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Author Kang, Jing ♦ Xu, Bing ♦ Yao, Ye ♦ Lin, Wei ♦ Hennessy, Conor
Source CiteSeerX
Content type Text
File Format PDF
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Dynamical Model Reveals Gene Co-localizations ♦ Experimental Data ♦ Dynamical Model ♦ Important Role ♦ Available Transcription Factor ♦ Nucleus Size ♦ Simple Standard Brownian Motion Model ♦ Gene Mobilization ♦ Dynamic Model ♦ Co-regulated Gene ♦ Chromatin Movement ♦ Transcription Factor ♦ Association Level ♦ Sub-diffusion Process ♦ Standard Brownian Motion ♦ Defined Subnuclear Region ♦ Biological Observation ♦ Pure Diffusion ♦ Direct Interaction ♦ Transcription Factor Number ♦ Gene Expression Pattern ♦ Observed Co-localization ♦ Recent Static Experimental Data ♦ Factory Number ♦ Preferential Co-localization ♦ Gene Co-localization
Abstract Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes, within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without any direct interaction, and suggests the occurrence may due to a limitation in the number of available transcription factors. Experimental data of chromatin movements demonstrates that fractional rather than standard Brownian motion is more appropriate to model gene mobilizations, and we tested our dynamical model against recent static experimental data, using a sub-diffusion process by which the genes tend to colocalize more easily. Moreover, in order to compare our model with recently obtained experimental data, we studied the association level between genes and factors, and presented data supporting the validation of this dynamic model. As further applications of our model, we applied it to test against more biological observations. We found that increasing transcription factor number, rather than factory number and nucleus size, might be the reason for decreasing gene co-localization. In the scenario of frequency- or amplitude-modulation of transcription factors, our model predicted that frequency-modulation may increase the co-localization between its targeted genes.
Educational Role Student ♦ Teacher
Age Range above 22 year
Educational Use Research
Education Level UG and PG ♦ Career/Technical Study