Modeling in vivo dynamics of RNA polymerase II meeting Nucleosomes
-
2016-04-20 https://doi.org/10.14419/ijet.v5i2.6098
-
Modeling, Nucleosome, Radial Basis Function Network, Random Walk, RNA polymerase. -
Abstract
Nucleosomes are shown to be barriers for RNA Polymerase II elongation along DNA, and their entry site behaves as the major obstacle. In this work, based on recent available in vivo data, we introduce a mathematical model for RNA Polymerase II reads. Moreover, as an alternative way, we use Radial Basis Function Network to predict RNA Polymerase II reads. Results of our models are in good agreement with experimental data. Furthermore, we introduce a random walk model which includes stalling, backtracking, and elongation phenomena. This model can predict and simulate the RNA Polymerase II trajectory on DNA, when it meets various nucleosomes.
-
References
[1] F. K. Hsieh, M. Fisher, A. Újvári, et al., Histone Sin mutations promotes nucleosome traversal and histone displacement by RNA polymerase II, EMBO Reports 11 (2010) 705–710. http://dx.doi.org/10.1038/embor.2010.113.
[2] A. Újvári, F. K. Hsieh, S. W. Luse, et al., Histone N-terminal tails interfere with nucleosome traversal by RNA polymerase II, Journal of Biological Chemistry283 (2008) 32236–32243.
[3] Ch. M. Weber, S. Ramachandran, S. Henikoff, Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase, Molecular Cell53, 5 (2014) 819-830. http://dx.doi.org/10.1016/j.molcel.2014.02.014.
[4] L. Bintu, T. Ishibashi, M. Dangkulwanich, et al., Nucleosomal Elements That Control the Topography of the Barrier to Transcription, Cell 151,4 (2012) 738–749. http://dx.doi.org/10.1016/j.cell.2012.10.009.
[5] G. Dos Santos, A. J. Schroeder, J. L. Goodman, et al., FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations, Nucleic Acids Research, 43, D1 (2015) D690-D697. http://dx.doi.org/10.1093/nar/gku1099.
[6] N. L. Johnson, S. Kotz, N. Balakrishnan, Continuous univariate distributions,2nd edition, John Wiley and Sons, New York,1994.
[7] N. R. Draper, H. Smith, Applied regression analysis,3rd edition, John Wiley and Sons, New York,1998. http://dx.doi.org/10.1002/9781118625590.
[8] J. Park, I. W. Sandberg, Universal approximation Using Radial-Basis-Function Network, Neural Computation, 3, 2(1991)246-257.
-
Downloads
Additional Files
-
How to Cite
Abedini-Nassab, R., & Zhang, X. (2016). Modeling in vivo dynamics of RNA polymerase II meeting Nucleosomes. International Journal of Engineering & Technology, 5(2), 33-37. https://doi.org/10.14419/ijet.v5i2.6098Received date: 2016-04-10
Accepted date: 2016-04-11
Published date: 2016-04-20