The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.02 - March-April (2013 vol.10)
pp: 300-307
Ngoc Tu Le , Sch. of Knowledge Sci., Japan Adv. Inst. of Sci. & Technol., Nomi, Japan
Tu Bao Ho , Sch. of Knowledge Sci., Japan Adv. Inst. of Sci. & Technol., Nomi, Japan
Bich Hai Ho , Inst. of Inf. Technol., Hanoi, Vietnam
ABSTRACT
Eukaryotic gene transcription is a complex process, which requires the orchestrated recruitment of a large number of proteins, such as sequence-specific DNA binding factors, chromatin remodelers and modifiers, and general transcription machinery, to regulatory regions. Previous works have shown that these regulatory proteins favor specific organizational theme along promoters. Details about how they cooperatively regulate transcriptional process, however, remain unclear. We developed a method to reconstruct a Bayesian network (BN) model representing functional relationships among various transcriptional components. The positive/negative influence between these components was measured from protein binding and nucleosome occupancy data and embedded into the model. Application on S.cerevisiae ChIP-Chip data showed that the proposed method can recover confirmed relationships, such as Isw1-Pol II, TFIIH-Pol II, TFIIB-TBP, Pol II-H3K36Me3, H3K4Me3-H3K14Ac, etc. Moreover, it can distinguish colocating components from functionally related ones. Novel relationships, e.g., ones between Mediator and chromatin remodeling complexes (CRCs), and the combinatorial regulation of Pol II recruitment and activity by CRCs and general transcription factors (GTFs), were also suggested. Conclusion: protein binding events during transcription positively influence each other. Among contributing components, GTFs and CRCs play pivotal roles in transcriptional regulation. These findings provide insights into the regulatory mechanism.
INDEX TERMS
Bioinformatics, Proteins, Stability analysis, Genomics, Machinery, Bayesian methods, Data models,nucleosome positioning, Bioinformatics, Proteins, Stability analysis, Genomics, Machinery, Bayesian methods, Data models, chromatin remodeling complex, Transcriptional relationship, Bayesian network, ChIP-Chip data, histone modification
CITATION
Ngoc Tu Le, Tu Bao Ho, Bich Hai Ho, "Computational Reconstruction of Transcriptional Relationships from ChIP-Chip Data", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 2, pp. 300-307, March-April 2013, doi:10.1109/TCBB.2012.102
REFERENCES
[1] K. Luger, A.W. Mader, A.K. Richmond, D.F. Sargent, and T.J. Richmond, "Crystal Structure of the Nucleosome Core Particle at 2.8 a Resolution," Nature, vol. 389, pp. 251-260, 1997.
[2] B. Li, M. Carey, and J.L. Workman, "The Role of Chromatin During Transcription," Cell, vol. 128, no. 4, pp. 707-719, 2007.
[3] S. Henikoff, "Nucleosome Destabilization in the Epigenetic Regulation of Gene Expression," Nature Rev. Genetics, vol. 9, no. 1, pp. 15-26, 2008.
[4] B.J. Venters and B.F. Pugh, "A Canonical Promoter Organization of the Transcription Machinery and its Regulators in the Saccharomyces Genome," Genome Research, vol. 19, no. 3, pp. 360-371, 2009.
[5] I. Albert, T.N. Mavrich, L.P. Tomsho, J. Qi, S.J. Zanton, S.C. Schuster, and B.F. Pugh, "Translational and Rotational Settings of h2a.z Nucleosomes Across the Saccharomyces Cerevisiae Genome," Nature, vol. 446, no. 7135, pp. 572-576, 2007.
[6] T.N. Mavrich, C. Jiang, I.P. Ioshikhes, X. Li, B.J. Venters, S.J. Zanton, L.P. Tomsho, J. Qi, R.L. Glaser, S.C. Schuster, D.S. Gilmour, IstvanAlbert, and B.F. Pugh, "Nucleosome Organization in the Drosophila Genome," Nature, vol. 453, pp. 358-362, 2008.
[7] C.T. Harbison, D.B. Gordon, T.I. Lee, N.J. Rinaldi, K.D. Macisaac, T.W. Danford, N.M. Hannett, J.B. Tagne, D.B. Reynolds, J. Yoo, E.G. Jennings, J. Zeitlinger, D.K. Pokholok, M. Kellis, P.A. Rolfe, K.T. Takusagawa, E.S. Lander, D.K. Gifford, E. Fraenkel, and R.A. Young, "Transcriptional Regulatory Code of a Eukaryotic Genome," Nature, vol. 431, no. 7004, pp. 99-104, 2004.
[8] R. Jothi, S. Cuddapah, A. Barski, K. Cui, and K. Zhao, "Genome-Wide Identification of in Vivo Protein-Dna Binding Sites from Chip-Seq Data," Nucleic Acids Research, vol. 36, no. 16, pp. 5221-5231, 2008.
[9] A. Barski, S. Cuddapah, K. Cui, T.-Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev, and K. Zhao, "High-Resolution Profiling of Histone Methylations in the Human Genome," Cell, vol. 129, no. 4, pp. 823-837, 2007.
[10] Z. Wang, C. Zang, J.A. Rosenfeld, D.E. Schones, A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, W. Peng, M.Q. Zhang, and K. Zhao, "Combinatorial Patterns of Histone Acetylations and Methylations in the Human Genome," Nature Genetic, vol. 40, no. 7, pp. 897-903, 2008.
[11] G.J. Filion, J.G. van Bemmel, U. Braunschweig, W. Talhout, J. Kind, L.D. Ward, W. Brugman, I.J. de Castro, R.M. Kerkhoven, H.J. Bussemaker, and B. van Steensel, "Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells," Cell, vol. 143, no. 2, pp. 212-224, 2010.
[12] Y. Wang, X.S. Zhang, and Y. Xia, "Predicting Eukaryotic Transcriptional Cooperativity by Bayesian Network Integration of Genome-Wide Data," Nucleic Acids Research, vol. 37, no. 18, pp. 5943-5958, 2009.
[13] Z. Dai, X. Dai, Q. Xiang, J. Feng, J. Wang, Y. Deng, and C. He, "Genome-Wide Analysis of Interactions Between Atp-Dependent Chromatin Remodeling and Histone Modifications," BMC Genomics, vol. 10, article 304, 2009.
[14] B. van Steensel, U. Braunschweig, G.J. Filion, M. Chen, J.G. van Bemmel, and T. Ideker, "Bayesian Network Analysis of Targeting Interactions in Chromatin," Genome Research, vol. 20, no. 2, pp. 190-200, 2009.
[15] M. Bansal, V. Belcastro, A. Ambesi-Impiombato, and D. di Bernardo, "How to Infer Gene Networks from Expression Profiles," Molecular Systems Biology, vol. 3, p. 78, 2007.
[16] N.T. Le and T.B. Ho, "Reconstruction of Histone Modification Network from Next-Generation Sequencing Data," Proc. IEEE 11th Int'l Conf. Bioinformatics and Bioeng. (BIBE), Oct. 2011.
[17] N. Friedman, M. Linial, I. Nachman, and D. Pe'er, "Using Bayesian Networks to Analyze Expression Data," J. Computational Biology, vol. 7, nos. 3/4, pp. 601-620, 2000.
[18] R. Jansen, H. Yu, D. Greenbaum, Y. Kluger, N.J. Krogan, S. Chung, A. Emili, M. Snyder, J.F. Greenblatt, and M. Gerstein, "A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data," Science, vol. 302, no. 6544, pp. 449-453, 2003.
[19] K. Sachs, O. Perez, D. Pe'er, D.A. Lauffenburger, and G.P. Nolan, "Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data," Science, vol. 308, no. 5127, pp. 523-529, 2005.
[20] H. Yu, S. Zhu, B. Zhou, H. Xue, and J.D. Han, "Inferring Causal Relationships among Different Histone Modifications and Gene Expression," Genome Research, vol. 18, no. 8, pp. 1314-1324, 2008.
[21] D.K. Pokholok, C.T. Harbison, S. Levine, M. Cole, N.M. Hannett, T.I. Lee, G.W. Bell, K. Walker, P.A. Rolfe, E. Herbolsheimer, J. Zeitlinger, F. Lewitter, D.K. Gifford, and R.A. Young, "Genome-Wide Map of Nucleosome Acetylation and Methylation in Yeast," Cell, vol. 122, no. 4, pp. 517-527, 2005.
[22] W. Lee, D. Tillo, N. Bray, R.H. Morse, R.W. Davis, T.R. Hughes, and C. Nislow, "A High-Resolution Atlas of Nucleosome Occupancy in Yeast," Nature Genetics, vol. 39, no. 10, pp. 1235-1244, 2007.
[23] D. Karolchik, A.S. Hinrichs, T.S. Furey, K.M. Roskin, C.W. Sugnet, D. Haussler, and W.J. Kent, "The Ucsc Table Browser Data Retrieval Tool," Nucleic Acids Research, vol. 32, pp. D493-D496, 2004.
[24] D. Heckerman, D. Geiger, and D.M. Chickering, "Learning Bayesian Networks: The Combination of Knowledge and Statistical Data," Machine Learning, vol. 20, pp. 197-243, 1995.
[25] F.V. Jensen and T.D. Nielsen, Bayesian Networks and Decision Graphs, second ed. Springer-Verlag, 2001.
[26] D.M. Chickering, "Learning Bayesian Networks is NP-Complete," Learning from Data: Artificial Intelligence and Statistics V, D. Fisher and H. Lenz, eds., pp. 121-130. Springer-Verlag, 1996.
[27] G. Cooper and E. Herskovits, "A Bayesian Method for the Induction of Probabilistic Networks from Data," Machine Learning, vol. 9, pp. 309-347, 1992.
[28] A.J. Hartemink, D.K. Gifford, T.S. Jaakkola, and R.A. Young, "Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks," Proc. Pacific Symp. Biocomputing, pp. 422-433, 2001.
[29] J. Yu, V.A. Smith, P.P. Wang, A.J. Hartemink, and E.D. Jarvis, "Advances to Bayesian Network Inference for Generating Causal Networks from Observational Biological Data," Bioinformatics, vol. 20, no. 18, pp. 3594-3603, 2004.
[30] V.A. Smith, E.D. Jarvis, and A.J. Hartemink, "Evaluating Functional Network Inference Using Simulations of Complex Biological Systems," Bioinformatics, vol. 18, no. Suppl 1, pp. S216-224, 2002.
[31] A. Jansen and K.J. Verstrepen, "Nucleosome Positioning in Saccharomyces Cerevisiae," Microbiology and Molecular Biology Rev., vol. 75, no. 2, pp. 301-320, 2011.
[32] A. Morillon, N. Karabetsou, A. Nair, and J. Mellor, "Dynamic Lysine Methylation on Histone h3 Defines the Regulatory Phase of Gene Transcription," Molecular Cell, vol. 18, no. 6, pp. 723-734, 2005.
[33] T.Y. Erkina, Y. Zou, S. Freeling, V.I. Vorobyev, and A.M. Erkine, "Functional Interplay between Chromatin Remodeling Complexes Rsc, Swi/Snf, and Iswi in Regulation of Yeast Heat Shock Genes," Nucleic Acids Research, vol. 38, no. 5, pp. 251-260, 2009.
[34] B. Li, M. Carey, and J.L. Workman, "The Role of Chromatin during Transcription," Cell, vol. 128, no. 4, pp. 707-719, 2007.
[35] B.J. Venters and B.F. Pugh, "How Eukaryotic Genes are Transcribed," Critical Rev. in Biochemistry Molecular Biology, vol. 44, nos. 2/3, pp. 117-141, 2009.
[36] H.H. Ng, F. Robert, R.A. Young, and K. Struhl, "Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity," Molecular Cell, vol. 11, no. 3, pp. 709-719, 2003.
[37] K. Luger, A.W. Mader, A.K. Richmond, D.F. Sargent, and T.J. Richmond, "The Language of Covalent Histone Modifications," Nature, vol. 403, no. 6765, pp. 41-45, 2000.
[38] W. Zhang, J.R. Bone, D.G. Edmondson, B.M. Turner, and S.Y. Roth, "Essential and Redundant Functions of Histone Acetylation Revealed by Mutation of Target Lysines and Loss of the Gcn5P Acetyltransferase," EMBO J., vol. 17, no. 11, pp. 3155-3167, 1998.
[39] R. Biddick and E.T. Young, "Yeast Mediator and its Role in Transcriptional Regulation," Comptes Rendus Biologies, vol. 328, no. 9, pp. 773-782, 2005.
[40] R.D. Kornberg, "Mediator and the Mechanism of Transcriptional Activation," Trends in Biochemical Sciences, vol. 30, no. 5, pp. 235-239, 2005.
[41] M.W. Adkins and J.K. Tyler, "Transcriptional Activators are Dispensable for Transcription in the Absence of Spt6-Mediated Chromatin Reassembly of Promoter Regions," Molecular Cell, vol. 21, no. 3, pp. 405-416, 2006.
[42] H. Zhang and J.C. Reese, "Exposing the Core Promoter is Sufficient to Activate Transcription and Alter Coactivator Requirement at Rnr3," Proc. Nat'l Academy of Sciences USA, vol. 104, no. 21, pp. 8833-8838, 2007.
[43] B. Xella, C. Goding, E. Agricola, E. di Mauro, and M. Caserta, "The Iswi and Chd1 Chromatin Remodelling Activities Influence Adh2 Expression and Chromatin Organization," Molecular Microbiology, vol. 59, no. 5, pp. 1531-1541, 2006.
[44] K.C. Lindstrom, J.C. Vary, M.R. Parthun, J. Delrow, and T. Tsukiyama, "Isw1 Functions in Parallel with the Nua4 and Swr1 Complexes in Stress-Induced Gene Repression," Molecular and Cellular Biology, vol. 26, no. 16, pp. 6117-6129, 2006.
[45] S. Chou, S. Chatterjee, M. Lee, and K. Struhl, "Transcriptional Activation in Yeast Cells Lacking Transcription Factor Iia," Genetics, vol. 153, no. 4, pp. 1573-1581, 1999.
[46] S.W. Hong, S.M. Hong, J.M. Yoo, Y.C.L.Y.S. Kim, J.T. Lis, and D.K. Lee, "Phosphorylation of the Rna Polymerase ii C-Terminal Domain by Tfiih Kinase is Not Essential for Transcription of Saccharomyces Cerevisiae Genome," Proc. Nat'l Academy of Sciences USA, vol. 106, no. 34, pp. 14 276-14 280, 2009.
[47] S.J. Zanton and B.F. Pugh, "Full and Partial Genome-Wide Assembly and Disassembly of the Yeast Transcription Machinery in Response to Heat Shock," Genes and Development, vol. 20, no. 16, pp. 2250-2265, 2006.
208 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool