Abstract
Conformation of a canonical nucleosome inhibits the direct access of the binding proteins to portions of nucleosomal DNA. Nucleosome dynamics establish certain pathways through which nucleosome gets remodeled (spontaneously, covalently or non-covalently) and the buried DNA sites become accessible. Currently for most pathways no single model is available to capture the temporal behavior of these pathways. Plus traditional diffusion-based models in most cases are not precise. In this work we have given a systematic overview of such pathways. Then, we manipulate the probability of a binding site on array of N nucleosomes and chromatin of length G base pairs . We further identify three of the widely accepted thermal-driven (passive) pathways and model those based on stochastic process and the Discrete-Event-Simulation. For the output of the models we have sought either the site access rate or the sliding rate of the nucleosome. We also show that results from these models match the experimental data where available.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Alberts, B., et al.: Molecular Biology of the Cell, 4th edn. Garland Science, New York (2002)
Richmond, T., Davey, C.A.: The Structure of DNA in Nucleosome Core. Nat. 423, 145–150 (2003)
Li, G., et al.: Rapid spontaneous accessibility of nucleosomal DNA. Nat. Struc. & Mol. Bio. 12, 46–53 (2005)
Beard, D.A., Schlick, T.: Computational Modeling Predicts the Structure and Dynamics of Chromatin Fiber. Els. J. Struc. 9, 105–114 (2001)
Ghosh, S., et al.: iSimBioSys: A Discrete Event Simulation Platform for ’in silico’ study of biological systems. In: Proc. of the 39th Annual Simulation Symp (ANSS’06) (2006)
Ghosh, P., et al.: A Stochastic model to estimate the time taken for Protein-Ligand Docking. In: IEEE CIBCB (2006)
Luger, K., et al.: Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997)
Flaus, A., Owen-Hughes, T.: Mechanism for Nucleosome Mobilization. J. Biopolymers 68, 563–578 (2003)
Mellor, J.: The Dynamics of Chromatin Remodeling at Promoters. J. Molecular Cell 19, 147–157 (2005)
Narlikar, G.J., Fan, H., Kingston, R.E.: Cooperation between Complexes that Regulate Chromatin Structure and Transcription. Cell 108, 475–487 (2002)
Saha, A., Wittmeyer, J., Cairns, B.R.: Chromatin remodelling: the industrial revolution of DNA around histones. Nat. rev. Mol. Cell Biol. 7(6), 437–447 (2006)
Kobor, M.S., et al.: A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2, E131 (2004)
Guo, X., Tatsuoka, K., Liu, A.R.: Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. Bioinformatics 22, 392–399 (2006)
Pennings, S., Meersseman, G., Bradbury, E.M.: Mobility of positioned nucleosomes on 5 S rDNA. J. Mol. Biol. 220(1), 101–110 (1991)
Levin, B.: Genes VIII. Prentice Hall, Upper Sadle River (2004)
Wiesenfeld, K., Jaramillo, F.: Minireview of stochastic c resonance. Chaos 8, 539–548 (1998)
Das, S., et al.: Parallel Discrete Event Simulation in Star Networks with Applications to Telecommunications. In: Int. Workshop on Modeling, Analysis and Sim. of Computer and Telecom. Sys. (1995)
Kulic, I.M., Schiessel, H.: Nucleosome repositioning via loop formation. Biophys. J. (2003)
Yakushevich, L.V.: Nonlinear Physics of DNA. Wiley-VCH, Weinheim (2004)
Kulic, I.M., Schiessel, H.: chromatin Dynamics: Nuicleosome go Mobile through Twist Defects. Phy. rev. lett. 91(14) (2003)
Kivshar, Y.S., Braun, O.M.: The Frenkel-Kontorova Model: Concepts, Methods, and Applications. Springer, Heidelberg (2004)
van Kampen, N.G.: Stochastic Processes in Physics and Chemistry. Elsevier, Amsterdam (1992)
Schiessel, H.: The physics of chromatin. Max-Planck-Institut für Polymerforschung, Theory Group, Mainz, Germany (2003)
Schiessel, H., et al.: Polymer Reptation and Nucleosome Repositioning. Phy. rev. lett. 86(19), 4414–4417 (2001)
Kleinrock, L.: Queueing Systems, vol. I: Theory. Wiley, New York (1975)
Ghosh, P., et al.: An Analytical Model to Estimate the time taken for Cytoplasmic Reactions for Stochastic Simulation of Complex Biological Systems. In: IEEE Granular Computing Conf. (2006)
Ghosh, P., et al.: A Model to estimate the time taken for protein-DNA binding for Stochastic discrete event simulation of biological processes. Accepted for pub. In: IEEE CIBCB, USA (2007)
Mazloom, A.R., Basu, K., Das, S.: A Random Walk Modelling Approach for Passive Metabolic Pathways in Gram-Negative Bacteria. In: IEEE CIBCB, Canada (2006)
Murthy, K.P.N., Kehr, K.W.: Mean first-passage time of random walks on a random lattice. Phys. rev A 40, 2082 (1989)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Mazloom, A.R., Basu, K., Mandal, S.S., Sorourian, M., Das, S. (2007). DNA Sites Buried in Nucleosome Become Accessible at Room Temperature: A Discrete-Event-Simulation Based Modeling Approach. In: Măndoiu, I., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2007. Lecture Notes in Computer Science(), vol 4463. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72031-7_55
Download citation
DOI: https://doi.org/10.1007/978-3-540-72031-7_55
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-72030-0
Online ISBN: 978-3-540-72031-7
eBook Packages: Computer ScienceComputer Science (R0)