Yeast Naked DNA Spatial Organization Predisposes to Transcriptional Regulation

  • Oriane Matte-Tailliez
  • Joan Hérisson
  • Nicolas Ferey
  • Olivier Magneau
  • Pierre Emmanuel Gros
  • François Képès
  • Rachid Gherbi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3980)


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.


Linear Distance Transcriptional Regulatory Network Virtual Reality Platform Interesting Geometric Property Sphere Digit 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 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)Google Scholar
  2. Gilbert, D.R., Schroeder, M., van Helden, J.: Interactive visualization and exploration of relationships between biological objects. Trends Biotech 18, 487–494 (2000)CrossRefGoogle Scholar
  3. 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)CrossRefGoogle Scholar
  4. 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)Google Scholar
  5. Li, C., Wang, J.: On 3-D representation of DNA primary sequences. Comb. Chem. & High Throughput Screen 7, 23–27 (2004)Google Scholar
  6. 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)CrossRefGoogle Scholar
  7. Guelzim, N., Bottani, S., Bourgine, P., Képès, F.: Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics 31, 64–68 (2002)CrossRefGoogle Scholar
  8. Képès, F.: Periodic Epi-organization of the Yeast Genome Revealed by the Distribution of Promoter Sites. J. Mol. Biol. 329, 859–865 (2003)CrossRefGoogle Scholar
  9. Nelson, C., Hersh, B.M., Carroll, S.B.: The regulatory content of intergenic DNA shapes genome architecture. Genome Biology 5, R25 (2004)CrossRefGoogle Scholar
  10. Cremer, T., Cremer, C.: Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Rev. Genet. 2, 292–301 (2001)CrossRefGoogle Scholar
  11. 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)CrossRefGoogle Scholar
  12. Képès, F.: Periodic transcriptional organization of the E. coli genome. J. Mol. Biol. 340, 957–964 (2004)CrossRefGoogle Scholar
  13. King, G.J.: Stability, structure and complexity of yeast chromosome III. Nucleic Acids Res 21, 4239–4245 (1993)CrossRefGoogle Scholar
  14. 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)CrossRefGoogle Scholar
  15. 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)CrossRefGoogle Scholar
  16. Carter, D., Chakalova, L., Osborne, C.S., Dai, Y., Fraser, P.: Long-range chromatin regulatory interactions in vivo. Nature Genetics 32, 623–626 (2002)CrossRefGoogle Scholar
  17. 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)CrossRefGoogle Scholar
  18. Cacchione, S., De Santis, P., Foti, D.P., Palleschi, A., Savino, M.: Periodical polydeoxynucleotides and DNA curvature. Biochemistry 28, 8706–8713 (1989)CrossRefGoogle Scholar
  19. 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)Google Scholar
  20. 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)Google Scholar
  21. 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)Google Scholar
  22. Shpigelman, A.S., Trifonov, E.N., Bolshoy, A.: CURVATURE: Software for the analysis of curved DNA. Comput. Appl. Biosci. 9, 435–440 (1993)Google Scholar
  23. Dekker, J., Rippe, K., Dekker, M., Kleckner, N.: Capturing Chromosome Conformation. Science 295, 1306–1311 (2002)CrossRefGoogle Scholar
  24. Spellman, P.T., Rubin, G.M.: Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1, 5 (2002)CrossRefGoogle Scholar
  25. Weitzman, J.B.: Transcriptional territories in the genome. J. Biol. 1, 2 (2002)CrossRefGoogle Scholar
  26. 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)CrossRefGoogle Scholar
  27. Cook, R.C.: Predicting three-dimensional genome structure from transcriptional activity. Nature Genetics 32, 347–352 (2002)CrossRefGoogle Scholar
  28. Cook, R.C.: Nongenic transcription, gene regulation and action at a distance. J. Cell Sci. 116, 4483–4491 (2003)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Oriane Matte-Tailliez
    • 1
    • 2
  • Joan Hérisson
    • 2
  • Nicolas Ferey
    • 2
  • Olivier Magneau
    • 3
  • Pierre Emmanuel Gros
    • 2
  • François Képès
    • 4
  • Rachid Gherbi
    • 2
  1. 1.Inference and Learning, LRIUMR CNRS 8326, Université Paris 11Orsay CedexFrance
  2. 2.Bioinformatics Team, LIMSI & IBISC CNRSGenopole Evry
  3. 3.VENISE transversal action on V&AR, LIMSI-CNRSOrsay CedexFrance
  4. 4.Epigenomics project & Atelier de Génomique Cognitive, CNRS UMR 8071EvryFrance

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