BayesPI - A new model to study protein-DNA interactions: A case study of condition-specific protein binding parameters for yeast transcription factors

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 345-

  Wang, Junbai ^a   Morigen, ^a  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN NETWORKS; BINDING ENERGY; DNA; PROTEINS; TRANSCRIPTION; TRANSCRIPTION FACTORS; YEAST;

BINDING AFFINITIES; BIOPHYSICAL MODEL; FLANKING SEQUENCE; NUCLEOTIDE AFFINITY; PROTEIN BINDING; PROTEIN-DNA INTERACTIONS; SPECIES SPECIFICS; SPECIFIC BINDING;

BINDING SITES;

TRANSCRIPTION FACTOR;

ARTICLE; BAYES THEOREM; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DNA SEQUENCE; GENETIC DATABASE; MATHEMATICAL COMPUTING; MOLECULAR RECOGNITION; NONHUMAN; OXIDATIVE STRESS; PROTEIN DNA INTERACTION;

EID: 70450265377     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-345     Document Type: Article

References (68)

1. Alberts B, Johnson AL, Lewis J, Raff M, Roberts K, Walter P. Molecular Biology of the Cell. 2002, New York and London: Garland Science.
2. Wang J. A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle. Journal of biomedical informatics 2007, 40(6):707-725. 10.1016/j.jbi.2007.02.003, 17418646.
3. Kornberg RD, Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 1999, 98(3):285-294. 10.1016/S0092-8674(00)81958-3, 10458604.
4. Morse RH. Getting into chromatin: how do transcription factors get past the histones?. Biochemistry and cell biology = Biochimie et biologie cellulaire 2003, 81(3):101-112. 10.1139/o03-039, 12897843.
5. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nature genetics 2007, 39(10):1235-1244. 10.1038/ng2117, 17873876.
6. Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC. Nucleosome organization in the Drosophila genome. Nature 2008, 453(7193):358-362. 10.1038/nature06929, 2735122, 18408708.
7. Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nature biotechnology 2007, 25(2):244-248. 10.1038/nbt1279, 17220878.
8. Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome research 2006, 16(12):1517-1528. 10.1101/gr.5655606, 1665635, 17053089.
9. Narlikar L, Gordan R, Hartemink AJ. A nucleosome-guided map of transcription factor binding sites in yeast. PLoS computational biology 2007, 3(11):e215. 10.1371/journal.pcbi.0030215, 2065891,2065891, 17997593.
10. Bussemaker HJ, Li H, Siggia ED. Regulatory element detection using correlation with expression. Nature genetics 2001, 27(2):167-171. 10.1038/84792, 11175784.
11. Roider HG, Kanhere A, Manke T, Vingron M. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics (Oxford, England) 2007, 23(2):134-141. 10.1093/bioinformatics/btl565, 17098775.
12. Foat BC, Morozov AV, Bussemaker HJ. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics (Oxford, England) 2006, 22(14):e141-149. 10.1093/bioinformatics/btl223, 16873464.
13. Kinney JB, Tkacik G, Callan CG. Precise physical models of protein-DNA interaction from high-throughput data. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(2):501-506. 10.1073/pnas.0609908104, 1766414, 17197415.
14. Wang J. Computational biology of genome expression and regulation--a review of microarray bioinformatics. J Environ Pathol Toxicol Oncol 2008, 27(3):157-179.
15. Berg OG, von Hippel PH. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. Journal of molecular biology 1987, 193(4):723-750. 10.1016/0022-2836(87)90354-8, 3612791.
16. Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004, 83(3):349-360. 10.1016/j.ygeno.2003.11.004, 14986705.
17. Das D, Nahle Z, Zhang MQ. Adaptively inferring human transcriptional subnetworks. Molecular systems biology 2006, 2:2006 0029. 10.1038/msb4100067, 1681499, 16760900.
18. Tanay A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome research 2006, 16(8):962-972. 10.1101/gr.5113606, 1524868, 16809671.
19. Zhou Q, Liu JS. Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic acids research 2008, 36(12):4137-4148. 10.1093/nar/gkn361, 2475627, 18556756.
20. Keles S, Warren CL, Carlson CD, Ansari AZ. CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data. Nucleic acids research 2008, 36(10):3171-3184. 10.1093/nar/gkn057, 2425502, 18411210.
21. Djordjevic M, Sengupta AM, Shraiman BI. A biophysical approach to transcription factor binding site discovery. Genome research 2003, 13(11):2381-2390. 10.1101/gr.1271603, 403756, 14597652.
22. Gerland U, Moroz JD, Hwa T. Physical constraints and functional characteristics of transcription factor-DNA interaction. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(19):12015-12020. 10.1073/pnas.192693599, 129390, 12218191.
23. Gerland U, Hwa T. On the selection and evolution of regulatory DNA motifs. Journal of molecular evolution 2002, 55(4):386-400. 10.1007/s00239-002-2335-z, 12355260.
24. Das D, Zhang MQ. Predictive models of gene regulation: application of regression methods to microarray data. Methods in molecular biology (Clifton, NJ) 2007, 377:95-110.
25. Mackay D. Bayesian Methods for Adaptive Models. PhD thesis, California Institute of Technology 1991,
26. Aurell E, d'Herouel AF, Malmnas C, Vergassola M. Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae. Physical biology 2007, 4(2):134-143. 10.1088/1478-3975/4/2/006, 17664657.
27. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431(7004):99-104. 10.1038/nature02800, 15343339.
28. Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. Divergence of transcription factor binding sites across related yeast species. Science (New York, NY) 2007, 317(5839):815-819.
29. Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America 2006, 103(32):12027-12032. 10.1073/pnas.0605003103, 1567692, 16880385.
30. Gao F, Foat BC, Bussemaker HJ. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC bioinformatics 2004, 5:31. 10.1186/1471-2105-5-31, 407845, 15113405.
31. Chen CY, Tsai HK, Hsu CM, May Chen MJ, Hung HG, Huang GT, Li WH. Discovering gapped binding sites of yeast transcription factors. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(7):2527-2532. 10.1073/pnas.0712188105, 2268170, 18272477.
32. Foat BC, Tepper RG, Bussemaker HJ. TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. Nucleic acids research 2008, (36 Database):D125-131. 2238954, 17947326.
33. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F. TRANSFAC: an integrated system for gene expression regulation. Nucleic acids research 2000, 28(1):316-319. 10.1093/nar/28.1.316, 102445, 10592259.
34. MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC bioinformatics 2006, 7:113. 10.1186/1471-2105-7-113, 1435934, 16522208.
35. Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL. Global nucleosome occupancy in yeast. Genome biology 2004, 5(9):R62. 10.1186/gb-2004-5-9-r62, 522869, 15345046.
36. Yarragudi A, Miyake T, Li R, Morse RH. Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae. Molecular and cellular biology 2004, 24(20):9152-9164. 10.1128/MCB.24.20.9152-9164.2004, 517901, 15456886.
37. Ryan MP, Stafford GA, Yu L, Morse RH. Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling. Molecular and cellular biology 2000, 20(16):5847-5857. 10.1128/MCB.20.16.5847-5857.2000, 86062, 10913168.
38. Lascaris RF, Groot E, Hoen PB, Mager WH, Planta RJ. Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic acids research 2000, 28(6):1390-1396. 10.1093/nar/28.6.1390, 111049, 10684934.
39. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature 2003, 425(6959):737-741. 10.1038/nature02046, 14562106.
40. Gorner W, Durchschlag E, Martinez-Pastor MT, Estruch F, Ammerer G, Hamilton B, Ruis H, Schuller C. Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes & development 1998, 12(4):586-597. 316529, 9472026, 10.1101/gad.12.4.586.
41. Fields DS, He Y, Al-Uzri AY, Stormo GD. Quantitative specificity of the Mnt repressor. Journal of molecular biology 1997, 271(2):178-194. 10.1006/jmbi.1997.1171, 9268651.
42. Sertil O, Kapoor R, Cohen BD, Abramova N, Lowry CV. Synergistic repression of anaerobic genes by Mot3 and Rox1 in Saccharomyces cerevisiae. Nucleic acids research 2003, 31(20):5831-5837. 219473, 14530431, 10.1093/nar/gkg792.
43. Deckert J, Perini R, Balasubramanian B, Zitomer RS. Multiple elements and auto-repression regulate Rox1, a repressor of hypoxic genes in Saccharomyces cerevisiae. Genetics 1995, 139(3):1149-1158. 1206446, 7768429.
44. Delaunay A, Isnard AD, Toledano MB. H2O2 sensing through oxidation of the Yap1 transcription factor. The EMBO journal 2000, 19(19):5157-5166. 302088, 11013218, 10.1093/emboj/19.19.5157.
45. Raitt DC, Johnson AL, Erkine AM, Makino K, Morgan B, Gross DS, Johnston LH. The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress. Molecular biology of the cell 2000, 11(7):2335-2347. 14923, 10888672.
46. Lee J, Godon C, Lagniel G, Spector D, Garin J, Labarre J, Toledano MB. Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast. The Journal of biological chemistry 1999, 274(23):16040-16046. 10.1074/jbc.274.23.16040, 10347154.
47. Bland JM, Altman DG. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1986, 1(8476):307-310.
48. Wang J, Nygaard V, Smith-Sorensen B, Hovig E, Myklebost O. MArray: analysing single, replicated or reversed microarray experiments. Bioinformatics (Oxford, England) 2002, 18(8):1139-1140. 10.1093/bioinformatics/18.8.1139, 12176840.
49. Zeitlinger J, Simon I, Harbison CT, Hannett NM, Volkert TL, Fink GR, Young RA. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 2003, 113(3):395-404. 10.1016/S0092-8674(03)00301-5, 12732146.
50. Jen-Jacobson L. Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. Biopolymers 1997, 44(2):153-180. 10.1002/(SICI)1097-0282(1997)44:2<153::AID-BIP4>3.0.CO;2-U, 9354759.
51. Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences of the United States of America 1998, 95(19):11163-11168. 21613, 9736707, 10.1073/pnas.95.19.11163.
52. Cheatham TE, Kollman PA. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. Journal of molecular biology 1996, 259(3):434-444. 10.1006/jmbi.1996.0330, 8676379.
53. Zhurkin VB, Ulyanov NB, Gorin AA, Jernigan RL. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proceedings of the National Academy of Sciences of the United States of America 1991, 88(16):7046-7050. 52230, 1871119, 10.1073/pnas.88.16.7046.
54. Tsong AE, Tuch BB, Li H, Johnson AD. Evolution of alternative transcriptional circuits with identical logic. Nature 2006, 443(7110):415-420. 10.1038/nature05099, 17006507.
55. Bond GL, Hu W, Levine A. A single nucleotide polymorphism in the MDM2 gene: from a molecular and cellular explanation to clinical effect. Cancer research 2005, 65(13):5481-5484. 10.1158/0008-5472.CAN-05-0825, 15994915.
56. Tuteja G, Jensen ST, White P, Kaestner KH. Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic acids research 2008, 36(12):4149-4157. 2475634, 18556755, 10.1093/nar/gkn366.
57. Segal L, Lapidot M, Solan Z, Ruppin E, Pilpel Y, Horn D. Nucleotide variation of regulatory motifs may lead to distinct expression patterns. Bioinformatics (Oxford, England) 2007, 23(13):i440-449. 10.1093/bioinformatics/btm183, 17646329.
58. Benos PV, Bulyk ML, Stormo GD. Additivity in protein-DNA interactions: how good an approximation is it?. Nucleic acids research 2002, 30(20):4442-4451. 137142, 12384591, 10.1093/nar/gkf578.
59. Man TK, Stormo GD. Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic acids research 2001, 29(12):2471-2478. 55749, 11410653, 10.1093/nar/29.12.2471.
60. Bulyk ML, Johnson PL, Church GM. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic acids research 2002, 30(5):1255-1261. 101241, 11861919, 10.1093/nar/30.5.1255.
61. Gull SF. Bayesian Inductive Inference and Maximum Entropy. Maximum-Entropy and Bayesian Methods in Science and Engineering 1988, 1:53-74.
62. Møller ME. A scaled conjugate gradient algorithm for fast supervised learning. Neural Networks 1993, 6(4).
63. Pearlmutter BA. Fast exact multiplication by the Hessian. Neural Computation 1994, 6(1).
64. Nabney I. NETLAB: Algorithms for Pattern Recognition. 2001, London, Springer.
65. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M. SGD: Saccharomyces Genome Database. Nucleic acids research 1998, 26(1):73-79. 147204, 9399804, 10.1093/nar/26.1.73.
66. Tsai HK, Huang GT, Chou MY, Lu HH, Li WH. Method for identifying transcription factor binding sites in yeast. Bioinformatics (Oxford, England) 2006, 22(14):1675-1681. 10.1093/bioinformatics/btl160, 16644789.
67. Murphy K. The Bayes Net Toolbox for MATLAB. Computing Science and Statistics 2001, 33:331-350.
68. Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nature genetics 2004, 36(8):900-905. 10.1038/ng1400, 15247917.