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Spatial stochastic simulation of transcription factor binding reveals mechaniscms to control gene activation

Klann, M. and Koeppl, H. (2012):
Spatial stochastic simulation of transcription factor binding reveals mechaniscms to control gene activation.
Tampere University of Technology, Tampere International Center for Signal Processing, In: 9th International Workshop on Computational Systems Biology (WCSB 2012), [Online-Edition: http://www.cs.tut.fi/wcsb12/WCSB2012.pdf],
[Conference or Workshop Item]

Abstract

The activation of genes is one of the most prominent yet most stochastic processes in the cell. Gene activation controls the state of the cell. But normally only one or a few copies of each gene exist, causing a highly stochastic process. In addition, transcription factors (TF) that activate the respective gene have to find the corresponding target site on the tremendously long DNA strand. In order to elucidate the process, we have developed a particle-tracking algorithm including both the spatial and stochastic aspects of the process. TFs can diffuse through the nucleus which is filled with DNA strands. They can unspecifically bind to the DNA backbone or directly to the target gene sequence in a reversible manner. The results of the detailed simulation show that the activation of the genes does not only depend on the number of TFs and the specific binding process to the target sequence but is strongly controlled by the unspecific binding process to all other nucleotide sequences along the DNA.

Item Type: Conference or Workshop Item
Erschienen: 2012
Creators: Klann, M. and Koeppl, H.
Title: Spatial stochastic simulation of transcription factor binding reveals mechaniscms to control gene activation
Language: English
Abstract:

The activation of genes is one of the most prominent yet most stochastic processes in the cell. Gene activation controls the state of the cell. But normally only one or a few copies of each gene exist, causing a highly stochastic process. In addition, transcription factors (TF) that activate the respective gene have to find the corresponding target site on the tremendously long DNA strand. In order to elucidate the process, we have developed a particle-tracking algorithm including both the spatial and stochastic aspects of the process. TFs can diffuse through the nucleus which is filled with DNA strands. They can unspecifically bind to the DNA backbone or directly to the target gene sequence in a reversible manner. The results of the detailed simulation show that the activation of the genes does not only depend on the number of TFs and the specific binding process to the target sequence but is strongly controlled by the unspecific binding process to all other nucleotide sequences along the DNA.

Volume: 61
Publisher: Tampere University of Technology, Tampere International Center for Signal Processing
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Event Title: 9th International Workshop on Computational Systems Biology (WCSB 2012)
Date Deposited: 04 Apr 2014 12:53
Official URL: http://www.cs.tut.fi/wcsb12/WCSB2012.pdf
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