Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum

Genome Biology

Volumn 9, Issue 12, 2008, Pages

  Brick, Kevin ^a   Watanabe, Junichi ^b   Pizzi, Elisabetta ^a  

^a ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; DNA; THYMINE;

ARTICLE; AT RICH SEQUENCE; EUKARYOTE; EXPRESSED SEQUENCE TAG; GENE MAPPING; MOLECULAR RECOGNITION; NONHUMAN; PHYSICAL CHEMISTRY; PLASMODIUM FALCIPARUM; PREDICTION; PROMOTER REGION; PROTOZOAL GENETICS; SEQUENCE ANALYSIS; SUPPORT VECTOR MACHINE; ALGORITHM; ANIMAL; DNA BASE COMPOSITION; GENETICS; GENOME;

EUKARYOTA; PLASMODIUM FALCIPARUM;

ALGORITHMS; ANIMALS; BASE COMPOSITION; GENOME, PROTOZOAN; PLASMODIUM FALCIPARUM; PROMOTER REGIONS, GENETIC;

EID: 59949101979     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-12-r178     Document Type: Article

References (85)

1. Cooper SJ Trinklein ND Anton ED Nguyen L Myers RM Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res 2006, 16:1-10. 1356123 16344566
2. Gershenzon NI Ioshikhes IP Synergy of human Pol II core promoter elements revealed by statistical sequence analysis. Bioinformatics 2005, 21:1295-1300. 15572469
3. Schones DE Zhao K Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 2008, 9:179-191. 18250624
4. Bird A Perceptions of epigenetics. Nature 2007, 447:396-398. 17522671
5. Segal E Fondufe-Mittendorf Y Chen L Thastrom A Field Y Moore IK Wang JP Widom J A genomic code for nucleosome positioning. Nature 2006, 442:772-778. 2623244 16862119
6. Bultrini E Pizzi E A new parameter to study compositional properties of non-coding regions in eukaryotic genomes. Gene 2006, 385:75-82. 16978802
7. Goni JR Perez A Torrents D Orozco M Determining promoter location based on DNA structure first-principles calculations. Genome Biol 2007, 8:R263. 2246265 18072969
8. Florquin K Saeys Y Degroeve S Rouze P Van de PY Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res 2005, 33:4255-4264. 1181242 16049029
9. Abeel T Saeys Y Bonnet E Rouze P Van de PY Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res 2008, 18:310-323. 2203629 18096745
10. Bajic VB Tan SL Suzuki Y Sugano S Promoter prediction analysis on the whole human genome. Nat Biotechnol 2004, 22:1467-1473. 15529174
11. Reese MG Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 2001, 26:51-56. 11765852
12. Ohler U Liao GC Niemann H Rubin GM Computational analysis of core promoters in the Drosophila genome. Genome Biol 2002, 3. RESEARCH0087 151189 12537576
13. Ohler U Niemann H Liao G Rubin GM Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 2001, 17(Suppl 1):S199-S206. 11473010
14. World Health Organization WHO (2004). The World Health Report 2004 - Changing History World Health Organization 2004.
15. Coleman BI Duraisingh MT Transcriptional control and gene silencing in Plasmodium falciparum. Cell Microbiol 2008, 10:1935-1946. 18637022
16. Llinas M Deitsch KW Voss TS Plasmodium gene regulation: Far more to factor in. Trends Parasitol 2008, 24:551-556. 18929512
17. De Silva EK Gehrke AR Olszewski K Leon I Chahal JS Bulyk ML Llinas M Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc Natl Acad Sci USA 2008, 105:8393-8398. 2423414 18541913
18. Gardner MJ Hall N Fung E White O Berriman M Hyman RW Carlton JM Pain A Nelson KE Bowman S Paulsen IT James K Eisen JA Rutherford K Salzberg SL Craig A Kyes S Chan MS Nene V Shallom SJ Suh B Peterson J Angiuoli S Pertea M Allen J Selengut J Haft D Mather MW Vaidya AB Martin DM et al Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-511. 12368864
19. Watanabe J Suzuki Y Sasaki M Sugano S Full-malaria 2004: An enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species. Nucleic Acids Res 2004, 32:D334-D338. 308849 14681428
20. FULL Malaria Database http://fullmal.hgc.jp/index.html
21. Kawaji H Frith MC Katayama S Sandelin A Kai C Kawai J Carninci P Hayashizaki Y Dynamic usage of transcription start sites within core promoters. Genome Biol 2006, 7:R118. 1794431 17156492
22. Frith MC Valen E Krogh A Hayashizaki Y Carninci P Sandelin A A code for transcription initiation in mammalian genomes. Genome Res 2008, 18:1-12. 2134772 18032727
23. Sandelin A Carninci P Lenhard B Ponjavic J Hayashizaki Y Hume DA Mammalian RNA polymerase II core promoters: Insights from genome-wide studies. Nat Rev Genet 2007, 8:424-436. 17486122
24. Gallagher PG Nilson DG Wong C Weisbein JL Garrett-Beal LJ Eber SW Bodine DM A dinucleotide deletion in the ankyrin promoter alters gene expression, transcription initiation and TFIID complex formation in hereditary spherocytosis. Hum Mol Genet 2005, 14:2501-2509. 16037067
25. Noble WS Support vector machine applications in computational biology. Kernel Methods in Computational Biology Cambridge, MA: The MIT Press Scholkopf B, Tsuda K, Vert J 2004, 71-92.
26. Noble WS What is a support vector machine? Nat Biotechnol 2006, 24:1565-1567. 17160063
27. Sonnenburg S Zien A Ratsch G ARTS: Accurate recognition of transcription starts in human. Bioinformatics 2006, 22:e472-e480. 16873509
28. Uljanov N James T Statistical analysis of DNA duplex structural features. Methods Enzymol 1995, 261:90-115. 8569515
29. Gabrielian A Pongor S Correlation of intrinsic DNA curvature with DNA property periodicity. FEBS Lett 1996, 393:65-68. 8804425
30. Polson HE Blackman MJ A role for poly(dA)poly(dT) tracts in directing activity of the Plasmodium falciparum calmodulin gene promoter. Mol Biochem Parasitol 2005, 141:179-189. 15850701
31. Tham WH Payne PD Brown GV Rogerson SJ Identification of basic transcriptional elements required for rif gene transcription. Int J Parasitol 2007, 37:605-615. 17196595
32. Alano P Silvestrini F Roca L Structure and polymorphism of the upstream region of the pfg27/25 gene, transcriptionally regulated in gametocytogenesis of Plasmodium falciparum. Mol Biochem Parasitol 1996, 79:207-217. 8855557
33. Bajic VB Brent MR Brown RH Frankish A Harrow J Ohler U Solovyev VV Tan SL Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol 2006. 7(Suppl 1):S3-13. 1810552 16925837
34. Yamashita R Suzuki Y Wakaguri H Tsuritani K Nakai K Sugano S DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res 2006, 34:D86-D89. 1347491 16381981
35. Olivieri A Silvestrini F Sanchez M Alano P A 140-bp AT-rich sequence mediates positive and negative transcriptional control of a Plasmodium falciparum developmentally regulated promoter. Int J Parasitol 2007, 38:299-312. 17976625
36. Yang MQ Koehly LM Elnitski LL Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol 2007, 3:e72. 1853124 17447839
37. Trinklein ND Aldred SF Hartman SJ Schroeder DI Otillar RP Myers RM An abundance of bidirectional promoters in the human genome. Genome Res 2004, 14:62-66. 314279 14707170
38. The Plasmodium Genome Resource http://www.plasmoDB.org
39. Le Roch KG Zhou Y Blair PL Grainger M Moch JK Haynes JD de l V Holder AA Batalov S Carucci DJ Winzeler EA Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 2003, 301:1503-1508. 12893887
40. Bozdech Z Llinas M Pulliam BL Wong ED Zhu J Derisi JL The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1:E5. 176545 12929205
41. Smith JD Chitnis CE Craig AG Roberts DJ Hudson-Taylor DE Peterson DS Pinches R Newbold CI Miller LH Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes. Cell 1995, 82:101-110. 7606775
42. Su XZ Heatwole VM Wertheimer SP Guinet F Herrfeldt JA Peterson DS Ravetch JA Wellems TE The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum -infected erythrocytes. Cell 1995, 82:89-100. 7606788
43. Deitsch KW Calderwood MS Wellems TE Malaria. Cooperative silencing elements in var genes. Nature 2001, 412:875-876. 11528468
44. Calderwood MS Gannoun-Zaki L Wellems TE Deitsch KW Plasmodium falciparum var genes are regulated by two regions with separate promoters, one upstream of the coding region and a second within the intron. J Biol Chem 2003, 278:34125-34132. 12832422
45. Patankar S Munasinghe A Shoaibi A Cummings LM Wirth DF Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite. Mol Biol Cell 2001, 12:3114-3125. 60160 11598196
46. Gunasekera AM Patankar S Schug J Eisen G Kissinger J Roos D Wirth DF Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Mol Biochem Parasitol 2004, 136:35-42. 15138065
47. Militello KT Patel V Chessler AD Fisher JK Kasper JM Gunasekera A Wirth DF RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum. RNA 2005, 11:365-370. 1370726 15703443
48. Slater GS Birney E Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31. 553969 15713233
49. Vlahovicek K Kajan L Pongor S DNA analysis servers: Plot.it, bend.it, model.it and IS. Nucleic Acids Res 2003, 31:3686-3687. 168966 12824394
50. plot.it Server http://hydra.icgeb.trieste.it/dna/plot_it.html
51. Berkley Drosophila Genome Project http://www.fruitfly.org
52. Chih-Chung C Chih-Jen L LIBSVM: A Library for Support Vector Machines http://www.csie.ntu.edu.tw/~cjlin/papers/libsvm.pdf
53. LibSVM Toolkit http://www.csie.ntu.edu.tw/~cjlin/libsvm
54. Chen YW Lin CJ Combining SVMs with Various Feature Selection Strategies. Feature Extraction: Foundations and Applications (Studies in Fuzziness and Soft Computing) Zadeh LA: New York: Springer Guyon I, Gunn S, Nikravesh M 1.0 2006, 315-323.
55. Malaria Promoter Predictor Site http://www.mapp-predictor.info/downloads
56. Rutherford K Parkhill J Crook J Horsnell T Rice P Rajandream MA Barrell B Artemis: Sequence visualization and annotation. Bioinformatics 2000, 16:944-945. 11120685
57. Munteanu MG Vlahovicek K Parthasarathy S Simon I Pongor S Rod models of DNA: Sequence-dependent anisotropic elastic modelling of local bending phenomena. Trends Biochem Sci 1998, 23:341-347. 9787640
58. Goodsell DS Dickerson RE Bending and curvature calculations in B-DNA. Nucleic Acids Res 1994, 22:5497-5503. 332108 7816643
59. Gromiha MM Munteanu MG Gabrielian A Pongor S Anisotropic elastic bending models of DNA. J Biol Phys 1996, 22:227-243.
60. Brukner I Sanchez R Suck D Pongor S Sequence-dependent bending propensity of DNA as revealed by DNase I: Parameters for tri nucleotides. EMBO J 1995, 14:1812-1818. 398274 7737131
61. Satchwell SC Drew HR Travers AA Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 1986, 191:659-675. 3806678
62. Ornstein RL Rein R Breen DL Macelroy RD An optimized potential function for the calculation of nucleic acid interaction energies. Biopolymers 1978, 17:2341-2360.
63. Olson WK Gorin AA Lu XJ Hock LM Zhurkin VB DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 1998, 95:11163-11168. 21613 9736707
64. Gorin AA Zhurkin VB Olson WK B-DNA twisting correlates with base-pair morphology. J Mol Biol 1995, 247:34-48. 7897660
65. Ivanov VI Minchenkova LE Chernov BK McPhie P Ryu S Garges S Barber AM Zhurkin VB Adhya S CRP-DNA complexes: Inducing the A-like form in the binding sites with an extended central spacer. J Mol Biol 1995, 245:228-240. 7844815
66. El Hassan MA Calladine CR Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J Mol Biol 1996, 259:95-103. 8648652
67. Sugimoto N Nakano S Yoneyama M Honda K Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 1996, 24:4501-4505. 146261 8948641
68. Breslauer KJ Frank R Blocker H Marky LA Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986, 83:3746-3750. 323600 3459152
69. Blake RD Encyclopedia of Molecular Biology and Molecular Medicine New York: Wiley 1996.
70. Sivolob AV Khrapunov SN Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending stiffness. J Mol Biol 1995, 247:918-931. 7723041
71. Ho PS Ellison MJ Quigley GJ Rich A A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J 1986, 5:2737-2744. 1167176 3780676
72. Aida M An ab initio molecular orbital study on the sequence-dependency of DNA conformation: An evaluation of intra- and inter-strand stacking interaction energy. J Theor Biol 1988, 130:327-335. 3419185
73. Bansal M Bhattacharyya D Ravi B NUPARM and NUCGEN: Software for analysis and generation of sequence dependent nucleic acid structures. Comput Appl Biosci 1995, 11:281-287. 7583696
74. Bolshoy A McNamara P Harrington RE Trifonov EN Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci USA 1991, 88:2312-2316. 51221 2006170
75. Calladine CR Drew HR Principles of sequence-dependent flexure of DNA. J Mol Biol 1986, 192:907-918. 3586013
76. De SP Palleschi A Savino M Scipioni A Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistry 1990, 29:9269-9273. 2271594
77. Hartmann B Malfoy B Lavery R Theoretical prediction of base sequence effects in DNA. Experimental reactivity of Z-DNA and B-Z transition enthalpies. J Mol Biol 1989, 207:433-444. 2754731
78. Chalikian TV Volker J Plum GE Breslauer KJ A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques. Proc Natl Acad Sci USA 1999, 96:7853-7858. 22151 10393911
79. Ivanov VI Krilov DY Shchyolkina AK Chernov BK Minchenkov LE Decimal code controlling the B to A transition of DNA. J Biomol Struct Dynamics 1995, 12:a102-108.
80. Lisser S Margalit H Determination of common structural features in Escherichia coli promoters by computer analysis. Eur J Biochem 1994, 223:823-830. 8055959
81. SantaLucia J Jr Allawi HT Seneviratne PA Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 1996, 35:3555-3562. 8639506
82. Sarai A Mazur J Nussinov R Jernigan RL Sequence dependence of DNA conformational flexibility. Biochemistry 1989, 28:7842-7849. 2611216
83. Gotoh O Takashira Y Stabilities of nearest neighbour doublets in double helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers 1980, 20:1033-1042.
84. Ulyanov NB James TL Statistical analysis of DNA duplex structural features. Methods Enzymol 1995, 261:90-120. 8569515
85. Lewis JP Sankey OF Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular relaxations. Biophys J 1995 69 1068 1076 1236334 8519960