cell Sci 114: 2561-2568
98. Larkin JC, Oppenheimer DG, Pollock S, Marks MD (1993) Arabidopsis GLABROUS1 gene requires downstream sequences for function. Plant Cell 5: 1739-1748
99. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262: 208-214
100. Lawrence CE, Reilly AA (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins 7: 41-51
101. Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30: 325-327
102. Li G, Chandrasekharan MB, Wolffe AP, Hall TC (2001) Chromatin structure and phaseolin gene regulation. Plant Mol Biol 46: 121-129
103. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080
104. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet 21: 20-24
105. Liu XS, Brutlag DL, Liu JS (2002) An algorithm for finding protein DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 20: 835-839
106. Liu XS, Brutlag DL, Liu JS (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 127-138
107. Marilley M, Pasero P (1996) Common DNA structural features exhibited by eukaryotic ribosomal gene promoters. Nucleic Acids Res 24: 2204-2211
108. Marsan L, Sagot MF (2000) Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J Comput Biol 7: 345-362
109. Mathé C, Sagot MF, Schiex T, Rouzé P (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 30: 4103-4117
110. Meyer P (2000) Transcriptional transgene silencing and chromatin components. Plant Mol Biol 43: 221-234
111. Meyer P, Niedenhof I, ten Lohuis M (1994) Evidence for cytosine methylation of non-symmetrical sequences in transgenic Petunia hybrida. EMBO J 13: 2084-2088
112. Meza TJ, Enerly E, Boru B, Larsen F, Mandal A, Aalen RB, Jakobsen KS (2002) A human CpG island randomly inserted into a plant genome is protected from methylation. Transgenic Res 11: 133-142
113. Mindell DP, Meyer A (2001) Homology evolving. Trends Ecol Evol 16: 434-440
114. Moreau Y, De Smet F, Thijs G, Marchal K, De Moor B (2002) Functional bioinformatics of microarray data: from expression to regulation. IEEE Proc 30: 1722-1743
115. Neuwald AF, Liu JS, Lawrence CE (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 4: 1618-1632
116. Ng HH, Bird A (1999) DNA methylation and chromatin modification. Curr Opin Genet Dev 9: 158-163
117. Nikolov DB, Burley SK (1997) RNA polymerase II transcription initiation: a structural view. Proc Natl Acad Sci USA 94: 15-22
118. Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK (1996) Crystal structure of a human TATA box-binding protein/TATA element complex. Proc Natl Acad Sci USA 93: 4862-4867
119. Ohler U (2000) Promoter prediction on a genomic scale: the Adh experience. Genome Res 10: 539-542
120. Ohler U, Harbeck S, Niemann H, Noth E, Reese MG (1999) Interpolated Markov chains for eukaryotic promoter recognition. Bioinformatics 15: 362-369
121. Ohler U, Niemann H (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet 17: 56-60
122. Ohler U, Niemann H, Liao GC, Rubin GM (2001) Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 17: S199-S206
123. Ohler U, Liao GC, Niemann H, Rubin GM (2000) Computational analysis of core promoters in the Drosophila genome. Genome Biol 3: 0087.1-0087.12
124. Oki M, Kamakaka RT (2002) Blockers and barriers to transcription: competing activities. Curr Opin Cell Biol 14: 299-304
125. Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 95: 11163-11168
126. Panstruga R, Buschges R, Piffanelli P, Schulze-Lefert P (1998) A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res 26: 1056-1062
127. Pedersen AG, Baldi P, Chauvin Y, Brunak S (1998) DNA structure in human RNA polymerase II promoters. J Mol Biol 281: 663-673
128. Pedersen AG, Baldi P, Chauvin Y, Brunak S (1999) The biology of eukaryotic promoter prediction: a review. Comput Chem 23: 191-207
129. Pesole G, Liuni S, D'Souza M (2000) PatSearch: a pattern marcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics 16: 439-450
130. Pitto L, Cernilogar F, Evangelista M, Lombardi L, Miarelli C, Rocchi P (2000) Characterization of carrot nuclear proteins that exhibit specific binding affinity towards conventional and nonconventional DNA methylation. Plant Mol Biol 44: 659-673
131. Ponger L, Mouchiroud D (2002) CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics 18: 631-633
132. Pradhan S, Urwin NA, Jenkins GI, Adams RL (1999) Effect of CWG methylation on expression of plant genes. Biochem J 341: 473-476
133. Praz V, Perier R, Bonnard C, Bucher P (2002) The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res 30: 322-324
134. Prestridge DS (1991) SIGNAL SCAN: A computer program that scans DNA sequences for eukaryotic transcriptional elements. CABIOS 7: 203-206
135. Prestridge DS (1995) Predicting Pol II promoter sequences using transcription factor binding sites. J Mol Biol 249: 923-932
136. Prince VE, Pickett FB (2002) Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 3: 827-837
137. Quiros CF, Grellet F, Sadowski J, Suzuki T, Li G, Wroblewski T (2001) Arabidopsis and Brassica comparative genomics: sequence, structure and gene content in the ABI1-Rps2-Ck1 chromosomal segment and related regions. Genetics 157: 1321-1330
138. Razin A (1998) CpG methylation, chromatin structure and gene silencing: a three-way connection. EMBO J 17: 4905-4908
139. Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE (2000) Genome annotation assessment in Drosophila melanogaster. Genome Res 10: 483-501
140. Reymond P, Weber H, Damond M, Farmer EE (2000) Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 12: 707-720
141. Richards EJ, Elgin SC (2002) Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108: 489-500
142. Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290: 2105-2110
143. Robertson KD (2002) DNA methylation and chromatin: unraveling the tangled web. Oncogene 21: 5361-5379
144. Robin S, Schbath S (2001) Numerical comparison of several approximations of the word count distribution in random sequences. J Comput Biol 8: 349-359
145. Rooney JW, Sun YL, Glimcher LH, Hoey T (1995) Novel NFAT sites that mediate activation of the interleukin-2 promoter in response to T-cell receptor stimulation. Mol Cell Biol 15: 6299-6310
146. Rossi V, Motto M, Pellegrini L (1997) Analysis of the methylation pattern of the maize opaque-2 (O2) promoter and in vitro binding studies indicate that the O2 B-Zip protein and other endosperm factors can bind to methylated target sequences. J Biol Chem 272: 13758-13765
147. Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quanfitation. Nat Biotechnol 16: 939-945
148. Sagot MF, Myers EW (1998) Identifying satellites and periodic repetitions in biological sequences. J Comput Biol 5: 539-553
149. Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Diaz-Peredo E, Sanchez-Solano F, Perez-Rueda E, Bonavides-Martinez C, Collado-Vides J (2001) RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res 29: 72-74
150. Schbath S (1997) An efficient statistic to detect over- and trader-represented words in DNA sequences. J Comp Biol 4: 189-192
151. Schbath S (2000) An overview on the distribution of word counts in Markov chains. J Comput Biol 7: 193-201
152. Schbath S, Prum B, de Turckheim E (1995) Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J Comput Biol 2: 417-437
153. Scherf M, Klingenhoff A, Werner T (2000) Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach. J Mol Biol 297: 599-606
154. Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296: 141-145
155. Sinha S, Tompa M (2000) A statistical method for finding transcription factor binding sites. Proc Int Conf Intell Syst Mol Biol 8: 344-354
156. Sinha S, Tompa M (2002) Discovery of novel transcription factor binding sites by statistical overrepresentafion. Nucleic Acids Res 30: 5549-5560
157. Sivolob AV, Khrapunov SN (1995) Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending stiffness. J Mol Biol 247: 918-931
158. Sorensen MB, Muller M, Skerritt J, Simpson D (1996) Hordein promoter methylation and transcriptional activity in wild-type and mutant barley endosperm. Mol Gen Genet 250: 750-760
159. Southern EM (2001) DNA microarrays: history and overview. Methods Mol Biol 170: 1-15
160. Stormo GD (1988) Computer methods for analyzing sequence recognition of nucleic acids. Annu Rev Biophys Biophys Chem 17: 241-263
161. Stormo GD (1990) Consensus patterns in DNA. Methods Enzymol 183: 211-221
162. Stormo GD, Hartzell GW, 3rd (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci USA 86: 1183-1187
163. Struhl K (1999) Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98: 1-4
164. Struhl K (2001) Gene regulation: a paradigm for precision. Science 293: 1054-1055
165. Sturaro M, Viotti A (2001) Methylation of the Opaque2 box in zein genes is parent-dependent and affects O2 DNA binding activity in vitro. Plant Mol Biol 46: 549-560
166. Sugimoto N, Nakano S, Yoneyama M, Honda K (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24: 4501-4505
167. Sved J, Bird A (1990) The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci USA 87: 4692-4696
168. Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99: 3740-3745
169. Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouzé P, Moreau Y (2001) A higher order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 17: 1113-1122
170. Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouzé P, Moreau Y (2002a) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol 9: 447-464
171. Thijs G, Moreau Y, De Smet F, Mathys J, Lescot M, Rombauts S, Rouzé P, De Moor B, Marchal K, Déhais P et al. (2002b) INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. Bioinformatics 18: 331-332
172. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680
173. Tjian R, Maniatis T (1994) Transcriptional activation: a complex puzzle with a few easy pieces. Cell 77: 5-8
174. Tompa M (2001) identifying functional elements by comparative DNA sequence analysis. Genome Res 11: 1143-1144
175. Travers A, Drew H (1997) DNA recognition and nucleosome organization. Biopolymers 44: 423-433
176. Tsunoda T, Takagi T (1998) Estimating transcription factor bindability on DNA. Bioinformatics 15: 622-630
177. 80 family of promoter signals. J Mol Biol 297: 335-353
178. Vanet A, Marsan L, Sagot MF (1999) Promoter sequences and algorithmical methods for identifying them. Res Microbiol 150: 779-799
179. van Helden J, Andre B, Collado-Vides J (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 281: 827-842
180. van Helden J, del Olmo M, Perez-Ortin JE (2000a) Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res 28: 1000-1010
181. van Helden J, Rios AF, Collado-Vides J (2000b) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res 28: 1808-1818
182. Vaucheret H, Fagard M (2001) Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet 17: 29-35
183. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al (2001) The sequence of the human genome. Science 291: 1304-1351
184. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414
185. Waibel AH, Hanazawa T, Hinton GE, Shikano K, Lang KJ (1989) Phoneme recognition using time-delay neural networks. IEEE Trans Acoustic Speech Signal Process 37: 328-339
186. Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE (2000) Human-mouse genome comparisons to locate regulatory sites. Nat Genet 26: 225-228
187. Weber H, Ziechmann C, Graessmann A (1990) In vitro DNA methylation inhibits gene expression in transgenic tobacco. EMBO J 9: 4409-4415
188. Werner T (2000) Computer-assisted analysis of transcription control regions: Matinspector and other programs. Methods Mol Biol 132: 337-349
189. 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: 316-319
190. Wingender E, Dietze P, Karas H, Knuppel R (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 24: 238-241
191. Wolfertstetter F, Frech K, Herrmann G, Werner T (1996) Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Comput Appl Biosci 12: 71-80
192. Wolffe AP, Matzke MA (1999) Epigenetics: regulation through repression. Science 286: 481-486
193. Workman CT, Stormo GD (2000) ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput 467-478
194. Zhang MQ (1998) Identification of human gene core promoters in silico. Genome Res 8: 319-326
195. Zhang SH, Lawton MA, Hunter T, Lamb CJ (1994) atpk1, a novel ribosomal protein kinase gene from Arabidopsis: I. Isolation, characterization, and expression. J Biol Chem 269: 17586-17592
196. Zhu J, Liu JS, Lawrence CE (1998) Bayesian adaptive sequence alignment algorithms. Bioinformatics 14: 25-39
197. Zhu J, Zhang MQ (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15: 607-611