Abstract
This paper presents a new structural-based approach to explore spatial organization of naked DNA on a whole chromosome sequence and its biological features related to gene regulation. A 3D trajectory representation on full-length yeast chromosomes based on Bolshoy’s conformation model is discussed. These trajectories are predicted by our visualizing system ADN-Viewer. Observations show interesting geometric properties of chromosomes dealing with variability of 3D structures and the fact that regions linearly distant could be spatially close. These new observed phenomena are correlated then with biological considerations. In particular, transcriptional co-regulation of the data of Lee et al., 2002 are exploited. A characterization parameter (RLS), ratio of linear distance and 3D one, was computed for each couple of genes. The co-regulated genes are found to be either linearly distant and spatially close, or linearly close. The co-regulated genes arranged in 1D-clusters could be detected directly in raw data. But, our model offers new predictions of co-regulated genes thanks to 3D-clusters. Then, we concluded that yeast naked DNA spatial organization seems to predispose to transcriptional regulation.
This work was supported by LIMSI-CNRS and Génopole ®.
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References
Rojdestvenski, I., Modjeska, D., Pettersson, F.: Sequence World: A Genetics Database in Virtual Reality. In: International Conference on Information Visualization IEEE, pp. 513–517 (2000)
Gilbert, D.R., Schroeder, M., van Helden, J.: Interactive visualization and exploration of relationships between biological objects. Trends Biotech 18, 487–494 (2000)
Férey, N., Gros, P.E., Hérisson, J., Gherbi, R.: Exploration by visualization of numerical and textual genomic data. J. Biol. Physics and Chem. 4, 102–110 (2004)
Randic, M., Vracko, M., Nandy, A., Basak, S.C.: On 3-D graphical representation of DNA primary sequences and their numerical characterization. J. Chem. Inf. Comput. Sci. 40, 1235–1244 (2000)
Li, C., Wang, J.: On 3-D representation of DNA primary sequences. Comb. Chem. & High Throughput Screen 7, 23–27 (2004)
Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., et al.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002)
Guelzim, N., Bottani, S., Bourgine, P., Képès, F.: Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics 31, 64–68 (2002)
Képès, F.: Periodic Epi-organization of the Yeast Genome Revealed by the Distribution of Promoter Sites. J. Mol. Biol. 329, 859–865 (2003)
Nelson, C., Hersh, B.M., Carroll, S.B.: The regulatory content of intergenic DNA shapes genome architecture. Genome Biology 5, R25 (2004)
Cremer, T., Cremer, C.: Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Rev. Genet. 2, 292–301 (2001)
Gerlich, D., Beaudouin, J., Kalbfuss, B., Daigle, N., Eils, R., Ellenberg, J.: Global chromosome positions are transmitted through mitosis in mammalian cells. Cell 112, 751–764 (2003)
Képès, F.: Periodic transcriptional organization of the E. coli genome. J. Mol. Biol. 340, 957–964 (2004)
King, G.J.: Stability, structure and complexity of yeast chromosome III. Nucleic Acids Res 21, 4239–4245 (1993)
Jáuregui, R., Abreu-Goodger, C., Moreno-Hagelsieb, G., Collado-Vides, J., Merino, E.: Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. Nucleic Acids Res 31, 6770–6777 (2003)
de Bruin, D., Zaman, Z., Liberatore, R.A., Ptashne, M.: Telomere looping permits gene activation by a downstream UAS in yeast. Nature 409, 109–113 (2001)
Carter, D., Chakalova, L., Osborne, C.S., Dai, Y., Fraser, P.: Long-range chromatin regulatory interactions in vivo. Nature Genetics 32, 623–626 (2002)
Bolshoy, A., McNamara, P., Harrington, R.E., Trifonov, E.N.: Curved DNA without A-A: Experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA 88, 2312–2316 (1991)
Cacchione, S., De Santis, P., Foti, D.P., Palleschi, A., Savino, M.: Periodical polydeoxynucleotides and DNA curvature. Biochemistry 28, 8706–8713 (1989)
Ponomarenko, M.P., Ponomarenko, J.V., Kel, A.E., Kolchanov, N.A.: Search for DNA conformational features for functional sites. In: Investigation of the TATA box. Proceedings of the International Pacific Symposium of Biocomputing, PSB (2000)
Gherbi, R., Hérisson, J.: Representation and Processing of Complex DNA Spatial Architecture and its Annotated Content. In: Proceedings of the International Pacific Symposium of Biocomputing, PSB (2002)
Gros, P.-E., Férey, N., Hérisson, J., Gherbi, R.: A Distributed Multimedia Database Visualization within an Immersive Environment for Bioinformatics. In: Proceedings of the International Conference of Bioinformatics and Applications, Lauderdale, FL, USA (2004)
Shpigelman, A.S., Trifonov, E.N., Bolshoy, A.: CURVATURE: Software for the analysis of curved DNA. Comput. Appl. Biosci. 9, 435–440 (1993)
Dekker, J., Rippe, K., Dekker, M., Kleckner, N.: Capturing Chromosome Conformation. Science 295, 1306–1311 (2002)
Spellman, P.T., Rubin, G.M.: Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1, 5 (2002)
Weitzman, J.B.: Transcriptional territories in the genome. J. Biol. 1, 2 (2002)
Meneghini, M.D., Wu, M., Madhani, H.D.: Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112, 725–736 (2003)
Cook, R.C.: Predicting three-dimensional genome structure from transcriptional activity. Nature Genetics 32, 347–352 (2002)
Cook, R.C.: Nongenic transcription, gene regulation and action at a distance. J. Cell Sci. 116, 4483–4491 (2003)
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Matte-Tailliez, O. et al. (2006). Yeast Naked DNA Spatial Organization Predisposes to Transcriptional Regulation. In: Gavrilova, M., et al. Computational Science and Its Applications - ICCSA 2006. ICCSA 2006. Lecture Notes in Computer Science, vol 3980. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11751540_24
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DOI: https://doi.org/10.1007/11751540_24
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