Open AccessModeling in vivo dynamics of RNA polymerase II meeting Nucleosomes
Author(s) -
Roozbeh Abedini-Nassab,
Xu Zhang
Publication year - 2016
Publication title -
international journal of engineering and technology
Language(s) - English
Resource type - Journals
ISSN - 2227-524X
DOI - 10.14419/ijet.v5i2.6098
Subject(s) - polymerase , rna polymerase , rna polymerase ii , computational biology , rna polymerase i , rna , physics , biology , dna , rna dependent rna polymerase , genetics , gene , gene expression , promoter
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.