Kang, J orcid.org/0000-0002-2770-1099, Xu, B, Yao, Y et al. (4 more authors) (2011) A Dynamical Model Reveals Gene Co-Localizations in Nucleus. PLoS Computational Biology, 7 (7). e1002094. ISSN 1553-734X
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 be 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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | 2011 Kang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
Keywords: | Transcription factors; DNA transcription; Brownian motion; Gene regulation; Transcriptional control; Gene expression; Chromatin; Simulation and modeling |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Medicine and Health (Leeds) > School of Dentistry (Leeds) > Oral Biology (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 24 Sep 2019 10:17 |
Last Modified: | 24 Sep 2019 10:17 |
Status: | Published |
Publisher: | Public Library of Science |
Identification Number: | 10.1371/journal.pcbi.1002094 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:149348 |